#CCP4I VERSION CCP4Interface 8.0.008 #CCP4I SCRIPT LOG mrbump #CCP4I DATE 20 Jan 2023 12:53:34 #CCP4I USER 'UNKNOWN' #CCP4I PROJECT Lyso-T #CCP4I JOB_ID 1 #CCP4I SCRATCH C:/Users/Rigaku/AppData/Local/Temp #CCP4I HOSTNAME DESKTOP-MN6A612 #CCP4I PID 1136 http_proxy not specified in environment ################################################################# ################################################################# ################################################################# ### CCP4 7.1: MRBUMP version 2.2.6 : 20 Sep 2021 ## ################################################################# User: Rigaku Run date: 20/01/2023 Run time: 12:53:35 Operating System: win32 Python Version: 3.7.1 (v3.7.1:260ec2c36a, Oct 20 2018, 14:57:15) [MSC v.1915 64 bit (AMD64)] Python location: C:\CCP4-8\8.0\libexec\python.exe ENTER KEYWORD INPUT FROM FILE OR FROM STANDARD INPUT PDB non-redundancy level for homologue search: 100 If Results in HTML required the file will be written to: C:/DATA/Marek/2023/CB080/Lyso-teach/results_1.html Number of ensembles processed by phaser: 1 Number of models to use in each phaser ensemble: 1 E value to use in fasta search: 0.020000 No value given for NMASU. Number of molecules will be calculated automatically ############################################################### Keyword input summary: ############################################################### CLEAN flag set to: False LITE flag set to: False Use Acorn to improve map set to: False Acorn will be invoked if the collected data resolution is better than: 1.700 Angstroms Enantiomorph search set to: False MR programs to be used: MOLREP PHASER Run in TRYALL mode set to: False PHAQUICK: False Use Buccaneer to do model building set to: True Test all spacegroups (phaser only) set to: False Number of cycles of restrained refinement to use in Refmac = 30 Refmac TWIN option run set to: False Number of cycles of model building in Buccaneer = 10 Use ARP/wARP to do model building set to: False Number of cycles of model building in ARP/wARP = 5 Use Shelxe to do c-alpha trace set to: False Number of cycles of auto-tracing in Shelxe = 15 Perform model building after SHELXE: False Use Buccaneer after SHELXE: True Use ARP/wARP after SHELXE: False Run Ctruncate to analyse data: TRUNCATE=True Job identifier: 1 Root directory: C:\DATA\Marek\2023\CB080\Lyso-teach Number of search models to use in MR: 30 Default sequence alignment program: MAFFT Debug set to: False SCOP search set to: False SSM search set to: False PQS search set to: False Generate PDBClip models set to: False Generate Molrep models set to: True Generate Chainsaw models set to: True Generate Sculptor models set to: True Generate UNMOD models set to: False Generate Polyalanine models set to: False Run local Fasta search set to: False Update database files set to: False Do FASTA search set to: False Do the Phmmer search set to: True List of PDB codes to ignore in the search: List of PDB codes to include in the search: Run in HTMLOUT mode set to: False Check web connection set to: True Cluster set to: False Do HHPRED search set to: False Do HHSCORE search set to: True Use Gesamt variance truncation to generate ensembles: False Use Gesamt ensemble instead of superposed: False Use Ensemble in MR set to: False ############################################################### Web connectivity test enabled. Checking PDB servers for file availability.... (Note: Disable this in the MrBUMP interface if running without a web connection) ################################################## Checking to see if the https_proxy has been set... ################################################## Proxy has not been set... Warning: Proxy not set! downloading ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/pdb/pdb1smw.ent.gz Warning: Proxy not set! HTTP Error: 404 http://ftp.pdbj.org/pdb/pdb1smw.ent.gz Warning: Problem downloading PDB file from source 3 (PDBJ server) Warning: Proxy not set! downloading https://files.rcsb.org/download/1SMW.pdb.gz ################################################# ########################################################################## Mode of operation: FULLMR - Search models will be created and used in Molecular Replacement. ########################################################################## Input MTZ file: C:/DATA/Marek/2023/CB080/molrep/lyso-2016-HD_sg96.mtz Input Sequence file: C:/DATA/Marek/2023/CB080/molrep/1JUG.fasta.pir Output MTZ file: C:/DATA/Marek/2023/CB080/Lyso-teach/lyso-2016-HD_sg96_mrbump_soln1.mtz Output PDB file: C:/DATA/Marek/2023/CB080/Lyso-teach/lyso-2016-HD_sg96_mrbump_soln1.pdb Output XML file: mafft.bat.exe not found in PATH probcons.exe not found in PATH t_coffee.exe not found in PATH Program 'mafft' was not found in the system PATH. Will use CLUSTALW to do multiple alignment of sequences instead. Database update: Keyword "UPDATE" set to False. MrBUMP will not attempt a database update. ################################### ### Target Information ### ################################### Matthews_Coef message: Estimated number of molecules using target molecular weight: 1 Matthews_Coef message: Score for this number of molecules: 1.000 Matthews_Coef message: Actual Vm: 2.050 and Solvent content: 40.110 % Sequence file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\input\1JUG.fasta.pir Reflection (MTZ) file: C:/DATA/Marek/2023/CB080/molrep/lyso-2016-HD_sg96.mtz Number of residues: 125 Molecular Weight (daltons): 13993.800 Estimated number of molecules to search for in a.s.u.: 1 Resolution of collected data (angstroms): 1.550 Input spacegroup: P43212 #################################### ### Input column data ### #################################### F : F_XDSdataset SIGF : SIGF_XDSdataset I : IMEAN_XDSdataset SIGI : SIGIMEAN_XDSdataset FREE : FreeR_flag IPLUS : I_XDSdataset(+) SIGIPLUS : SIGI_XDSdataset(+) IMINUS : I_XDSdataset(-) SIGIMINUS : SIGI_XDSdataset(-) FPLUS : F_XDSdataset(+) SIGFPLUS : SIGF_XDSdataset(+) FMINUS : F_XDSdataset(-) SIGFMINUS : SIGF_XDSdataset(-) Analysing MTZ file with Ctruncate... Analysis of MTZ with Ctruncate completed successfully... (Log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\logs\ctruncate.log) Here's a summary of its findings: ############################# ### Ctruncate Results ### ############################# TRANSLATIONAL NCS: No translational NCS detected ANISOTROPY CORRECTION: Eigenvalue ratios: 1.0000 1.0000 0.9332 TWINNING ANALYSIS: No twinning detected. ################################### ### PHMMER search ### ################################### Creating the sequence database for search... PDB redundancy level: 100 1jug_A1_PHR KILKKQELCKNLVAQGMNGYQHITLPNWVCTAFHESSYNTRATNHNTDGSTDYGILQINSRYWCHDGKTPGSKNACNISCSKLLDDDITDDLKCAKKIAGEAKGLTPWVAWKSKCRGHDLSKFKC 100.00 100.00 1.90 XRAY 5v8g_A1_PHR VYSRCELAAAMKRLGLDNYRGYSLGNWVCAANYESSFNTQATNRNTDGSTDYGILQINSRWWCDDGKTPGSKNACGIPCSVLLRSDITEAVRCAKRIVSDGNGMNAWVAWRNRCRGTDVSKW 57.38 55.00 1.20 XRAY 1i22_D1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSKLLDDNIADDVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 55.65 55.00 1.80 XRAY 3lhm_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLDDNIADDVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 54.84 54.00 1.80 XRAY 1lmq_A1_PHR VYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRYWCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSY 55.74 54.00 1.60 XRAY 6d9i_B1_PHR VYSRCELAAAMKRLGLDNYRGYSLGNWVCAANYESGFNTQATNRNTDGSTDYGILQINSRWWCDDGKTPRSKNACGIPCSVLLRSDITEAVRCAKRIVSDGNGMNAWVAWRNRCRGTDVSKW 55.74 54.00 1.15 XRAY 1lze_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRYWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 55.00 52.00 1.80 XRAY 1i20_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADDVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 54.03 53.00 1.90 XRAY 1di3_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDGSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 54.03 53.00 1.80 XRAY 5v92_B1_PHR VYSRCELAAAMKRLGLDNYRGYSLGNWVCAANYESGFNTQATNRNTDGSTDYGILQINSRWWCDDGKTPRSKNACGIRCSVLLRSDITEAVRCAKRIVRDGNGMNAWVAWRNRCRGTDVSKW 55.74 54.00 1.11 XRAY 1kxy_A1_PHR VFGRCELAAAMKRHGLNNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 55.00 52.00 1.79 XRAY 1ge3_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQGRDVRQY 54.03 53.00 1.80 XRAY 1i1z_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLDDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 54.03 53.00 1.80 XRAY 1fly_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDANGMNAWVAWRNRCKGTDVQ 55.00 52.00 1.83 XRAY 1lzg_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRFWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 54.17 51.00 1.80 XRAY 6p4a_C1_PHR VFGRCELAAAMKRHGLDNYQGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSENLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 55.00 52.00 2.20 XRAY 1gfr_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGARNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 2iff_Y1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGKTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 55.00 52.00 2.65 XRAY 1oub_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVARDPQGIRAWVAWRNRCQNRDVRQY 54.03 53.00 1.80 XRAY 1iot_A1_PHR VFGRCELAAALKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 55.00 52.00 1.75 XRAY 1d6q_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVREPQGIRAWVAWRNRCQNRDVRQY 54.03 53.00 1.96 XRAY 6p4d_A1_PHR VFGRCELAAAMKRHGLDNYQGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSENLCNIPCSALLSSDITASVNCAKKIVSRGNGMNAWVAWRNRCKGTDVQ 55.00 52.00 1.05 XRAY 1wqm_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQF 54.03 53.00 1.80 XRAY 1gf3_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADSVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 2ihl_A1_PHR GRCELAAAMKRHGLDKYQGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDVHGMNAWVAWRNRCKGTDVN 55.93 52.00 1.40 XRAY 1b7s_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGASNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 2.00 XRAY 2vb1_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 54.17 51.00 0.65 XRAY 7cvj_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 54.17 51.00 1.50 XRAY 1kxx_A1_PHR VFGRCELAAAMKRHGLNNYRGYSLGDWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 54.17 51.00 1.71 XRAY 1gfk_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGANNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1uia_A1_PHR VFGRCELAAAMKXXGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 54.17 51.00 1.76 XRAY 1uic_A1_PHR VFGRCELAAAMKRAGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 54.17 51.00 1.95 XRAY 1ip1_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESAYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1gb8_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAMNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1ouh_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAANACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1gaz_A1_PHR KIFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 54.03 53.00 1.80 XRAY 1ip2_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAADRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1uif_A1_PHR FGRCELAAAMKRVGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 54.62 51.00 1.85 XRAY 1lhj_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDGQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1gfj_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGADNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1heo_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGVLQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 53.33 51.00 1.80 XRAY 1hem_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITATVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 54.17 51.00 1.80 XRAY 1ge4_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQARDVRQY 53.23 52.00 1.80 XRAY 1di5_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVXDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 2.20 XRAY 1uid_A1_PHR FGRCELAAAMKRFGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 54.62 51.00 1.95 XRAY 1di4_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNXXDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 2.00 XRAY 1ios_A1_PHR FGRCELAAAFKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 54.62 51.00 1.76 XRAY 1b7o_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESQYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1uie_A1_PHR FGRCELAAAMKRGGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 54.62 51.00 1.95 XRAY 1oue_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1ip6_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1ip7_B1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.90 XRAY 1lmt_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.60 XRAY 1lz5_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1lz6_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 2nwd_X1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.04 XRAY 1gb7_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGALNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1gfh_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAYNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1ior_A1_PHR VFGRCELAAALKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGIFQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 54.17 51.00 1.76 XRAY 1gb5_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAGNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1gf7_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVTRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1lhl_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNPGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1hen_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGVLQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITATVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 53.33 51.00 1.80 XRAY 1gb0_A1_PHR KLFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1b7p_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACGLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 2.00 XRAY 1gb9_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAFNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1b5u_A1_PHR KVFERCELARTLKRLGMDGYRGIALANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1yam_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGVRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1yaq_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNVADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1yan_A1_PHR KVFERCELARTLKRLGMDGYRGVSLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1yao_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGVFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1yap_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQVNSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1a2y_C1_PHR VFGRCELAAAMKRHGLANYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 54.17 51.00 1.50 XRAY 1gb6_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAINACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1gbw_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWIAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 3qy4_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSSNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 54.17 51.00 1.65 XRAY 134l_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNECQNRDVRQY 53.23 52.00 1.77 XRAY 1gez_A1_PHR KVFERCELSRTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1gb2_A1_PHR MFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.85 52.00 1.80 XRAY 1at5_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSXXNGMNAWVAWRNRCKGTDVQ 54.17 51.00 1.80 XRAY 1ir9_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKMVSDGNGMNAWVAWRNRCKGTDVQ 53.33 51.00 1.90 XRAY 1ir7_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNMPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 53.33 51.00 1.90 XRAY 1ir8_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQMNSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 53.33 51.00 1.63 XRAY 1h6m_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFQSNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 53.33 51.00 1.64 XRAY 1jse_A1_PHR RCELAAAMKRLGLDNYRGYSLGNWVCAAKFESNFNTHATNRNTDGSTDYGILQINSRWWCNDGRTPGSKNLCNIPCSALLSSDITASVNCAKKIASGGNGMNAWVAWRNRCKGTDV 57.76 53.00 1.12 XRAY 1gb3_A1_PHR FFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.85 52.00 1.80 XRAY 1oud_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDARQ 53.66 52.00 1.80 XRAY 1cj6_A1_PHR KVFERCELARALKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 2meb_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGLFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 2mee_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQLNSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1gdx_A1_PHR KVFERCELARTLKRLGMDGYAGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1eq5_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRNPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1dkk_B1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNSQATNRNTDGSTDYGVLQINSRWWCNDGKTPGSRNLCNIPCSALLSSDITATVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 53.33 51.00 1.90 XRAY 1oui_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAAACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1gf4_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADATACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1lsn_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITAAVNCAKKIVSNGNGMNAWVAWRNRCKGTDVQ 54.17 51.00 1.90 XRAY 1her_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNSQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 53.33 51.00 1.80 XRAY 1wqp_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNFNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1cj7_A1_PHR KVFERCELARVLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1oug_A1_PHR FERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.28 52.00 1.80 XRAY 1gf9_A1_PHR FERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.28 52.00 1.80 XRAY 1ge2_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACALSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 2.00 XRAY 1b5v_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRATDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 2.17 XRAY 3ln2_B1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVDDPQGIRAWVAWRNHCQNRDVRQY 53.23 52.00 2.04 XRAY 1eq4_A1_PHR KVFERCQLARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1b5y_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWEAGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 2.20 XRAY 1b5z_B1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCAALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 2.20 XRAY 1b5x_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLACSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 2.00 XRAY 1b5w_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINARYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 2.17 XRAY 2mec_B1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGMFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 2.20 XRAY 2mef_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQMNSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1gby_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWMAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1gbx_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWLAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1gf0_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLSKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1gf5_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACSKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 2hea_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGARAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1kxw_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGDWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 53.33 51.00 1.96 XRAY 3a3r_X1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQIDSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 53.33 51.00 1.90 XRAY 1gfg_A1_PHR ERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.72 51.00 1.80 XRAY 1gf8_A1_PHR ERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.72 51.00 1.80 XRAY 1gdw_A1_PHR KVFERCELARTLKRLGMDGYGGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1jka_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWDSGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.66 XRAY 1ioq_A1_PHR FGRCELAAAFKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGIFQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 53.78 51.00 1.79 XRAY 133l_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNHCQNRDVRQY 53.23 52.00 1.77 XRAY 1lsm_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGLLQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITATVNCAKKIVSSGNGMNAWVAWRNRCKGTDVQ 53.33 51.00 1.70 XRAY 1heq_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNSQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITATVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 53.33 51.00 1.80 XRAY 1gfa_A1_PHR ERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.72 51.00 1.80 XRAY 1wqn_A1_PHR KVFERCELARTLKRLGMDGFRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1wqo_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGFNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1wqq_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDFGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1tcy_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRFWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.70 XRAY 1gfe_A1_PHR ERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.72 51.00 1.80 XRAY 3ojp_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTNYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 53.33 51.00 1.81 XRAY 1laa_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTEYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.77 XRAY 1gay_A1_PHR ERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 53.72 51.00 1.80 XRAY 2mea_B1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGFFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 2.20 XRAY 2med_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQFNSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1nby_C1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAAKIVSDGNGMNAWVAWRNRCKGTDVQ 53.33 51.00 1.80 XRAY 1nbz_C1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKAIVSDGNGMNAWVAWRNRCKGTDVQ 53.33 51.00 1.85 XRAY 1flq_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKATDVQ 53.33 51.00 1.80 XRAY 1ouj_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRAVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1ouc_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWAAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1flw_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPASRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 53.33 51.00 1.81 XRAY 1flu_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDARTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 53.33 51.00 1.79 XRAY 1fn5_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDASTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 53.33 51.00 1.78 XRAY 1gf6_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRTVRDPQGIRAWVAWRNRCQNRDVRQY 53.23 52.00 1.80 XRAY 1lsy_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTSYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 53.33 51.00 1.90 XRAY 1hep_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNSQATNRNTDGSTDYGVLQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITATVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 52.50 50.00 1.80 XRAY 3ok0_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFASNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 53.33 51.00 1.82 XRAY 1ckg_B1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSVDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 2.20 XRAY 1eqe_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRNVR 53.28 52.00 1.80 XRAY 1ckd_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRAVNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1cj9_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNVRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1ckh_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKVPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 2.00 XRAY 1ndg_C1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSAWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 53.33 51.00 1.90 XRAY 1ckf_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSADYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1b7m_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACMKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 2.20 XRAY 1gbz_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWFAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1ckc_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRAANYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1cj8_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNARATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1b7l_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLLKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1bb3_B1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACLKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1gev_A1_PHR KVFERCETARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 2.10 XRAY 2hef_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNAADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 2heb_A1_PHR KVFERCELARTLKRLGMDGYRGASLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 2.20 XRAY 2hec_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGAFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 2hed_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQANSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1w08_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKNPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 2.50 XRAY 2mei_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQYNSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1gft_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWYAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1oua_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGTFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 2meh_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQTNSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1tdy_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRWWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.70 XRAY 1ip5_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQAIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1ip4_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPAAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1ip3_B1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDAKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1lhh_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWPAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1ge1_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFAINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.70 XRAY 1jkb_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWASGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.66 XRAY 3wvy_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTAGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 53.33 51.00 1.56 XRAY 2meg_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQSNSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1lhk_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIAPAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1inu_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWRAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1lyy_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNHGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1b7r_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFGINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1gbo_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWGAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1gfu_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWDAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1gfv_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWNAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1tby_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRLWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.77 XRAY 1b7n_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWLSGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 2hee_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQGNSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1lz4_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNAAHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1b7q_A1_PHR KVFERCELARTLKRLGMDGYRGISLALWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 2.00 XRAY 1tay_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRAWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.70 XRAY 3ww6_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRDTDGSTSYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 52.50 50.00 1.53 XRAY 1jkc_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAFVAWRNRCQNRDVRQY 52.42 52.00 1.60 XRAY 1lhi_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTGGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 3ww5_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRETDGSTSYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 52.50 50.00 1.53 XRAY 1ghl_B1_PHR GRCELAAAMKRMGLDNYRGYSLGNWVCAAKFESNFNTGATNRNTDGSTDYGILQINSRWWCNDGRTPGSKNLCHIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRKHCKGTDVN 55.08 51.00 2.10 XRAY 1ge0_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGGNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 1jhl_A1_PHR GRCELAAAMKRMGLDNYRGYSLGNWVCAAKFESNFNTGATNRNTDGSTDYGILQINSRWWCNDGRTPGSKNLCHIPCSALLSSDITASVNCAKKIVSDGDGMNAWVAWRKHCKGTDVN 55.08 51.00 2.40 XRAY 2bqg_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNAAHLSCSALLQDNIADAVAAAKRVARDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 6p4b_D1_PHR VFGRCELAAAMKRHGLDNYQGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSENLSNIPCSALLSSDITASVNSAKKIVSDGNGMNAWVAWRNRCKGTDVQ 53.33 51.00 1.90 XRAY 7ap7_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYRCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 52.42 52.00 1.15 XRAY 6t5s_A1_PHR IIPRCELVKILREHGFEGFEGTTIADWICLVQHESDYNTEAYNNNG-PSRDYGIFQINSKYWCNDGKTSGAVDGCHISCSELMTNDLEDDIKCAKKIARDAHGLTPWYGWKNHCEGRDLSSY 53.72 52.00 1.50 XRAY 1jkd_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAAVAWRNRCQNRDVRQY 52.42 52.00 1.80 XRAY 2bqm_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAANAAHLSCSALLQDNIADAVAAAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 51.61 51.00 1.80 XRAY 2bqj_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNAAHLSCSALLQDNIADAVAAAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 51.61 51.00 1.80 XRAY 2bqk_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNAAHLSCSALLQDNIADAVAAAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 51.61 51.00 1.80 XRAY 1lz2_A1_PHR RCELAAAMKRLGLDNYRGYSLGNWVCAAKFESNFNTHATNRNTNGSTDYGILQINSRWWCDNGRTPGSRNLCNIPCSALLSSDITASVNCAKKIASGGDGMNAWVAWRNRCKGTDV 55.17 51.00 2.80 XRAY 1bb4_B1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACLKRVVRDPQGIRAHVAWRNRCQNRDVRQY 51.61 51.00 2.23 XRAY 2bqf_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNAAHLSCSALLQDNVADAVAAAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 50.81 50.00 1.80 XRAY 2bqb_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNAAHLSCSALLQDNIADAVAAAKRVVRDPQGVRAWVAWRNRCQNRDVRQY 51.61 51.00 1.80 XRAY 2bqc_A1_PHR KVFERCELARTLKRLGMDGYRGVSLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNAAHLSCSALLQDNIADAVAAAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 50.81 50.00 1.80 XRAY 2bqd_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGVFQINSRYWCNDGKTPGAVNAAHLSCSALLQDNIADAVAAAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 50.81 50.00 1.80 XRAY 2bqe_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQVNSRYWCNDGKTPGAVNAAHLSCSALLQDNIADAVAAAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 50.81 50.00 1.80 XRAY 1fbi_Y1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNSQATNRNTDGSTDYGVLQINSRWWCNDGRTPGSRNLCNIPCSALQSSDITATANCAKKIVSDGNGMNAWVAWRKHCKGTDV 52.10 49.00 3.00 XRAY 2bqi_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNAAHLSCSALLQDNIADAVAAAKRVVRDPQGIRAWVAWRNRCQNRDARQ 52.03 51.00 1.80 XRAY 1hhl_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNSQATNRNTDGSTDYGVLQINSRWWCNDGRTPGSRNLCNIPCSALQSSDITATANCAKKIVSDGDGMNAWVAWRKHCKGTDV 52.10 49.00 1.90 XRAY 6t6c_A1_PHR IIPRCELVKILREHGFEGFEGTTIADWICLVQHASDYNTEAYNNNG-PSRDYGIFQINSKYWCNDGKTSGAVDGCHISCSELMTNDLEDDIKCAKKIARDAHGLTPWYGWKNHCEGRDLSSY 52.89 51.00 1.25 XRAY 2bqn_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNAAHLSCSALLQDNIADAAAAAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 51.61 51.00 1.80 XRAY 2bql_A1_PHR FERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNAAHLSCSALLQDNIADAVAAAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 51.64 50.00 1.80 XRAY 2bqo_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNAAHLSCSALLQDNIADAVAAAKRAVRDPQGIRAWVAWRNRCQNRDVRQY 51.61 51.00 1.80 XRAY 2bqh_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNAAHLSCSALLQDNIADAVAAAKRVVRDPQGIRAWAAWRNRCQNRDVRQY 50.81 50.00 1.80 XRAY 1qsw_D1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYCANDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 51.61 51.00 1.85 XRAY 1ix0_A1_PHR KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQANSRYWCNDGKTPGAVNAAHLSCSALLQDNIADAVAAAKRVVRDPQGIRAWVAWRNRCQNRDVRQY 50.81 50.00 1.80 XRAY 2gv0_A1_PHR KIYEQCELAREFKRHGMDGYHGYSLGDWVCTAKHESNFNTAATNYNRGDQSTDYGILQINSRWWCNDGKTPKAKNACGIECSELLKADITAAVNCAKRIVRDPNGMGAWVAWTKYCKGKDVSQW 54.84 54.00 1.90 XRAY 2z2f_A1_PHR KVFERCELARTLKKLGLDGYKGVSLANWLCLTKWESSYNTKATNYNPSSESTDYGIFQINSKWWCNDGKTPNAVDGCHVSCSELMENDIAKAVACAKHIVSE-QGITAWVAWKSHCRDHDVSSY 51.22 50.00 1.50 XRAY 1qqy_A1_PHR KIFSKCELARKLKSMGMDGFHGYSLANWVCMAEYESNFNTQAFNGRNSNGSSDYGIFQLNSKWWCKSN-SHSSANACNIMCSKFLDDNIDDDIACAKRVVKDPNGMSAWVAWVKHCKGKDLSKY 50.41 50.00 1.85 XRAY 5xuw_B1_PHR KVFSKCELAHKLKAQEMDGFGGYSLANWVCMAEYESNFNTRAFNGKNANGSYDYGLFQLNSKWWCKDNKR-SSSNACNIMCSKLLDDNIDDDISCAKRVVRDPKGMSAWKAWVKHCKDKDLSEY 51.22 50.00 1.76 XRAY 2z2e_B1_PHR KIFSKCELARKLKSMGMDGFHGYSLANWVCMAEYESNFNTQAFQGRQSQGSSDYGIFQLNSKWWCKS-QSHSSANACNIMCSKFLDDNIDDDIACAKRVVKDPQGMSAWVAWVKHCKGKDLSKY 48.78 48.00 2.01 XRAY 2eql_A1_PHR KVFSKCELAHKLKAQEMDGFGGYSLANWVCMAEYESNFNTRAFNGKNANGSSDYGLFQLNNKWWCKDNKR-SSSNACNIMCSKLLDENIDDDISCAKRVVRDPKGMSAWKAWVKHCKDKDLSEY 49.59 49.00 2.50 XRAY 3b0k_B1_PHR DLKDYGGVSLPEWVCTAFHTSGYDTQAIVQNND-STEYGLFQINNKIWCKDDQNPHSRNICNISCDKFLDDDLTDDIVCAKKILDK-VGINYWLAHKALCS 52.53 42.00 1.60 XRAY 6ip9_A1_PHR KDLKGYGGVSLPEWVCTTFHTSGYDTQAIVQNND-STEYGLFQINNKIWCKDDQNPHSSNICNISCDKFLDDDLTDDIMCVKKILDK-VGINYWLAHKALCS 51.00 41.00 1.85 XRAY 1hfz_D1_PHR KDLKGYGGVSLPEWVCTTFHTSGYDTQAIVQNND-STEYGLFQINNKIWCKDDQNPHSSNICNISCDKFLDDDLTDDIVCVKKILDK-VGINYWLAHKALCS 51.00 41.00 2.30 XRAY 1fkq_A1_PHR DLKDYGGVSLPEWVCVAFHTSGYDTQAIVQNND-STEYGLFQINNKIWCKDDQNPHSRNICNISCDKFLDDDLTDDIVCAKKILDK-VGINYWLAHKALCS 51.52 41.00 1.80 XRAY 1fkv_A1_PHR DLKDYGGVSLPEWVCIAFHTSGYDTQAIVQNND-STEYGLFQINNKIWCKDDQNPHSRNICNISCDKFLDDDLTDDIVCAKKILDK-VGINYWLAHKALCS 51.52 41.00 2.00 XRAY 4yf2_C1_PHR KVFSRCELAKEMHDFGLDGYRGYNLADWVCLAYYTSGFNTNAVDHEADGSTNNGIFQISSRRWCRTLASNG-PNLCRIYCTDLLNNDLKDSIVCAMKIVQEPLGLGYWEAWRHHCQGRDLSD 43.80 42.00 2.15 XRAY 1alc_A1_PHR KCELSQNLY--DIDGYGRIALPELICTMFHTSGYDTQAIVEN-DESTEYGLFQISNALWCKSSQSPQSRNICDITCDKFLDDDITDDIMCAKKIL-DIKGIDYWIAHKALCT 50.00 44.00 1.70 XRAY 1yro_C1_PHR IKDIDGYQGISLLEWACVLFHTSGYDTQAVV-NDNGSTEYGLFQISDRFWCKSSEFPESENICGISCDKLLDDELDDDIACAKKILA-IKGIDYWKAYKPMCS-EKLEQWRC 46.79 41.00 1.90 XRAY 1b9o_A1_PHR LLKDIDGYGGIALPELICTMFHTSGYDTQAIVEN-DESTEYGLFQISNKLWCKSSQVPQSRNICDISCDKFLDDDITDDIMCAKKIL-DIKGIDYWLAHKALCT 49.02 40.00 1.15 XRAY 1hml_A1_PHR LLKDIDGYGGIALPELICTMFHTSGYDTQAIVENNE-STEYGLFQISNKLWCKSSQVPQSRNICDISCDKFLDDDITDDIMCAKKIL-DIKGIDYWLAHKALCT 48.04 39.00 1.70 XRAY 3b0o_B1_PHR LKDIDGYGGIALPELICTMFHTSGYDTQAIVENNE-STEYGLFQISNKLWCKSSQVPQSRNICDISCDKFLDDDITDDIMCAKKIL-DIKGIDYWLAHKALCT 48.51 39.00 1.61 XRAY 1hfx_A1_PHR DLAGYRDITLPEWLCIIFHISGYDTQAIVKNSDH-KEYGLFQINDKDFCESSTTVQSRNICDISCDKLLDDDLTDDIMCVKKIL-DIKGIDYWLAHKPLCS 48.48 39.00 1.90 XRAY 1gd6_A1_PHR KHGFEENLMRNWVCLVEHESSRDTSKTNTNRNGSKDYGLFQINDRYWCSKGASPGK--DCNVKCSDLLTDDITKAAKCAKKIYKR-HRFDAWYGWKNHCQGS 49.49 40.00 2.50 XRAY 6ukc_A1_PHR DIKNWVCIAEFESSFNTAAINRNRNRSTDYGIFQINNKYWCGS--D-YGKNVCKIPCSDLMSDDITEALRCAETIRRDTERFRGRGKGYSAWVAYNSKCKNRDLDQY 49.04 41.00 2.25 XRAY 3zvq_A1_PHR VFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTP 56.52 31.00 2.00 XRAY 2fbd_B1_PHR GVPKSELPQWTCIAEHESSYRTNVVGPTNSNGSNDYGIFQINNYYWCQPSNGRFSYNECHLSCDALLTDNISNSVTCARKIKSQ-QGWTAWSTWKY-CSG 45.92 36.00 1.90 XRAY 1iiz_A1_PHR QGFDENLMRDWVCLVENESARYTDKIANVNKNGSRDYGLFQINDKYWCSKGSTPGK--DCNVTCSQLLTDDITVASTCAKKIYKRTK-FDAWSGWDNHCNH 43.88 35.00 2.40 XRAY 3cb7_B1_PHR NQLARWTCIAEHESSYNTKAVGSLNSNGSRDYGIFQINNYYWCSPPSGAFSYDECKIKCEDFLVDSIEPAVKCAQLVL-KQQGWTAWSTWKY-CD 44.09 33.00 1.90 XRAY 3zvq_B1_PHR SRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQ 50.00 20.00 2.00 XRAY Number of templates after user specified chains are included: 251 Fasta log message: Number of matches: 251 --------------------------------------------------------- Fasta: Getting Template Sequences and Multiple Alignment: --------------------------------------------------------- Top match from FASTA search: 1jug_A1_PHR ######################################################################################### ##### Template Model Search Results ##### ######################################################################################### CHAIN_ID EVALUE SCORE localSEQID overallSEQID resolution experiment SOURCE 1jug_A1_PHR 1.0e-87 293.5 100.0 100.0 1.9 XRAY Phmmer 5v8g_A1_PHR 4.7e-48 165.2 57.4 55.0 1.2 XRAY Phmmer 1i22_D1_PHR 5.9e-48 164.9 55.6 55.0 1.8 XRAY Phmmer 3lhm_A1_PHR 3.8e-47 162.3 54.8 54.0 1.8 XRAY Phmmer 1lmq_A1_PHR 4.8e-47 161.9 55.7 54.0 1.6 XRAY Phmmer 6d9i_B1_PHR 2.1e-46 159.9 55.7 54.0 1.1 XRAY Phmmer 1lze_A1_PHR 2.3e-46 159.7 55.0 52.0 1.8 XRAY Phmmer 1i20_A1_PHR 2.5e-46 159.6 54.0 53.0 1.9 XRAY Phmmer 1di3_A1_PHR 2.8e-46 159.4 54.0 53.0 1.8 XRAY Phmmer 5v92_B1_PHR 3.7e-46 159.0 55.7 54.0 1.1 XRAY Phmmer 1ge3_A1_PHR 4.2e-46 158.9 54.0 53.0 1.8 XRAY Phmmer 1kxy_A1_PHR 4.3e-46 158.9 55.0 52.0 1.8 XRAY Phmmer 1i1z_A1_PHR 4.8e-46 158.7 54.0 53.0 1.8 XRAY Phmmer 1fly_A1_PHR 4.9e-46 158.7 55.0 52.0 1.8 XRAY Phmmer 1lzg_A1_PHR 6.5e-46 158.3 54.2 51.0 1.8 XRAY Phmmer 6p4a_C1_PHR 8.3e-46 157.9 55.0 52.0 2.2 XRAY Phmmer 1gfr_A1_PHR 8.7e-46 157.8 53.2 52.0 1.8 XRAY Phmmer 1oub_A1_PHR 9.1e-46 157.8 54.0 53.0 1.8 XRAY Phmmer 2iff_Y1_PHR 9.3e-46 157.8 55.0 52.0 2.6 XRAY Phmmer 1d6q_A1_PHR 1.1e-45 157.5 54.0 53.0 2.0 XRAY Phmmer 1iot_A1_PHR 1.1e-45 157.5 55.0 52.0 1.8 XRAY Phmmer 6p4d_A1_PHR 1.3e-45 157.3 55.0 52.0 1.1 XRAY Phmmer 1wqm_A1_PHR 1.5e-45 157.1 54.0 53.0 1.8 XRAY Phmmer 1gf3_A1_PHR 1.7e-45 156.9 53.2 52.0 1.8 XRAY Phmmer 1b7s_A1_PHR 1.8e-45 156.8 53.2 52.0 2.0 XRAY Phmmer 2ihl_A1_PHR 1.8e-45 156.9 55.9 52.0 1.4 XRAY Phmmer 1gfk_A1_PHR 2.0e-45 156.7 53.2 52.0 1.8 XRAY Phmmer 1kxx_A1_PHR 2.0e-45 156.7 54.2 51.0 1.7 XRAY Phmmer 2vb1_A1_PHR 2.0e-45 156.7 54.2 51.0 0.7 XRAY Phmmer 7cvj_A1_PHR 2.0e-45 156.7 54.2 51.0 1.5 XRAY Phmmer 1uia_A1_PHR 2.1e-45 156.7 54.2 51.0 1.8 XRAY Phmmer 1ip1_A1_PHR 2.2e-45 156.5 53.2 52.0 1.8 XRAY Phmmer 1uic_A1_PHR 2.2e-45 156.6 54.2 51.0 1.9 XRAY Phmmer 1gb8_A1_PHR 2.3e-45 156.5 53.2 52.0 1.8 XRAY Phmmer 1ouh_A1_PHR 2.4e-45 156.4 53.2 52.0 1.8 XRAY Phmmer 1gaz_A1_PHR 2.5e-45 156.4 54.0 53.0 1.8 XRAY Phmmer 1ip2_A1_PHR 2.5e-45 156.4 53.2 52.0 1.8 XRAY Phmmer 1uif_A1_PHR 2.5e-45 156.4 54.6 51.0 1.9 XRAY Phmmer 1gfj_A1_PHR 2.6e-45 156.3 53.2 52.0 1.8 XRAY Phmmer 1lhj_A1_PHR 2.6e-45 156.3 53.2 52.0 1.8 XRAY Phmmer 1hem_A1_PHR 2.7e-45 156.3 54.2 51.0 1.8 XRAY Phmmer 1heo_A1_PHR 2.7e-45 156.3 53.3 51.0 1.8 XRAY Phmmer 1ge4_A1_PHR 2.8e-45 156.2 53.2 52.0 1.8 XRAY Phmmer 1di5_A1_PHR 2.9e-45 156.2 53.2 52.0 2.2 XRAY Phmmer 1b7o_A1_PHR 3.0e-45 156.1 53.2 52.0 1.8 XRAY Phmmer 1di4_A1_PHR 3.0e-45 156.1 53.2 52.0 2.0 XRAY Phmmer 1uid_A1_PHR 3.0e-45 156.1 54.6 51.0 1.9 XRAY Phmmer 1ios_A1_PHR 3.1e-45 156.1 54.6 51.0 1.8 XRAY Phmmer 1ip6_A1_PHR 3.1e-45 156.1 53.2 52.0 1.8 XRAY Phmmer 1ip7_B1_PHR 3.1e-45 156.0 53.2 52.0 1.9 XRAY Phmmer 1lmt_A1_PHR 3.1e-45 156.0 53.2 52.0 1.6 XRAY Phmmer 1lz5_A1_PHR 3.1e-45 156.0 53.2 52.0 1.8 XRAY Phmmer 1lz6_A1_PHR 3.1e-45 156.0 53.2 52.0 1.8 XRAY Phmmer 1oue_A1_PHR 3.1e-45 156.1 53.2 52.0 1.8 XRAY Phmmer 1uie_A1_PHR 3.1e-45 156.1 54.6 51.0 1.9 XRAY Phmmer 2nwd_X1_PHR 3.1e-45 156.0 53.2 52.0 1.0 XRAY Phmmer 1gb7_A1_PHR 3.2e-45 156.0 53.2 52.0 1.8 XRAY Phmmer 1gfh_A1_PHR 3.4e-45 155.9 53.2 52.0 1.8 XRAY Phmmer 1gb5_A1_PHR 3.5e-45 155.9 53.2 52.0 1.8 XRAY Phmmer 1gf7_A1_PHR 3.5e-45 155.9 53.2 52.0 1.8 XRAY Phmmer 1ior_A1_PHR 3.5e-45 155.9 54.2 51.0 1.8 XRAY Phmmer 1lhl_A1_PHR 3.6e-45 155.9 53.2 52.0 1.8 XRAY Phmmer 1hen_A1_PHR 3.8e-45 155.8 53.3 51.0 1.8 XRAY Phmmer 1gb0_A1_PHR 4.0e-45 155.7 53.2 52.0 1.8 XRAY Phmmer 1b7p_A1_PHR 4.1e-45 155.7 53.2 52.0 2.0 XRAY Phmmer 1gb9_A1_PHR 4.1e-45 155.6 53.2 52.0 1.8 XRAY Phmmer 1b5u_A1_PHR 4.2e-45 155.6 53.2 52.0 1.8 XRAY Phmmer 1gb6_A1_PHR 4.4e-45 155.6 53.2 52.0 1.8 XRAY Phmmer 1gbw_A1_PHR 4.4e-45 155.6 52.4 52.0 1.8 XRAY Phmmer 1yam_A1_PHR 4.4e-45 155.6 53.2 52.0 1.8 XRAY Phmmer 1yan_A1_PHR 4.4e-45 155.6 52.4 52.0 1.8 XRAY Phmmer 1yao_A1_PHR 4.4e-45 155.6 52.4 52.0 1.8 XRAY Phmmer 1yap_A1_PHR 4.4e-45 155.6 52.4 52.0 1.8 XRAY Phmmer 1yaq_A1_PHR 4.4e-45 155.6 52.4 52.0 1.8 XRAY Phmmer 134l_A1_PHR 4.5e-45 155.5 53.2 52.0 1.8 XRAY Phmmer 1a2y_C1_PHR 4.5e-45 155.6 54.2 51.0 1.5 XRAY Phmmer 1gez_A1_PHR 4.6e-45 155.5 53.2 52.0 1.8 XRAY Phmmer 3qy4_A1_PHR 4.6e-45 155.5 54.2 51.0 1.6 XRAY Phmmer 1gb2_A1_PHR 4.9e-45 155.4 52.8 52.0 1.8 XRAY Phmmer 1at5_A1_PHR 5.1e-45 155.4 54.2 51.0 1.8 XRAY Phmmer 1h6m_A1_PHR 5.2e-45 155.4 53.3 51.0 1.6 XRAY Phmmer 1ir7_A1_PHR 5.2e-45 155.4 53.3 51.0 1.9 XRAY Phmmer 1ir8_A1_PHR 5.2e-45 155.4 53.3 51.0 1.6 XRAY Phmmer 1ir9_A1_PHR 5.2e-45 155.4 53.3 51.0 1.9 XRAY Phmmer 1gb3_A1_PHR 5.6e-45 155.2 52.8 52.0 1.8 XRAY Phmmer 1jse_A1_PHR 5.6e-45 155.2 57.8 53.0 1.1 XRAY Phmmer 1oud_A1_PHR 5.6e-45 155.2 53.7 52.0 1.8 XRAY Phmmer 1cj6_A1_PHR 5.7e-45 155.2 53.2 52.0 1.8 XRAY Phmmer 2meb_A1_PHR 6.1e-45 155.1 52.4 52.0 1.8 XRAY Phmmer 2mee_A1_PHR 6.1e-45 155.1 52.4 52.0 1.8 XRAY Phmmer 1eq5_A1_PHR 6.3e-45 155.1 53.2 52.0 1.8 XRAY Phmmer 1gdx_A1_PHR 6.3e-45 155.1 53.2 52.0 1.8 XRAY Phmmer 1oui_A1_PHR 6.4e-45 155.0 53.2 52.0 1.8 XRAY Phmmer 1dkk_B1_PHR 6.6e-45 155.0 53.3 51.0 1.9 XRAY Phmmer 1gf4_A1_PHR 6.8e-45 155.0 53.2 52.0 1.8 XRAY Phmmer 1lsn_A1_PHR 7.1e-45 154.9 54.2 51.0 1.9 XRAY Phmmer 1her_A1_PHR 7.2e-45 154.9 53.3 51.0 1.8 XRAY Phmmer 1oug_A1_PHR 7.3e-45 154.8 53.3 52.0 1.8 XRAY Phmmer 1wqp_A1_PHR 7.3e-45 154.9 53.2 52.0 1.8 XRAY Phmmer 1cj7_A1_PHR 7.4e-45 154.8 53.2 52.0 1.8 XRAY Phmmer 1gf9_A1_PHR 7.4e-45 154.8 53.3 52.0 1.8 XRAY Phmmer 1b5v_A1_PHR 7.7e-45 154.8 52.4 52.0 2.2 XRAY Phmmer 1ge2_A1_PHR 7.7e-45 154.8 53.2 52.0 2.0 XRAY Phmmer 3ln2_B1_PHR 7.8e-45 154.8 53.2 52.0 2.0 XRAY Phmmer 1eq4_A1_PHR 7.9e-45 154.7 52.4 52.0 1.8 XRAY Phmmer 1b5w_A1_PHR 8.0e-45 154.7 52.4 52.0 2.2 XRAY Phmmer 1b5x_A1_PHR 8.0e-45 154.7 52.4 52.0 2.0 XRAY Phmmer 1b5y_A1_PHR 8.0e-45 154.7 52.4 52.0 2.2 XRAY Phmmer 1b5z_B1_PHR 8.0e-45 154.7 52.4 52.0 2.2 XRAY Phmmer 1gby_A1_PHR 8.4e-45 154.7 52.4 52.0 1.8 XRAY Phmmer 2mec_B1_PHR 8.4e-45 154.7 52.4 52.0 2.2 XRAY Phmmer 2mef_A1_PHR 8.4e-45 154.7 52.4 52.0 1.8 XRAY Phmmer 1gbx_A1_PHR 8.5e-45 154.6 52.4 52.0 1.8 XRAY Phmmer 1gf0_A1_PHR 8.8e-45 154.6 52.4 52.0 1.8 XRAY Phmmer 1gf5_A1_PHR 8.8e-45 154.6 52.4 52.0 1.8 XRAY Phmmer 1gfg_A1_PHR 8.8e-45 154.6 53.7 51.0 1.8 XRAY Phmmer 1gf8_A1_PHR 8.9e-45 154.6 53.7 51.0 1.8 XRAY Phmmer 2hea_A1_PHR 8.9e-45 154.6 53.2 52.0 1.8 XRAY Phmmer 1gdw_A1_PHR 9.0e-45 154.6 53.2 52.0 1.8 XRAY Phmmer 1jka_A1_PHR 9.0e-45 154.6 52.4 52.0 1.7 XRAY Phmmer 1kxw_A1_PHR 9.1e-45 154.6 53.3 51.0 2.0 XRAY Phmmer 3a3r_X1_PHR 9.1e-45 154.6 53.3 51.0 1.9 XRAY Phmmer 133l_A1_PHR 9.6e-45 154.5 53.2 52.0 1.8 XRAY Phmmer 1ioq_A1_PHR 9.7e-45 154.5 53.8 51.0 1.8 XRAY Phmmer 1gfa_A1_PHR 1.0e-44 154.4 53.7 51.0 1.8 XRAY Phmmer 1heq_A1_PHR 1.0e-44 154.4 53.3 51.0 1.8 XRAY Phmmer 1lsm_A1_PHR 1.0e-44 154.4 53.3 51.0 1.7 XRAY Phmmer 1tcy_A1_PHR 1.0e-44 154.4 52.4 52.0 1.7 XRAY Phmmer 1wqn_A1_PHR 1.0e-44 154.4 52.4 52.0 1.8 XRAY Phmmer 1wqo_A1_PHR 1.0e-44 154.4 52.4 52.0 1.8 XRAY Phmmer 1wqq_A1_PHR 1.0e-44 154.4 52.4 52.0 1.8 XRAY Phmmer 1gay_A1_PHR 1.1e-44 154.3 53.7 51.0 1.8 XRAY Phmmer 1gfe_A1_PHR 1.1e-44 154.3 53.7 51.0 1.8 XRAY Phmmer 1laa_A1_PHR 1.1e-44 154.3 52.4 52.0 1.8 XRAY Phmmer 2mea_B1_PHR 1.1e-44 154.3 52.4 52.0 2.2 XRAY Phmmer 2med_A1_PHR 1.1e-44 154.3 52.4 52.0 1.8 XRAY Phmmer 3ojp_A1_PHR 1.1e-44 154.3 53.3 51.0 1.8 XRAY Phmmer 1flq_A1_PHR 1.2e-44 154.2 53.3 51.0 1.8 XRAY Phmmer 1nby_C1_PHR 1.2e-44 154.2 53.3 51.0 1.8 XRAY Phmmer 1nbz_C1_PHR 1.2e-44 154.2 53.3 51.0 1.9 XRAY Phmmer 1ouc_A1_PHR 1.2e-44 154.1 52.4 52.0 1.8 XRAY Phmmer 1ouj_A1_PHR 1.2e-44 154.1 53.2 52.0 1.8 XRAY Phmmer 1flu_A1_PHR 1.3e-44 154.1 53.3 51.0 1.8 XRAY Phmmer 1flw_A1_PHR 1.3e-44 154.1 53.3 51.0 1.8 XRAY Phmmer 1fn5_A1_PHR 1.3e-44 154.1 53.3 51.0 1.8 XRAY Phmmer 1gf6_A1_PHR 1.3e-44 154.0 53.2 52.0 1.8 XRAY Phmmer 1ckg_B1_PHR 1.4e-44 153.9 52.4 52.0 2.2 XRAY Phmmer 1hep_A1_PHR 1.4e-44 154.0 52.5 50.0 1.8 XRAY Phmmer 1lsy_A1_PHR 1.4e-44 154.0 53.3 51.0 1.9 XRAY Phmmer 3ok0_A1_PHR 1.4e-44 153.9 53.3 51.0 1.8 XRAY Phmmer 1b7l_A1_PHR 1.5e-44 153.8 52.4 52.0 1.8 XRAY Phmmer 1b7m_A1_PHR 1.5e-44 153.8 52.4 52.0 2.2 XRAY Phmmer 1bb3_B1_PHR 1.5e-44 153.8 52.4 52.0 1.8 XRAY Phmmer 1cj8_A1_PHR 1.5e-44 153.8 52.4 52.0 1.8 XRAY Phmmer 1cj9_A1_PHR 1.5e-44 153.9 52.4 52.0 1.8 XRAY Phmmer 1ckc_A1_PHR 1.5e-44 153.8 52.4 52.0 1.8 XRAY Phmmer 1ckd_A1_PHR 1.5e-44 153.9 52.4 52.0 1.8 XRAY Phmmer 1ckf_A1_PHR 1.5e-44 153.8 52.4 52.0 1.8 XRAY Phmmer 1ckh_A1_PHR 1.5e-44 153.9 52.4 52.0 2.0 XRAY Phmmer 1eqe_A1_PHR 1.5e-44 153.9 53.3 52.0 1.8 XRAY Phmmer 1gbz_A1_PHR 1.5e-44 153.8 52.4 52.0 1.8 XRAY Phmmer 1ndg_C1_PHR 1.5e-44 153.9 53.3 51.0 1.9 XRAY Phmmer 1gev_A1_PHR 1.6e-44 153.7 52.4 52.0 2.1 XRAY Phmmer 1gft_A1_PHR 1.7e-44 153.6 52.4 52.0 1.8 XRAY Phmmer 1w08_A1_PHR 1.7e-44 153.7 52.4 52.0 2.5 XRAY Phmmer 2heb_A1_PHR 1.7e-44 153.7 52.4 52.0 2.2 XRAY Phmmer 2hec_A1_PHR 1.7e-44 153.7 52.4 52.0 1.8 XRAY Phmmer 2hed_A1_PHR 1.7e-44 153.7 52.4 52.0 1.8 XRAY Phmmer 2hef_A1_PHR 1.7e-44 153.7 52.4 52.0 1.8 XRAY Phmmer 2mei_A1_PHR 1.7e-44 153.6 52.4 52.0 1.8 XRAY Phmmer 1oua_A1_PHR 1.8e-44 153.6 52.4 52.0 1.8 XRAY Phmmer 2meh_A1_PHR 1.8e-44 153.6 52.4 52.0 1.8 XRAY Phmmer 1tdy_A1_PHR 2.1e-44 153.4 52.4 52.0 1.7 XRAY Phmmer 1ge1_A1_PHR 2.2e-44 153.3 52.4 52.0 1.7 XRAY Phmmer 1ip3_B1_PHR 2.2e-44 153.3 52.4 52.0 1.8 XRAY Phmmer 1ip4_A1_PHR 2.2e-44 153.3 52.4 52.0 1.8 XRAY Phmmer 1ip5_A1_PHR 2.2e-44 153.3 52.4 52.0 1.8 XRAY Phmmer 1jkb_A1_PHR 2.2e-44 153.3 52.4 52.0 1.7 XRAY Phmmer 1lhh_A1_PHR 2.2e-44 153.3 52.4 52.0 1.8 XRAY Phmmer 3wvy_A1_PHR 2.3e-44 153.3 53.3 51.0 1.6 XRAY Phmmer 2meg_A1_PHR 2.5e-44 153.1 52.4 52.0 1.8 XRAY Phmmer 1lhk_A1_PHR 2.7e-44 153.0 52.4 52.0 1.8 XRAY Phmmer 1b7r_A1_PHR 3.2e-44 152.8 52.4 52.0 1.8 XRAY Phmmer 1inu_A1_PHR 3.2e-44 152.8 52.4 52.0 1.8 XRAY Phmmer 1lyy_A1_PHR 3.2e-44 152.8 52.4 52.0 1.8 XRAY Phmmer 1gbo_A1_PHR 3.4e-44 152.7 52.4 52.0 1.8 XRAY Phmmer 1gfu_A1_PHR 3.5e-44 152.6 52.4 52.0 1.8 XRAY Phmmer 1gfv_A1_PHR 3.7e-44 152.6 52.4 52.0 1.8 XRAY Phmmer 1b7n_A1_PHR 4.1e-44 152.4 52.4 52.0 1.8 XRAY Phmmer 1tby_A1_PHR 4.1e-44 152.4 52.4 52.0 1.8 XRAY Phmmer 2hee_A1_PHR 4.7e-44 152.2 52.4 52.0 1.8 XRAY Phmmer 1lz4_A1_PHR 4.8e-44 152.2 52.4 52.0 1.8 XRAY Phmmer 1b7q_A1_PHR 5.2e-44 152.1 52.4 52.0 2.0 XRAY Phmmer 1tay_A1_PHR 5.9e-44 151.9 52.4 52.0 1.7 XRAY Phmmer 1jkc_A1_PHR 6.2e-44 151.8 52.4 52.0 1.6 XRAY Phmmer 3ww6_A1_PHR 6.3e-44 151.9 52.5 50.0 1.5 XRAY Phmmer 1lhi_A1_PHR 6.8e-44 151.7 52.4 52.0 1.8 XRAY Phmmer 3ww5_A1_PHR 7.4e-44 151.6 52.5 50.0 1.5 XRAY Phmmer 1ghl_B1_PHR 7.6e-44 151.6 55.1 51.0 2.1 XRAY Phmmer 1ge0_A1_PHR 8.4e-44 151.4 52.4 52.0 1.8 XRAY Phmmer 1jhl_A1_PHR 9.3e-44 151.3 55.1 51.0 2.4 XRAY Phmmer 2bqg_A1_PHR 2.2e-43 150.1 52.4 52.0 1.8 XRAY Phmmer 6p4b_D1_PHR 2.4e-43 150.0 53.3 51.0 1.9 XRAY Phmmer 7ap7_A1_PHR 2.4e-43 149.9 52.4 52.0 1.1 XRAY Phmmer 1jkd_A1_PHR 2.5e-43 149.9 52.4 52.0 1.8 XRAY Phmmer 6t5s_A1_PHR 2.5e-43 149.9 53.7 52.0 1.5 XRAY Phmmer 2bqm_A1_PHR 5.8e-43 148.7 51.6 51.0 1.8 XRAY Phmmer 2bqj_A1_PHR 7.4e-43 148.4 51.6 51.0 1.8 XRAY Phmmer 2bqk_A1_PHR 7.8e-43 148.3 51.6 51.0 1.8 XRAY Phmmer 1lz2_A1_PHR 8.2e-43 148.2 55.2 51.0 2.8 XRAY Phmmer 1bb4_B1_PHR 9.5e-43 148.0 51.6 51.0 2.2 XRAY Phmmer 1fbi_Y1_PHR 1.1e-42 147.8 52.1 49.0 3.0 XRAY Phmmer 2bqb_A1_PHR 1.1e-42 147.8 51.6 51.0 1.8 XRAY Phmmer 2bqc_A1_PHR 1.1e-42 147.8 50.8 50.0 1.8 XRAY Phmmer 2bqd_A1_PHR 1.1e-42 147.8 50.8 50.0 1.8 XRAY Phmmer 2bqe_A1_PHR 1.1e-42 147.8 50.8 50.0 1.8 XRAY Phmmer 2bqf_A1_PHR 1.1e-42 147.8 50.8 50.0 1.8 XRAY Phmmer 2bqi_A1_PHR 1.3e-42 147.5 52.0 51.0 1.8 XRAY Phmmer 1hhl_A1_PHR 1.4e-42 147.5 52.1 49.0 1.9 XRAY Phmmer 2bqn_A1_PHR 1.5e-42 147.3 51.6 51.0 1.8 XRAY Phmmer 6t6c_A1_PHR 1.6e-42 147.4 52.9 51.0 1.2 XRAY Phmmer 2bql_A1_PHR 1.7e-42 147.1 51.6 50.0 1.8 XRAY Phmmer 2bqo_A1_PHR 2.9e-42 146.4 51.6 51.0 1.8 XRAY Phmmer 2bqh_A1_PHR 3.0e-42 146.4 50.8 50.0 1.8 XRAY Phmmer 1qsw_D1_PHR 3.3e-42 146.2 51.6 51.0 1.9 XRAY Phmmer 1ix0_A1_PHR 4.1e-42 146.0 50.8 50.0 1.8 XRAY Phmmer 2gv0_A1_PHR 4.8e-42 145.8 54.8 54.0 1.9 XRAY Phmmer 2z2f_A1_PHR 4.2e-41 142.7 51.2 50.0 1.5 XRAY Phmmer 1qqy_A1_PHR 5.0e-39 136.0 50.4 50.0 1.9 XRAY Phmmer 5xuw_B1_PHR 2.7e-38 133.7 51.2 50.0 1.8 XRAY Phmmer 2z2e_B1_PHR 3.0e-38 133.5 48.8 48.0 2.0 XRAY Phmmer 2eql_A1_PHR 1.0e-37 131.7 49.6 49.0 2.5 XRAY Phmmer 3b0k_B1_PHR 7.3e-33 115.9 52.5 42.0 1.6 XRAY Phmmer 6ip9_A1_PHR 1.5e-32 114.9 51.0 41.0 1.9 XRAY Phmmer 1hfz_D1_PHR 2.4e-32 114.4 51.0 41.0 2.3 XRAY Phmmer 1fkq_A1_PHR 3.2e-32 114.0 51.5 41.0 1.8 XRAY Phmmer 1fkv_A1_PHR 4.1e-32 113.6 51.5 41.0 2.0 XRAY Phmmer 4yf2_C1_PHR 7.3e-31 109.5 43.8 42.0 2.1 XRAY Phmmer 1alc_A1_PHR 9.6e-31 109.1 50.0 44.0 1.7 XRAY Phmmer 1b9o_A1_PHR 1.3e-30 108.6 49.0 40.0 1.1 XRAY Phmmer 1yro_C1_PHR 1.3e-30 108.8 46.8 41.0 1.9 XRAY Phmmer 1hml_A1_PHR 2.5e-30 107.7 48.0 39.0 1.7 XRAY Phmmer 3b0o_B1_PHR 2.6e-30 107.7 48.5 39.0 1.6 XRAY Phmmer 1hfx_A1_PHR 4.0e-28 100.6 48.5 39.0 1.9 XRAY Phmmer 1gd6_A1_PHR 4.9e-28 100.3 49.5 40.0 2.5 XRAY Phmmer 6ukc_A1_PHR 1.0e-27 99.9 49.0 41.0 2.2 XRAY Phmmer 3zvq_A1_PHR 5.2e-24 87.3 56.5 31.0 2.0 XRAY Phmmer 2fbd_B1_PHR 3.0e-23 84.8 45.9 36.0 1.9 XRAY Phmmer 1iiz_A1_PHR 3.5e-22 81.4 43.9 35.0 2.4 XRAY Phmmer 3cb7_B1_PHR 1.9e-20 75.9 44.1 33.0 1.9 XRAY Phmmer 3zvq_B1_PHR 4.0e-14 55.4 50.0 20.0 2.0 XRAY Phmmer For inline graphs use a Java browser Warning: Proxy not set! downloading https://files.rcsb.org/download/1JUG.pdb.gz Warning: Proxy not set! downloading https://files.rcsb.org/download/5V8G.pdb.gz Warning: Proxy not set! downloading https://files.rcsb.org/download/1I22.pdb.gz Warning: Proxy not set! downloading https://files.rcsb.org/download/3LHM.pdb.gz Warning: Proxy not set! downloading https://files.rcsb.org/download/1LMQ.pdb.gz Warning: Proxy not set! downloading https://files.rcsb.org/download/6D9I.pdb.gz Warning: Proxy not set! downloading https://files.rcsb.org/download/1LZE.pdb.gz Warning: Proxy not set! downloading https://files.rcsb.org/download/1I20.pdb.gz Warning: Proxy not set! downloading https://files.rcsb.org/download/1DI3.pdb.gz Warning: Proxy not set! downloading https://files.rcsb.org/download/5V92.pdb.gz Warning: Proxy not set! downloading https://files.rcsb.org/download/1GE3.pdb.gz Warning: Proxy not set! downloading https://files.rcsb.org/download/1KXY.pdb.gz Warning: Proxy not set! downloading https://files.rcsb.org/download/1I1Z.pdb.gz Warning: Proxy not set! downloading https://files.rcsb.org/download/1FLY.pdb.gz Warning: Proxy not set! downloading https://files.rcsb.org/download/1LZG.pdb.gz Warning: Proxy not set! downloading https://files.rcsb.org/download/6P4A.pdb.gz Warning: Proxy not set! downloading https://files.rcsb.org/download/1GFR.pdb.gz Warning: Proxy not set! downloading https://files.rcsb.org/download/1OUB.pdb.gz Warning: Proxy not set! downloading https://files.rcsb.org/download/2IFF.pdb.gz Warning: Proxy not set! downloading https://files.rcsb.org/download/1D6Q.pdb.gz Warning: Proxy not set! downloading https://files.rcsb.org/download/1IOT.pdb.gz Warning: Proxy not set! downloading https://files.rcsb.org/download/6P4D.pdb.gz Warning: Proxy not set! downloading https://files.rcsb.org/download/1WQM.pdb.gz Warning: Proxy not set! downloading https://files.rcsb.org/download/1GF3.pdb.gz Warning: Proxy not set! downloading https://files.rcsb.org/download/1B7S.pdb.gz Warning: Proxy not set! downloading https://files.rcsb.org/download/2IHL.pdb.gz Warning: Proxy not set! downloading https://files.rcsb.org/download/1GFK.pdb.gz Warning: Proxy not set! downloading https://files.rcsb.org/download/1KXX.pdb.gz Warning: Proxy not set! downloading https://files.rcsb.org/download/2VB1.pdb.gz Warning: Proxy not set! downloading https://files.rcsb.org/download/7CVJ.pdb.gz ------------------------------- Processing PDB files (PDBclip): ------------------------------- ------------- Process PDBs ------------- PDB Processing log: Number of valid search models after PDB processing = 30 ########################################### ### Search Model Preparation ### ########################################### The following types of model will be generated: CHNSAW -- Chainsaw generated model, side chains pruned according to sequence alignment. SCLPTR -- Sculptor generated model, side chains pruned according to sequence alignment. MOLREP -- Molrep generated model, side chains pruned according to sequence alignment. ------------------------------------------------------------- Models Construct log message: Manipulating models with Molrep ------------------------------------------------------------- --------------------------------------------------------------- Models Construct log message: Manipulating models with Chainsaw --------------------------------------------------------------- --------------------------------------------------------------- Models Construct log message: Manipulating models with Sculptor --------------------------------------------------------------- ##################################################################### ##### Search Model Preparation Results ##### ##################################################################### CHAINID RESOL(A) MOLREP-SCORE CHAINSAW-SCORE SOURCE MODEL NO. ---------------------------------------------------------------------------- 1jug_A1_PHR 0.000 0.664 1.000 PHR 0 5v8g_A1_PHR 0.000 0.517 0.580 PHR 1 1i22_D1_PHR 0.000 0.521 0.550 PHR 2 3lhm_A1_PHR 0.000 0.518 0.540 PHR 3 1lmq_A1_PHR 0.000 0.512 0.560 PHR 4 6d9i_B1_PHR 0.000 0.511 0.560 PHR 5 1lze_A1_PHR 0.000 0.514 0.550 PHR 6 1i20_A1_PHR 0.000 0.515 0.540 PHR 7 1di3_A1_PHR 0.000 0.515 0.540 PHR 8 5v92_B1_PHR 0.000 0.510 0.560 PHR 9 1ge3_A1_PHR 0.000 0.514 0.540 PHR 10 1kxy_A1_PHR 0.000 0.514 0.550 PHR 11 1i1z_A1_PHR 0.000 0.514 0.540 PHR 12 1fly_A1_PHR 0.000 0.514 0.550 PHR 13 1lzg_A1_PHR 0.000 0.512 0.550 PHR 14 6p4a_C1_PHR 0.000 0.513 0.550 PHR 15 1gfr_A1_PHR 0.000 0.513 0.530 PHR 16 1oub_A1_PHR 0.000 0.513 0.540 PHR 17 2iff_Y1_PHR 0.000 0.513 0.550 PHR 18 1d6q_A1_PHR 0.000 0.512 0.540 PHR 19 1iot_A1_PHR 0.000 0.512 0.550 PHR 20 6p4d_A1_PHR 0.000 0.512 0.550 PHR 21 1wqm_A1_PHR 0.000 0.512 0.540 PHR 22 1gf3_A1_PHR 0.000 0.512 0.530 PHR 23 1b7s_A1_PHR 0.000 0.512 0.530 PHR 24 2ihl_A1_PHR 0.000 0.517 0.560 PHR 25 1gfk_A1_PHR 0.000 0.512 0.530 PHR 26 1kxx_A1_PHR 0.000 0.511 0.550 PHR 27 2vb1_A1_PHR 0.000 0.511 0.550 PHR 28 7cvj_A1_PHR 0.000 0.511 0.550 PHR 29 For inline graphs use a Java browser Model Preparation log: Use Ensemble set to 'False' - no ensemble will be created. Model Preparation log: A total of 90 models have been created for processing in Molecular Replacement Model Preparation log: The following list of models has been created for MR: Number of domains found: 3 These models will be placed in the folder: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models Scoring models using Phaser eLLG... ######################################################################################################## ##### Search models for MR ##### ######################################################################################################## Target Range: 1 -- Residue range: 1-125 (Target length: 125 (*1)) -- C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1 Model name RID ENS eLLG e-value Score(P/H/C) SeqID Coverage Resolution Expt Source 1jug_A1_PHR_SC_s1.00_r1-125 1 1 3381.70 1.0e-87 293.5 100.0 0.99 1.9 XRAY Phmmer 1jug_A1_PHR_MO_s1.00_r1-125 1 1 3381.70 1.0e-87 293.5 100.0 0.99 1.9 XRAY Phmmer 1jug_A1_PHR_CH_s1.00_r1-125 1 1 3381.70 1.0e-87 293.5 100.0 0.99 1.9 XRAY Phmmer 1i22_D1_PHR_MO_s0.56_r1-123 1 1 565.30 5.9e-48 164.9 55.6 0.98 1.8 XRAY Phmmer 5v8g_A1_PHR_MO_s0.57_r2-123 1 1 564.20 4.7e-48 165.2 57.4 0.97 1.2 XRAY Phmmer 1lmq_A1_PHR_MO_s0.56_r2-123 1 1 548.60 4.8e-47 161.9 55.7 0.97 1.6 XRAY Phmmer 3lhm_A1_PHR_MO_s0.55_r1-123 1 1 540.30 3.8e-47 162.3 54.8 0.98 1.8 XRAY Phmmer 5v92_B1_PHR_MO_s0.56_r2-123 1 1 523.80 3.7e-46 159.0 55.7 0.97 1.1 XRAY Phmmer 6d9i_B1_PHR_MO_s0.56_r2-123 1 1 523.30 2.1e-46 159.9 55.7 0.97 1.1 XRAY Phmmer 1i20_A1_PHR_MO_s0.54_r1-123 1 1 518.80 2.5e-46 159.6 54.0 0.98 1.9 XRAY Phmmer 1d6q_A1_PHR_MO_s0.54_r1-123 1 1 517.90 1.1e-45 157.5 54.0 0.98 2.0 XRAY Phmmer 1i1z_A1_PHR_MO_s0.54_r1-123 1 1 516.20 4.8e-46 158.7 54.0 0.98 1.8 XRAY Phmmer 1i22_D1_PHR_SC_s0.56_r1-123 1 1 515.70 5.9e-48 164.9 55.6 0.98 1.8 XRAY Phmmer 1wqm_A1_PHR_MO_s0.54_r1-123 1 1 514.50 1.5e-45 157.1 54.0 0.98 1.8 XRAY Phmmer 1oub_A1_PHR_MO_s0.54_r1-123 1 1 514.50 9.1e-46 157.8 54.0 0.98 1.8 XRAY Phmmer 1ge3_A1_PHR_MO_s0.54_r1-123 1 1 514.50 4.2e-46 158.9 54.0 0.98 1.8 XRAY Phmmer 1di3_A1_PHR_MO_s0.54_r1-123 1 1 514.50 2.8e-46 159.4 54.0 0.98 1.8 XRAY Phmmer 5v8g_A1_PHR_SC_s0.57_r2-123 1 1 508.60 4.7e-48 165.2 57.4 0.97 1.2 XRAY Phmmer 5v8g_A1_PHR_CH_s0.57_r2-123 1 1 508.60 4.7e-48 165.2 57.4 0.97 1.2 XRAY Phmmer 1i22_D1_PHR_CH_s0.56_r1-123 1 1 507.90 5.9e-48 164.9 55.6 0.98 1.8 XRAY Phmmer 2ihl_A1_PHR_MO_s0.56_r4-121 1 1 507.10 1.8e-45 156.9 55.9 0.94 1.4 XRAY Phmmer 1lze_A1_PHR_MO_s0.55_r2-121 1 1 500.20 2.3e-46 159.7 55.0 0.95 1.8 XRAY Phmmer 1gfr_A1_PHR_MO_s0.53_r1-123 1 1 499.40 8.7e-46 157.8 53.2 0.98 1.8 XRAY Phmmer 1gfk_A1_PHR_MO_s0.53_r1-123 1 1 497.30 2.0e-45 156.7 53.2 0.98 1.8 XRAY Phmmer 1iot_A1_PHR_MO_s0.55_r2-121 1 1 496.60 1.1e-45 157.5 55.0 0.95 1.8 XRAY Phmmer 1fly_A1_PHR_MO_s0.55_r2-121 1 1 496.60 4.9e-46 158.7 55.0 0.95 1.8 XRAY Phmmer 6p4d_A1_PHR_MO_s0.55_r2-121 1 1 496.40 1.3e-45 157.3 55.0 0.95 1.1 XRAY Phmmer 1gf3_A1_PHR_MO_s0.53_r1-123 1 1 496.40 1.7e-45 156.9 53.2 0.98 1.8 XRAY Phmmer 1b7s_A1_PHR_MO_s0.53_r1-123 1 1 496.40 1.8e-45 156.8 53.2 0.98 2.0 XRAY Phmmer 2iff_Y1_PHR_MO_s0.55_r2-121 1 1 495.70 9.3e-46 157.8 55.0 0.95 2.6 XRAY Phmmer 1kxy_A1_PHR_MO_s0.55_r2-121 1 1 495.70 4.3e-46 158.9 55.0 0.95 1.8 XRAY Phmmer 6p4a_C1_PHR_MO_s0.55_r2-121 1 1 494.70 8.3e-46 157.9 55.0 0.95 2.2 XRAY Phmmer 1lmq_A1_PHR_SC_s0.56_r2-123 1 1 493.90 4.8e-47 161.9 55.7 0.97 1.6 XRAY Phmmer 1lmq_A1_PHR_CH_s0.56_r2-123 1 1 492.90 4.8e-47 161.9 55.7 0.97 1.6 XRAY Phmmer 3lhm_A1_PHR_SC_s0.55_r1-123 1 1 492.80 3.8e-47 162.3 54.8 0.98 1.8 XRAY Phmmer 3lhm_A1_PHR_CH_s0.55_r1-123 1 1 485.30 3.8e-47 162.3 54.8 0.98 1.8 XRAY Phmmer 1lzg_A1_PHR_MO_s0.54_r2-121 1 1 480.20 6.5e-46 158.3 54.2 0.95 1.8 XRAY Phmmer 7cvj_A1_PHR_MO_s0.54_r2-121 1 1 477.50 2.0e-45 156.7 54.2 0.95 1.5 XRAY Phmmer 2vb1_A1_PHR_MO_s0.54_r2-121 1 1 477.50 2.0e-45 156.7 54.2 0.95 0.7 XRAY Phmmer 1kxx_A1_PHR_MO_s0.54_r2-121 1 1 477.50 2.0e-45 156.7 54.2 0.95 1.7 XRAY Phmmer 1wqm_A1_PHR_SC_s0.54_r1-123 1 1 471.90 1.5e-45 157.1 54.0 0.98 1.8 XRAY Phmmer 1i20_A1_PHR_SC_s0.54_r1-123 1 1 471.50 2.5e-46 159.6 54.0 0.98 1.9 XRAY Phmmer 1d6q_A1_PHR_SC_s0.54_r1-123 1 1 471.50 1.1e-45 157.5 54.0 0.98 2.0 XRAY Phmmer 1i1z_A1_PHR_SC_s0.54_r1-123 1 1 470.60 4.8e-46 158.7 54.0 0.98 1.8 XRAY Phmmer 6d9i_B1_PHR_SC_s0.56_r2-123 1 1 469.60 2.1e-46 159.9 55.7 0.97 1.1 XRAY Phmmer 6d9i_B1_PHR_CH_s0.56_r2-123 1 1 469.60 2.1e-46 159.9 55.7 0.97 1.1 XRAY Phmmer 5v92_B1_PHR_SC_s0.56_r2-123 1 1 468.90 3.7e-46 159.0 55.7 0.97 1.1 XRAY Phmmer 5v92_B1_PHR_CH_s0.56_r2-123 1 1 468.90 3.7e-46 159.0 55.7 0.97 1.1 XRAY Phmmer 1oub_A1_PHR_SC_s0.54_r1-123 1 1 467.40 9.1e-46 157.8 54.0 0.98 1.8 XRAY Phmmer 1ge3_A1_PHR_SC_s0.54_r1-123 1 1 467.40 4.2e-46 158.9 54.0 0.98 1.8 XRAY Phmmer 1di3_A1_PHR_SC_s0.54_r1-123 1 1 467.40 2.8e-46 159.4 54.0 0.98 1.8 XRAY Phmmer 1wqm_A1_PHR_CH_s0.54_r1-123 1 1 464.70 1.5e-45 157.1 54.0 0.98 1.8 XRAY Phmmer 1i20_A1_PHR_CH_s0.54_r1-123 1 1 464.30 2.5e-46 159.6 54.0 0.98 1.9 XRAY Phmmer 1d6q_A1_PHR_CH_s0.54_r1-123 1 1 464.30 1.1e-45 157.5 54.0 0.98 2.0 XRAY Phmmer 1i1z_A1_PHR_CH_s0.54_r1-123 1 1 463.40 4.8e-46 158.7 54.0 0.98 1.8 XRAY Phmmer 1oub_A1_PHR_CH_s0.54_r1-123 1 1 460.30 9.1e-46 157.8 54.0 0.98 1.8 XRAY Phmmer 1ge3_A1_PHR_CH_s0.54_r1-123 1 1 460.30 4.2e-46 158.9 54.0 0.98 1.8 XRAY Phmmer 1di3_A1_PHR_CH_s0.54_r1-123 1 1 460.30 2.8e-46 159.4 54.0 0.98 1.8 XRAY Phmmer 2ihl_A1_PHR_SC_s0.56_r4-121 1 1 455.70 1.8e-45 156.9 55.9 0.94 1.4 XRAY Phmmer 2ihl_A1_PHR_CH_s0.56_r4-121 1 1 455.70 1.8e-45 156.9 55.9 0.94 1.4 XRAY Phmmer 1lze_A1_PHR_SC_s0.55_r2-121 1 1 451.10 2.3e-46 159.7 55.0 0.95 1.8 XRAY Phmmer 1lze_A1_PHR_CH_s0.55_r2-121 1 1 451.10 2.3e-46 159.7 55.0 0.95 1.8 XRAY Phmmer 1gf3_A1_PHR_SC_s0.53_r1-123 1 1 451.00 1.7e-45 156.9 53.2 0.98 1.8 XRAY Phmmer 1gfr_A1_PHR_SC_s0.53_r1-123 1 1 450.20 8.7e-46 157.8 53.2 0.98 1.8 XRAY Phmmer 1gfk_A1_PHR_SC_s0.53_r1-123 1 1 450.20 2.0e-45 156.7 53.2 0.98 1.8 XRAY Phmmer 1b7s_A1_PHR_SC_s0.53_r1-123 1 1 450.20 1.8e-45 156.8 53.2 0.98 2.0 XRAY Phmmer 6p4d_A1_PHR_CH_s0.55_r2-121 1 1 448.70 1.3e-45 157.3 55.0 0.95 1.1 XRAY Phmmer 2iff_Y1_PHR_SC_s0.55_r2-121 1 1 448.00 9.3e-46 157.8 55.0 0.95 2.6 XRAY Phmmer 2iff_Y1_PHR_CH_s0.55_r2-121 1 1 448.00 9.3e-46 157.8 55.0 0.95 2.6 XRAY Phmmer 1kxy_A1_PHR_SC_s0.55_r2-121 1 1 447.80 4.3e-46 158.9 55.0 0.95 1.8 XRAY Phmmer 1kxy_A1_PHR_CH_s0.55_r2-121 1 1 447.80 4.3e-46 158.9 55.0 0.95 1.8 XRAY Phmmer 6p4a_C1_PHR_SC_s0.55_r2-121 1 1 447.10 8.3e-46 157.9 55.0 0.95 2.2 XRAY Phmmer 6p4a_C1_PHR_CH_s0.55_r2-121 1 1 447.10 8.3e-46 157.9 55.0 0.95 2.2 XRAY Phmmer 1iot_A1_PHR_SC_s0.55_r2-121 1 1 446.80 1.1e-45 157.5 55.0 0.95 1.8 XRAY Phmmer 1iot_A1_PHR_CH_s0.55_r2-121 1 1 446.80 1.1e-45 157.5 55.0 0.95 1.8 XRAY Phmmer 1fly_A1_PHR_SC_s0.55_r2-121 1 1 445.00 4.9e-46 158.7 55.0 0.95 1.8 XRAY Phmmer 1fly_A1_PHR_CH_s0.55_r2-121 1 1 445.00 4.9e-46 158.7 55.0 0.95 1.8 XRAY Phmmer 1gf3_A1_PHR_CH_s0.53_r1-123 1 1 444.10 1.7e-45 156.9 53.2 0.98 1.8 XRAY Phmmer 1gfr_A1_PHR_CH_s0.53_r1-123 1 1 443.20 8.7e-46 157.8 53.2 0.98 1.8 XRAY Phmmer 1gfk_A1_PHR_CH_s0.53_r1-123 1 1 443.20 2.0e-45 156.7 53.2 0.98 1.8 XRAY Phmmer 1b7s_A1_PHR_CH_s0.53_r1-123 1 1 443.20 1.8e-45 156.8 53.2 0.98 2.0 XRAY Phmmer 7cvj_A1_PHR_CH_s0.54_r2-121 1 1 439.60 2.0e-45 156.7 54.2 0.95 1.5 XRAY Phmmer 2vb1_A1_PHR_CH_s0.54_r2-121 1 1 439.60 2.0e-45 156.7 54.2 0.95 0.7 XRAY Phmmer 7cvj_A1_PHR_SC_s0.54_r2-121 1 1 429.20 2.0e-45 156.7 54.2 0.95 1.5 XRAY Phmmer 1lzg_A1_PHR_SC_s0.54_r2-121 1 1 428.70 6.5e-46 158.3 54.2 0.95 1.8 XRAY Phmmer 1lzg_A1_PHR_CH_s0.54_r2-121 1 1 428.70 6.5e-46 158.3 54.2 0.95 1.8 XRAY Phmmer 1kxx_A1_PHR_SC_s0.54_r2-121 1 1 428.70 2.0e-45 156.7 54.2 0.95 1.7 XRAY Phmmer 1kxx_A1_PHR_CH_s0.54_r2-121 1 1 428.70 2.0e-45 156.7 54.2 0.95 1.7 XRAY Phmmer 6p4d_A1_PHR_SC_s0.55_r2-121 1 1 426.60 1.3e-45 157.3 55.0 0.95 1.1 XRAY Phmmer 2vb1_A1_PHR_SC_s0.54_r2-121 1 1 390.50 2.0e-45 156.7 54.2 0.95 0.7 XRAY Phmmer ######################################################################################################## ##### Outputting sequence search file ##### ######################################################################################################## ######################################################################################################## ##### Outputting models file ##### ######################################################################################################## ############################################################## ### Molecular Replacement and Refinement ### ############################################################## ********************************************************************************* ********************************************************************************* ********************************************************************************* ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 0: 1jug_A1_PHR_SC_s1.00_r1-125 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\sculptor Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\sculpt_1jug_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 1.00 Search model type: SCLPTR Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\sculptor\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: refmac failed to complete successfully Log file can be found here: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\sculptor\mr\molrep\refine\refmac_molrep_1jug_A1_PHR_SC_s1.00_r1-125.log Finished job, checking results.... ######################################################################### Job has completed for model '1jug_A1_PHR_SC_s1.00_r1-125' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 1jug_A1_PHR_SC_s1.00_r1-125: ##### ################################################################################################# Template Model: 1jug_A1_PHR_SC_s1.00_r1-125 produced a poor solution (Final Rfree = 1.000) Molrep log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\sculptor\mr\molrep\molrep.log Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\sculptor\mr\molrep\refine\refmac_molrep_1jug_A1_PHR_SC_s1.00_r1-125.log $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 1 MR programs being used: MOLREP PHASER Best search model so far: 1jug_A1_PHR_SC_s1.00_r1-125 using MOLREP Initial Rfree: 1.000 Final Rfree: 1.000 Solution Type: POOR Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\sculptor\mr\molrep\refine\refmac_molrep_1jug_A1_PHR_SC_s1.00_r1-125.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\sculptor\mr\molrep\refine\refmac_molrep_HKLOUT_1jug_A1_PHR_SC_s1.00_r1-125.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\sculptor\mr\molrep\refine\refmac_molrep_1jug_A1_PHR_SC_s1.00_r1-125.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\sculptor\mr\molrep\build\buccaneer\buccaneer_molrep_1jug_A1_PHR_SC_s1.00_r1-125.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 1: 1jug_A1_PHR_SC_s1.00_r1-125 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\sculptor Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\sculpt_1jug_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 1.00 Search model type: SCLPTR Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\sculptor\mr\phaser\phaser_1jug_A1_PHR_SC_s1.00_r1-125.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\sculptor\mr\phaser\phaser_1jug_A1_PHR_SC_s1.00_r1-125.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\sculptor\mr\phaser\phaser_1jug_A1_PHR_SC_s1.00_r1-125.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: refmac failed to complete successfully Log file can be found here: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\sculptor\mr\phaser\refine\refmac_phaser_1jug_A1_PHR_SC_s1.00_r1-125.log Error: Could not find output PDB from Refmac, can't continue Finished job, checking results.... ######################################################################### Job has completed for model '1jug_A1_PHR_SC_s1.00_r1-125' ######################################################################### ###################################################################### ##### Results from Phaser for 1jug_A1_PHR_SC_s1.00_r1-125: ##### ###################################################################### Template Model: 1jug_A1_PHR_SC_s1.00_r1-125 produced a poor solution (Final Rfree = 1.000) Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\sculptor\mr\phaser\phaser_1jug_A1_PHR_SC_s1.00_r1-125.log Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\sculptor\mr\phaser\refine\refmac_phaser_1jug_A1_PHR_SC_s1.00_r1-125.log $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 2 MR programs being used: MOLREP PHASER Best search model so far: 1jug_A1_PHR_SC_s1.00_r1-125 using MOLREP Initial Rfree: 1.000 Final Rfree: 1.000 Solution Type: POOR Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\sculptor\mr\molrep\refine\refmac_molrep_1jug_A1_PHR_SC_s1.00_r1-125.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\sculptor\mr\molrep\refine\refmac_molrep_HKLOUT_1jug_A1_PHR_SC_s1.00_r1-125.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\sculptor\mr\molrep\refine\refmac_molrep_1jug_A1_PHR_SC_s1.00_r1-125.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\sculptor\mr\molrep\build\buccaneer\buccaneer_molrep_1jug_A1_PHR_SC_s1.00_r1-125.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 2: 1jug_A1_PHR_MO_s1.00_r1-125 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1jug_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 1.00 Search model type: MOLREP Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1jug_A1_PHR_MO_s1.00_r1-125.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1jug_A1_PHR_MO_s1.00_r1-125.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\molrep\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1jug_A1_PHR_MO_s1.00_r1-125' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 1jug_A1_PHR_MO_s1.00_r1-125: ##### ################################################################################################# Template Model: 1jug_A1_PHR_MO_s1.00_r1-125 has produced a marginal solution, final Rfree = 0.433 Molrep log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\molrep\molrep.log Molrep PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\molrep\molrep_1jug_A1_PHR_MO_s1.00_r1-125.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1jug_A1_PHR_MO_s1.00_r1-125.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1jug_A1_PHR_MO_s1.00_r1-125.pdb #################################################################################################### ##### Refinement results from Refmac for 1jug_A1_PHR_MO_s1.00_r1-125: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1jug_A1_PHR_MO_s1.00_r1-125: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.5086 0.5175 0.360 94880. 5019.1 0.0150 1.329 3.341 2.105 0.147 1 0.4784 0.4869 0.400 93907. 4978.9 0.0096 0.801 2.436 1.495 0.140 2 0.4673 0.4738 0.431 93072. 4934.4 0.0088 0.723 2.176 1.317 0.141 3 0.4621 0.4653 0.452 92615. 4909.1 0.0066 0.546 2.021 1.213 0.138 4 0.4579 0.4607 0.460 92284. 4890.8 0.0062 0.508 1.924 1.144 0.135 5 0.4544 0.4577 0.468 92060. 4879.4 0.0059 0.479 1.853 1.092 0.133 6 0.4515 0.4546 0.480 91905. 4870.9 0.0057 0.461 1.789 1.047 0.130 7 0.4487 0.4521 0.484 91749. 4862.7 0.0055 0.445 1.738 1.011 0.128 8 0.4461 0.4487 0.491 91646. 4857.5 0.0054 0.439 1.696 0.984 0.126 9 0.4447 0.4473 0.495 91598. 4855.0 0.0052 0.421 1.651 0.955 0.124 10 0.4435 0.4461 0.501 91579. 4854.3 0.0051 0.409 1.612 0.930 0.123 11 0.4423 0.4442 0.503 91623. 4856.9 0.0050 0.399 1.571 0.907 0.121 12 0.4412 0.4427 0.506 91604. 4855.8 0.0049 0.391 1.539 0.887 0.120 13 0.4400 0.4419 0.509 91573. 4854.7 0.0048 0.383 1.517 0.871 0.119 14 0.4385 0.4411 0.511 91548. 4853.6 0.0048 0.377 1.499 0.857 0.117 15 0.4371 0.4405 0.516 91532. 4853.7 0.0047 0.370 1.483 0.845 0.116 16 0.4355 0.4402 0.518 91556. 4855.5 0.0046 0.362 1.467 0.833 0.115 17 0.4342 0.4395 0.520 91499. 4853.1 0.0045 0.356 1.451 0.822 0.113 18 0.4332 0.4405 0.522 91453. 4851.9 0.0044 0.350 1.437 0.811 0.112 19 0.4322 0.4401 0.524 91398. 4849.1 0.0044 0.343 1.422 0.801 0.111 20 0.4315 0.4400 0.525 91311. 4844.5 0.0043 0.337 1.409 0.791 0.110 21 0.4306 0.4396 0.530 91257. 4842.2 0.0042 0.332 1.397 0.783 0.109 22 0.4298 0.4387 0.534 91243. 4842.4 0.0041 0.325 1.385 0.775 0.109 23 0.4290 0.4380 0.535 91262. 4843.4 0.0040 0.319 1.374 0.767 0.108 24 0.4282 0.4373 0.537 91238. 4842.6 0.0040 0.313 1.364 0.760 0.108 25 0.4275 0.4365 0.537 91237. 4842.6 0.0039 0.309 1.354 0.754 0.107 26 0.4268 0.4356 0.538 91235. 4842.9 0.0038 0.305 1.346 0.749 0.106 27 0.4262 0.4351 0.539 91238. 4843.2 0.0038 0.301 1.338 0.744 0.106 28 0.4255 0.4346 0.540 91228. 4842.8 0.0038 0.298 1.331 0.739 0.105 29 0.4250 0.4340 0.540 91265. 4845.2 0.0037 0.295 1.325 0.735 0.104 30 0.4244 0.4331 0.543 91284. 4846.7 0.0037 0.293 1.319 0.732 0.104 $$ Output MTZ file from Refmac for model 1jug_A1_PHR_MO_s1.00_r1-125 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1jug_A1_PHR_MO_s1.00_r1-125.mtz Output PDB file from Refmac for model 1jug_A1_PHR_MO_s1.00_r1-125: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1jug_A1_PHR_MO_s1.00_r1-125.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 3 MR programs being used: MOLREP PHASER Best search model so far: 1jug_A1_PHR_MO_s1.00_r1-125 using MOLREP Initial Rfree: 0.509 Final Rfree: 0.433 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1jug_A1_PHR_MO_s1.00_r1-125.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1jug_A1_PHR_MO_s1.00_r1-125.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1jug_A1_PHR_MO_s1.00_r1-125.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_1jug_A1_PHR_MO_s1.00_r1-125.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 3: 1jug_A1_PHR_MO_s1.00_r1-125 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1jug_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 1.00 Search model type: MOLREP Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\phaser\phaser_1jug_A1_PHR_MO_s1.00_r1-125.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\phaser\phaser_1jug_A1_PHR_MO_s1.00_r1-125.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\phaser\phaser_1jug_A1_PHR_MO_s1.00_r1-125.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_HKLOUT_1jug_A1_PHR_MO_s1.00_r1-125.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1jug_A1_PHR_MO_s1.00_r1-125.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\phaser\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\phaser\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1jug_A1_PHR_MO_s1.00_r1-125' ######################################################################### ###################################################################### ##### Results from Phaser for 1jug_A1_PHR_MO_s1.00_r1-125: ##### ###################################################################### Template Model: 1jug_A1_PHR_MO_s1.00_r1-125 has produced a marginal solution, final Rfree = 0.433 Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\phaser\phaser_1jug_A1_PHR_MO_s1.00_r1-125.log Phaser PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\phaser\phaser_1jug_A1_PHR_MO_s1.00_r1-125.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1jug_A1_PHR_MO_s1.00_r1-125.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1jug_A1_PHR_MO_s1.00_r1-125.pdb #################################################################################################### ##### Refinement results from Refmac for 1jug_A1_PHR_MO_s1.00_r1-125: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1jug_A1_PHR_MO_s1.00_r1-125: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4965 0.4870 0.420 93717. 4958.3 0.0150 1.330 3.340 2.104 0.147 1 0.4772 0.4718 0.427 93287. 4941.8 0.0139 1.178 2.428 1.490 0.138 2 0.4680 0.4660 0.442 92634. 4910.3 0.0073 0.625 2.148 1.304 0.139 3 0.4632 0.4628 0.454 92294. 4892.5 0.0065 0.549 2.006 1.205 0.138 4 0.4588 0.4599 0.463 92032. 4878.6 0.0061 0.505 1.906 1.135 0.136 5 0.4549 0.4580 0.470 91958. 4874.7 0.0059 0.482 1.831 1.084 0.133 6 0.4512 0.4552 0.479 91819. 4867.6 0.0058 0.469 1.776 1.045 0.131 7 0.4477 0.4527 0.487 91731. 4862.8 0.0057 0.457 1.729 1.012 0.130 8 0.4460 0.4505 0.491 91709. 4861.1 0.0054 0.436 1.681 0.979 0.127 9 0.4447 0.4499 0.493 91682. 4859.7 0.0053 0.425 1.643 0.953 0.125 10 0.4428 0.4487 0.499 91667. 4859.4 0.0052 0.416 1.611 0.932 0.124 11 0.4414 0.4481 0.502 91678. 4860.3 0.0051 0.408 1.581 0.912 0.123 12 0.4402 0.4475 0.507 91569. 4854.9 0.0051 0.402 1.555 0.895 0.122 13 0.4389 0.4461 0.511 91534. 4853.8 0.0050 0.396 1.534 0.881 0.120 14 0.4373 0.4441 0.516 91475. 4851.0 0.0049 0.391 1.516 0.868 0.119 15 0.4359 0.4423 0.519 91443. 4849.7 0.0049 0.385 1.497 0.856 0.118 16 0.4347 0.4403 0.522 91436. 4849.6 0.0047 0.375 1.480 0.844 0.116 17 0.4339 0.4399 0.523 91494. 4852.4 0.0046 0.366 1.463 0.831 0.115 18 0.4330 0.4394 0.525 91474. 4851.6 0.0045 0.359 1.447 0.819 0.114 19 0.4322 0.4389 0.526 91444. 4850.2 0.0044 0.351 1.431 0.808 0.113 20 0.4311 0.4400 0.528 91333. 4845.1 0.0044 0.344 1.417 0.799 0.112 21 0.4302 0.4394 0.532 91319. 4845.0 0.0043 0.339 1.404 0.790 0.111 22 0.4294 0.4392 0.534 91314. 4845.6 0.0042 0.333 1.389 0.780 0.110 23 0.4287 0.4382 0.535 91319. 4846.5 0.0042 0.328 1.377 0.772 0.109 24 0.4280 0.4371 0.536 91316. 4846.5 0.0041 0.322 1.366 0.765 0.109 25 0.4272 0.4370 0.538 91266. 4844.2 0.0040 0.316 1.355 0.757 0.108 26 0.4265 0.4364 0.538 91235. 4842.9 0.0039 0.312 1.345 0.751 0.107 27 0.4259 0.4358 0.539 91208. 4842.0 0.0039 0.308 1.337 0.745 0.107 28 0.4253 0.4347 0.541 91170. 4840.1 0.0039 0.304 1.330 0.741 0.106 29 0.4247 0.4338 0.542 91160. 4840.0 0.0038 0.301 1.323 0.736 0.105 30 0.4242 0.4329 0.544 91158. 4840.0 0.0038 0.298 1.316 0.732 0.105 $$ Output MTZ file from Refmac for model 1jug_A1_PHR_MO_s1.00_r1-125 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1jug_A1_PHR_MO_s1.00_r1-125.mtz Output PDB file from Refmac for model 1jug_A1_PHR_MO_s1.00_r1-125: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1jug_A1_PHR_MO_s1.00_r1-125.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 4 MR programs being used: MOLREP PHASER Best search model so far: 1jug_A1_PHR_MO_s1.00_r1-125 using PHASER Initial Rfree: 0.496 Final Rfree: 0.433 Solution Type: MARGINAL Solution Spacegroup: P 43 21 2 Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1jug_A1_PHR_MO_s1.00_r1-125.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_HKLOUT_1jug_A1_PHR_MO_s1.00_r1-125.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1jug_A1_PHR_MO_s1.00_r1-125.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\phaser\build\buccaneer\buccaneer_phaser_1jug_A1_PHR_MO_s1.00_r1-125.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 4: 1jug_A1_PHR_CH_s1.00_r1-125 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\chainsaw Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\CHAINSAW_1jug_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 1.00 Search model type: CHNSAW Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\chainsaw\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\chainsaw\mr\molrep\refine\refmac_molrep_HKLOUT_1jug_A1_PHR_CH_s1.00_r1-125.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\chainsaw\mr\molrep\refine\refmac_molrep_1jug_A1_PHR_CH_s1.00_r1-125.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\chainsaw\mr\molrep\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\chainsaw\mr\molrep\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1jug_A1_PHR_CH_s1.00_r1-125' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 1jug_A1_PHR_CH_s1.00_r1-125: ##### ################################################################################################# Template Model: 1jug_A1_PHR_CH_s1.00_r1-125 has produced a marginal solution, final Rfree = 0.433 Molrep log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\chainsaw\mr\molrep\molrep.log Molrep PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\chainsaw\mr\molrep\molrep_1jug_A1_PHR_CH_s1.00_r1-125.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\chainsaw\mr\molrep\refine\refmac_molrep_1jug_A1_PHR_CH_s1.00_r1-125.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\chainsaw\mr\molrep\refine\refmac_molrep_1jug_A1_PHR_CH_s1.00_r1-125.pdb #################################################################################################### ##### Refinement results from Refmac for 1jug_A1_PHR_CH_s1.00_r1-125: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1jug_A1_PHR_CH_s1.00_r1-125: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.5086 0.5175 0.360 94880. 5019.1 0.0150 1.329 3.341 2.105 0.147 1 0.4784 0.4869 0.400 93907. 4978.9 0.0096 0.801 2.436 1.495 0.140 2 0.4673 0.4738 0.431 93072. 4934.4 0.0088 0.723 2.176 1.317 0.141 3 0.4621 0.4653 0.452 92615. 4909.1 0.0066 0.546 2.021 1.213 0.138 4 0.4579 0.4607 0.460 92284. 4890.8 0.0062 0.508 1.924 1.144 0.135 5 0.4544 0.4577 0.468 92060. 4879.4 0.0059 0.479 1.853 1.092 0.133 6 0.4515 0.4546 0.480 91905. 4870.9 0.0057 0.461 1.789 1.047 0.130 7 0.4487 0.4521 0.484 91749. 4862.7 0.0055 0.445 1.738 1.011 0.128 8 0.4461 0.4487 0.491 91646. 4857.5 0.0054 0.439 1.696 0.984 0.126 9 0.4447 0.4473 0.495 91598. 4855.0 0.0052 0.421 1.651 0.955 0.124 10 0.4435 0.4461 0.501 91579. 4854.3 0.0051 0.409 1.612 0.930 0.123 11 0.4423 0.4442 0.503 91623. 4856.9 0.0050 0.399 1.571 0.907 0.121 12 0.4412 0.4427 0.506 91604. 4855.8 0.0049 0.391 1.539 0.887 0.120 13 0.4400 0.4419 0.509 91573. 4854.7 0.0048 0.383 1.517 0.871 0.119 14 0.4385 0.4411 0.511 91548. 4853.6 0.0048 0.377 1.499 0.857 0.117 15 0.4371 0.4405 0.516 91532. 4853.7 0.0047 0.370 1.483 0.845 0.116 16 0.4355 0.4402 0.518 91556. 4855.5 0.0046 0.362 1.467 0.833 0.115 17 0.4342 0.4395 0.520 91499. 4853.1 0.0045 0.356 1.451 0.822 0.113 18 0.4332 0.4405 0.522 91453. 4851.9 0.0044 0.350 1.437 0.811 0.112 19 0.4322 0.4401 0.524 91398. 4849.1 0.0044 0.343 1.422 0.801 0.111 20 0.4315 0.4400 0.525 91311. 4844.5 0.0043 0.337 1.409 0.791 0.110 21 0.4306 0.4396 0.530 91257. 4842.2 0.0042 0.332 1.397 0.783 0.109 22 0.4298 0.4387 0.534 91243. 4842.4 0.0041 0.325 1.385 0.775 0.109 23 0.4290 0.4380 0.535 91262. 4843.4 0.0040 0.319 1.374 0.767 0.108 24 0.4282 0.4373 0.537 91238. 4842.6 0.0040 0.313 1.364 0.760 0.108 25 0.4275 0.4365 0.537 91237. 4842.6 0.0039 0.309 1.354 0.754 0.107 26 0.4268 0.4356 0.538 91235. 4842.9 0.0038 0.305 1.346 0.749 0.106 27 0.4262 0.4351 0.539 91238. 4843.2 0.0038 0.301 1.338 0.744 0.106 28 0.4255 0.4346 0.540 91228. 4842.8 0.0038 0.298 1.331 0.739 0.105 29 0.4250 0.4340 0.540 91265. 4845.2 0.0037 0.295 1.325 0.735 0.104 30 0.4244 0.4331 0.543 91284. 4846.7 0.0037 0.293 1.319 0.732 0.104 $$ Output MTZ file from Refmac for model 1jug_A1_PHR_CH_s1.00_r1-125 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\chainsaw\mr\molrep\refine\refmac_molrep_HKLOUT_1jug_A1_PHR_CH_s1.00_r1-125.mtz Output PDB file from Refmac for model 1jug_A1_PHR_CH_s1.00_r1-125: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\chainsaw\mr\molrep\refine\refmac_molrep_1jug_A1_PHR_CH_s1.00_r1-125.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 5 MR programs being used: MOLREP PHASER Best search model so far: 1jug_A1_PHR_MO_s1.00_r1-125 using PHASER Initial Rfree: 0.496 Final Rfree: 0.433 Solution Type: MARGINAL Solution Spacegroup: P 43 21 2 Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1jug_A1_PHR_MO_s1.00_r1-125.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_HKLOUT_1jug_A1_PHR_MO_s1.00_r1-125.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1jug_A1_PHR_MO_s1.00_r1-125.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\phaser\build\buccaneer\buccaneer_phaser_1jug_A1_PHR_MO_s1.00_r1-125.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 5: 1jug_A1_PHR_CH_s1.00_r1-125 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\chainsaw Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\CHAINSAW_1jug_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 1.00 Search model type: CHNSAW Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\chainsaw\mr\phaser\phaser_1jug_A1_PHR_CH_s1.00_r1-125.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\chainsaw\mr\phaser\phaser_1jug_A1_PHR_CH_s1.00_r1-125.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\chainsaw\mr\phaser\phaser_1jug_A1_PHR_CH_s1.00_r1-125.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\chainsaw\mr\phaser\refine\refmac_phaser_HKLOUT_1jug_A1_PHR_CH_s1.00_r1-125.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\chainsaw\mr\phaser\refine\refmac_phaser_1jug_A1_PHR_CH_s1.00_r1-125.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\chainsaw\mr\phaser\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\chainsaw\mr\phaser\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1jug_A1_PHR_CH_s1.00_r1-125' ######################################################################### ###################################################################### ##### Results from Phaser for 1jug_A1_PHR_CH_s1.00_r1-125: ##### ###################################################################### Template Model: 1jug_A1_PHR_CH_s1.00_r1-125 has produced a marginal solution, final Rfree = 0.433 Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\chainsaw\mr\phaser\phaser_1jug_A1_PHR_CH_s1.00_r1-125.log Phaser PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\chainsaw\mr\phaser\phaser_1jug_A1_PHR_CH_s1.00_r1-125.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\chainsaw\mr\phaser\refine\refmac_phaser_1jug_A1_PHR_CH_s1.00_r1-125.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\chainsaw\mr\phaser\refine\refmac_phaser_1jug_A1_PHR_CH_s1.00_r1-125.pdb #################################################################################################### ##### Refinement results from Refmac for 1jug_A1_PHR_CH_s1.00_r1-125: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1jug_A1_PHR_CH_s1.00_r1-125: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4965 0.4870 0.420 93717. 4958.3 0.0150 1.330 3.340 2.104 0.147 1 0.4772 0.4718 0.427 93287. 4941.8 0.0139 1.178 2.428 1.490 0.138 2 0.4680 0.4660 0.442 92634. 4910.3 0.0073 0.625 2.148 1.304 0.139 3 0.4632 0.4628 0.454 92294. 4892.5 0.0065 0.549 2.006 1.205 0.138 4 0.4588 0.4599 0.463 92032. 4878.6 0.0061 0.505 1.906 1.135 0.136 5 0.4549 0.4580 0.470 91958. 4874.7 0.0059 0.482 1.831 1.084 0.133 6 0.4512 0.4552 0.479 91819. 4867.6 0.0058 0.469 1.776 1.045 0.131 7 0.4477 0.4527 0.487 91731. 4862.8 0.0057 0.457 1.729 1.012 0.130 8 0.4460 0.4505 0.491 91709. 4861.1 0.0054 0.436 1.681 0.979 0.127 9 0.4447 0.4499 0.493 91682. 4859.7 0.0053 0.425 1.643 0.953 0.125 10 0.4428 0.4487 0.499 91667. 4859.4 0.0052 0.416 1.611 0.932 0.124 11 0.4414 0.4481 0.502 91678. 4860.3 0.0051 0.408 1.581 0.912 0.123 12 0.4402 0.4475 0.507 91569. 4854.9 0.0051 0.402 1.555 0.895 0.122 13 0.4389 0.4461 0.511 91534. 4853.8 0.0050 0.396 1.534 0.881 0.120 14 0.4373 0.4441 0.516 91475. 4851.0 0.0049 0.391 1.516 0.868 0.119 15 0.4359 0.4423 0.519 91443. 4849.7 0.0049 0.385 1.497 0.856 0.118 16 0.4347 0.4403 0.522 91436. 4849.6 0.0047 0.375 1.480 0.844 0.116 17 0.4339 0.4399 0.523 91494. 4852.4 0.0046 0.366 1.463 0.831 0.115 18 0.4330 0.4394 0.525 91474. 4851.6 0.0045 0.359 1.447 0.819 0.114 19 0.4322 0.4389 0.526 91444. 4850.2 0.0044 0.351 1.431 0.808 0.113 20 0.4311 0.4400 0.528 91333. 4845.1 0.0044 0.344 1.417 0.799 0.112 21 0.4302 0.4394 0.532 91319. 4845.0 0.0043 0.339 1.404 0.790 0.111 22 0.4294 0.4392 0.534 91314. 4845.6 0.0042 0.333 1.389 0.780 0.110 23 0.4287 0.4382 0.535 91319. 4846.5 0.0042 0.328 1.377 0.772 0.109 24 0.4280 0.4371 0.536 91316. 4846.5 0.0041 0.322 1.366 0.765 0.109 25 0.4272 0.4370 0.538 91266. 4844.2 0.0040 0.316 1.355 0.757 0.108 26 0.4265 0.4364 0.538 91235. 4842.9 0.0039 0.312 1.345 0.751 0.107 27 0.4259 0.4358 0.539 91208. 4842.0 0.0039 0.308 1.337 0.745 0.107 28 0.4253 0.4347 0.541 91170. 4840.1 0.0039 0.304 1.330 0.741 0.106 29 0.4247 0.4338 0.542 91160. 4840.0 0.0038 0.301 1.323 0.736 0.105 30 0.4242 0.4329 0.544 91158. 4840.0 0.0038 0.298 1.316 0.732 0.105 $$ Output MTZ file from Refmac for model 1jug_A1_PHR_CH_s1.00_r1-125 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\chainsaw\mr\molrep\refine\refmac_molrep_HKLOUT_1jug_A1_PHR_CH_s1.00_r1-125.mtz Output PDB file from Refmac for model 1jug_A1_PHR_CH_s1.00_r1-125: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\chainsaw\mr\molrep\refine\refmac_molrep_1jug_A1_PHR_CH_s1.00_r1-125.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 6 MR programs being used: MOLREP PHASER Best search model so far: 1jug_A1_PHR_MO_s1.00_r1-125 using PHASER Initial Rfree: 0.496 Final Rfree: 0.433 Solution Type: MARGINAL Solution Spacegroup: P 43 21 2 Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1jug_A1_PHR_MO_s1.00_r1-125.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_HKLOUT_1jug_A1_PHR_MO_s1.00_r1-125.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1jug_A1_PHR_MO_s1.00_r1-125.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1jug_A1_PHR\molrep\mr\phaser\build\buccaneer\buccaneer_phaser_1jug_A1_PHR_MO_s1.00_r1-125.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 6: 1i22_D1_PHR_MO_s0.56_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1i22_D1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.56 Search model type: MOLREP Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1i22_D1_PHR_MO_s0.56_r1-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\molrep\refine\refmac_molrep_1i22_D1_PHR_MO_s0.56_r1-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\molrep\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1i22_D1_PHR_MO_s0.56_r1-123' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 1i22_D1_PHR_MO_s0.56_r1-123: ##### ################################################################################################# Template Model: 1i22_D1_PHR_MO_s0.56_r1-123 has produced a marginal solution, final Rfree = 0.394 Molrep log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\molrep\molrep.log Molrep PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\molrep\molrep_1i22_D1_PHR_MO_s0.56_r1-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\molrep\refine\refmac_molrep_1i22_D1_PHR_MO_s0.56_r1-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\molrep\refine\refmac_molrep_1i22_D1_PHR_MO_s0.56_r1-123.pdb #################################################################################################### ##### Refinement results from Refmac for 1i22_D1_PHR_MO_s0.56_r1-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1i22_D1_PHR_MO_s0.56_r1-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4881 0.4834 0.425 93785. 4964.5 0.0317 2.736 3.654 2.228 0.385 1 0.4587 0.4529 0.463 92804. 4917.2 0.0111 0.949 2.719 1.622 0.271 2 0.4446 0.4407 0.497 92108. 4881.3 0.0089 0.746 2.401 1.414 0.202 3 0.4347 0.4351 0.518 91723. 4862.1 0.0078 0.646 2.203 1.284 0.159 4 0.4277 0.4321 0.532 91463. 4850.1 0.0071 0.582 2.065 1.195 0.141 5 0.4223 0.4286 0.542 91240. 4840.0 0.0065 0.533 1.964 1.129 0.131 6 0.4181 0.4260 0.548 91126. 4835.1 0.0060 0.494 1.883 1.079 0.125 7 0.4149 0.4223 0.555 91057. 4831.7 0.0056 0.459 1.811 1.034 0.121 8 0.4122 0.4188 0.565 90971. 4827.0 0.0053 0.431 1.749 0.996 0.118 9 0.4105 0.4152 0.570 90886. 4822.5 0.0050 0.409 1.692 0.961 0.116 10 0.4085 0.4126 0.574 90799. 4818.4 0.0047 0.389 1.650 0.935 0.115 11 0.4066 0.4111 0.579 90757. 4815.9 0.0045 0.371 1.610 0.910 0.113 12 0.4054 0.4089 0.583 90690. 4813.6 0.0044 0.361 1.573 0.887 0.112 13 0.4036 0.4075 0.588 90644. 4810.8 0.0042 0.341 1.535 0.866 0.111 14 0.4024 0.4059 0.593 90616. 4809.4 0.0040 0.328 1.505 0.848 0.110 15 0.4012 0.4045 0.595 90564. 4807.2 0.0039 0.317 1.479 0.833 0.109 16 0.4002 0.4034 0.597 90556. 4807.3 0.0037 0.307 1.456 0.819 0.108 17 0.3991 0.4023 0.598 90523. 4805.5 0.0036 0.299 1.436 0.806 0.108 18 0.3982 0.4014 0.600 90510. 4804.8 0.0036 0.293 1.418 0.795 0.107 19 0.3973 0.4007 0.603 90510. 4805.0 0.0035 0.286 1.401 0.784 0.106 20 0.3965 0.4001 0.605 90489. 4804.4 0.0034 0.280 1.385 0.774 0.105 21 0.3957 0.3993 0.608 90493. 4805.1 0.0033 0.274 1.371 0.765 0.105 22 0.3949 0.3986 0.609 90468. 4804.2 0.0032 0.269 1.358 0.756 0.104 23 0.3942 0.3978 0.610 90462. 4804.2 0.0032 0.265 1.346 0.748 0.103 24 0.3935 0.3973 0.611 90465. 4804.8 0.0031 0.261 1.335 0.741 0.102 25 0.3930 0.3971 0.611 90469. 4805.5 0.0031 0.257 1.324 0.734 0.102 26 0.3924 0.3964 0.612 90456. 4804.7 0.0030 0.254 1.315 0.728 0.101 27 0.3919 0.3958 0.614 90445. 4804.8 0.0030 0.250 1.305 0.722 0.101 28 0.3913 0.3952 0.614 90437. 4804.7 0.0030 0.247 1.296 0.716 0.101 29 0.3908 0.3950 0.615 90432. 4804.8 0.0029 0.245 1.288 0.711 0.100 30 0.3904 0.3944 0.615 90409. 4803.9 0.0029 0.242 1.280 0.706 0.100 $$ Output MTZ file from Refmac for model 1i22_D1_PHR_MO_s0.56_r1-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1i22_D1_PHR_MO_s0.56_r1-123.mtz Output PDB file from Refmac for model 1i22_D1_PHR_MO_s0.56_r1-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\molrep\refine\refmac_molrep_1i22_D1_PHR_MO_s0.56_r1-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 7 MR programs being used: MOLREP PHASER Best search model so far: 1i22_D1_PHR_MO_s0.56_r1-123 using MOLREP Initial Rfree: 0.488 Final Rfree: 0.394 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\molrep\refine\refmac_molrep_1i22_D1_PHR_MO_s0.56_r1-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1i22_D1_PHR_MO_s0.56_r1-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\molrep\refine\refmac_molrep_1i22_D1_PHR_MO_s0.56_r1-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_1i22_D1_PHR_MO_s0.56_r1-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 7: 1i22_D1_PHR_MO_s0.56_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1i22_D1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.56 Search model type: MOLREP Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\phaser\phaser_1i22_D1_PHR_MO_s0.56_r1-123.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\phaser\phaser_1i22_D1_PHR_MO_s0.56_r1-123.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\phaser\phaser_1i22_D1_PHR_MO_s0.56_r1-123.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\phaser\refine\refmac_phaser_HKLOUT_1i22_D1_PHR_MO_s0.56_r1-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\phaser\refine\refmac_phaser_1i22_D1_PHR_MO_s0.56_r1-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\phaser\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\phaser\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1i22_D1_PHR_MO_s0.56_r1-123' ######################################################################### ###################################################################### ##### Results from Phaser for 1i22_D1_PHR_MO_s0.56_r1-123: ##### ###################################################################### Template Model: 1i22_D1_PHR_MO_s0.56_r1-123 has produced a marginal solution, final Rfree = 0.397 Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\phaser\phaser_1i22_D1_PHR_MO_s0.56_r1-123.log Phaser PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\phaser\phaser_1i22_D1_PHR_MO_s0.56_r1-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\phaser\refine\refmac_phaser_1i22_D1_PHR_MO_s0.56_r1-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\phaser\refine\refmac_phaser_1i22_D1_PHR_MO_s0.56_r1-123.pdb #################################################################################################### ##### Refinement results from Refmac for 1i22_D1_PHR_MO_s0.56_r1-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1i22_D1_PHR_MO_s0.56_r1-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4783 0.4742 0.447 92378. 4883.0 0.0317 2.736 3.655 2.228 0.385 1 0.4648 0.4620 0.457 92420. 4889.7 0.0191 1.664 3.068 1.860 0.325 2 0.4541 0.4488 0.476 92190. 4880.7 0.0094 0.813 2.568 1.526 0.238 3 0.4480 0.4423 0.492 91926. 4868.1 0.0080 0.676 2.306 1.354 0.181 4 0.4431 0.4385 0.503 91684. 4856.4 0.0072 0.599 2.131 1.240 0.151 5 0.4386 0.4351 0.512 91502. 4847.7 0.0065 0.543 2.001 1.156 0.137 6 0.4342 0.4324 0.520 91424. 4843.7 0.0061 0.502 1.905 1.095 0.128 7 0.4289 0.4291 0.530 91239. 4835.5 0.0058 0.474 1.832 1.049 0.123 8 0.4232 0.4265 0.541 91120. 4830.0 0.0055 0.453 1.773 1.013 0.121 9 0.4211 0.4247 0.546 91076. 4829.0 0.0050 0.413 1.712 0.974 0.117 10 0.4188 0.4230 0.550 91037. 4827.8 0.0048 0.390 1.662 0.943 0.114 11 0.4166 0.4215 0.557 90992. 4825.5 0.0045 0.374 1.619 0.917 0.113 12 0.4143 0.4194 0.563 90983. 4825.8 0.0044 0.359 1.584 0.895 0.112 13 0.4120 0.4173 0.565 90909. 4822.6 0.0043 0.353 1.551 0.876 0.111 14 0.4103 0.4150 0.573 90868. 4820.7 0.0042 0.341 1.524 0.861 0.110 15 0.4083 0.4122 0.579 90795. 4817.5 0.0041 0.334 1.499 0.847 0.109 16 0.4058 0.4106 0.583 90749. 4815.4 0.0040 0.325 1.479 0.835 0.109 17 0.4042 0.4088 0.585 90685. 4812.4 0.0039 0.318 1.460 0.824 0.108 18 0.4028 0.4068 0.588 90648. 4810.9 0.0038 0.311 1.442 0.813 0.108 19 0.4016 0.4053 0.592 90613. 4809.4 0.0037 0.304 1.425 0.802 0.107 20 0.4004 0.4044 0.596 90578. 4808.5 0.0036 0.297 1.409 0.792 0.107 21 0.3992 0.4032 0.598 90525. 4806.0 0.0035 0.291 1.394 0.782 0.106 22 0.3983 0.4023 0.599 90510. 4805.5 0.0035 0.285 1.380 0.773 0.105 23 0.3973 0.4012 0.602 90487. 4804.2 0.0034 0.280 1.368 0.764 0.104 24 0.3969 0.4004 0.605 90515. 4806.3 0.0033 0.275 1.355 0.756 0.104 25 0.3956 0.3996 0.607 90463. 4803.8 0.0033 0.270 1.343 0.748 0.103 26 0.3949 0.3990 0.608 90448. 4803.2 0.0032 0.267 1.333 0.741 0.103 27 0.3942 0.3985 0.608 90441. 4803.1 0.0032 0.262 1.323 0.735 0.102 28 0.3935 0.3977 0.609 90425. 4802.6 0.0031 0.259 1.314 0.729 0.102 29 0.3929 0.3973 0.610 90412. 4802.3 0.0031 0.256 1.305 0.723 0.101 30 0.3923 0.3967 0.610 90420. 4803.1 0.0030 0.253 1.296 0.718 0.101 $$ Output MTZ file from Refmac for model 1i22_D1_PHR_MO_s0.56_r1-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1i22_D1_PHR_MO_s0.56_r1-123.mtz Output PDB file from Refmac for model 1i22_D1_PHR_MO_s0.56_r1-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\molrep\refine\refmac_molrep_1i22_D1_PHR_MO_s0.56_r1-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 8 MR programs being used: MOLREP PHASER Best search model so far: 1i22_D1_PHR_MO_s0.56_r1-123 using MOLREP Initial Rfree: 0.488 Final Rfree: 0.394 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\molrep\refine\refmac_molrep_1i22_D1_PHR_MO_s0.56_r1-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1i22_D1_PHR_MO_s0.56_r1-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\molrep\refine\refmac_molrep_1i22_D1_PHR_MO_s0.56_r1-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_1i22_D1_PHR_MO_s0.56_r1-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 8: 5v8g_A1_PHR_MO_s0.57_r2-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_5v8g_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.57 Search model type: MOLREP Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v8g_A1_PHR_MO_s0.57_r2-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v8g_A1_PHR_MO_s0.57_r2-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '5v8g_A1_PHR_MO_s0.57_r2-123' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 5v8g_A1_PHR_MO_s0.57_r2-123: ##### ################################################################################################# Template Model: 5v8g_A1_PHR_MO_s0.57_r2-123 has produced a marginal solution, final Rfree = 0.374 Molrep log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\molrep.log Molrep PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\molrep_5v8g_A1_PHR_MO_s0.57_r2-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v8g_A1_PHR_MO_s0.57_r2-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v8g_A1_PHR_MO_s0.57_r2-123.pdb #################################################################################################### ##### Refinement results from Refmac for 5v8g_A1_PHR_MO_s0.57_r2-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 5v8g_A1_PHR_MO_s0.57_r2-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4489 0.4378 0.537 92252. 4864.4 0.0344 2.530 2.388 1.465 0.255 1 0.4178 0.4197 0.570 91219. 4822.5 0.0089 0.669 1.769 1.080 0.201 2 0.4036 0.4091 0.593 90631. 4795.0 0.0064 0.500 1.602 0.975 0.165 3 0.4004 0.4062 0.601 90473. 4787.5 0.0053 0.426 1.506 0.913 0.142 4 0.3976 0.4041 0.607 90270. 4777.4 0.0048 0.387 1.436 0.870 0.129 5 0.3945 0.3971 0.613 89897. 4758.6 0.0045 0.362 1.382 0.836 0.120 6 0.3917 0.3948 0.618 89735. 4752.2 0.0043 0.345 1.339 0.810 0.114 7 0.3886 0.3926 0.623 89618. 4747.3 0.0041 0.333 1.304 0.789 0.110 8 0.3855 0.3896 0.629 89501. 4742.8 0.0040 0.325 1.275 0.771 0.106 9 0.3820 0.3855 0.635 89342. 4736.4 0.0040 0.322 1.253 0.757 0.104 10 0.3810 0.3847 0.638 89298. 4735.6 0.0038 0.307 1.225 0.739 0.102 11 0.3800 0.3838 0.640 89264. 4734.5 0.0036 0.297 1.203 0.725 0.100 12 0.3788 0.3827 0.643 89222. 4733.0 0.0035 0.290 1.181 0.712 0.099 13 0.3778 0.3828 0.645 89226. 4733.9 0.0035 0.285 1.164 0.701 0.098 14 0.3766 0.3822 0.649 89175. 4732.0 0.0034 0.280 1.148 0.691 0.097 15 0.3753 0.3812 0.651 89147. 4731.5 0.0034 0.276 1.134 0.682 0.096 16 0.3746 0.3808 0.651 89137. 4731.4 0.0032 0.268 1.119 0.672 0.095 17 0.3739 0.3804 0.653 89129. 4731.2 0.0032 0.263 1.106 0.664 0.094 18 0.3729 0.3791 0.655 89084. 4728.2 0.0031 0.259 1.095 0.657 0.094 19 0.3721 0.3786 0.657 89027. 4725.6 0.0031 0.255 1.084 0.650 0.093 20 0.3713 0.3780 0.659 88971. 4723.0 0.0030 0.251 1.073 0.644 0.093 21 0.3704 0.3775 0.660 88955. 4722.6 0.0030 0.248 1.065 0.639 0.092 22 0.3696 0.3765 0.661 88936. 4721.8 0.0029 0.246 1.056 0.634 0.092 23 0.3692 0.3760 0.661 88917. 4720.9 0.0029 0.241 1.047 0.628 0.091 24 0.3687 0.3757 0.662 88917. 4721.2 0.0028 0.238 1.039 0.623 0.091 25 0.3682 0.3752 0.663 88907. 4721.3 0.0028 0.235 1.031 0.618 0.090 26 0.3678 0.3749 0.664 88909. 4721.8 0.0028 0.233 1.024 0.614 0.090 27 0.3674 0.3746 0.665 88906. 4721.9 0.0027 0.231 1.017 0.610 0.089 28 0.3669 0.3744 0.665 88883. 4720.9 0.0027 0.229 1.011 0.607 0.089 29 0.3666 0.3741 0.666 88881. 4721.2 0.0027 0.227 1.005 0.603 0.088 30 0.3662 0.3738 0.667 88877. 4721.3 0.0027 0.225 0.999 0.600 0.088 $$ Output MTZ file from Refmac for model 5v8g_A1_PHR_MO_s0.57_r2-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v8g_A1_PHR_MO_s0.57_r2-123.mtz Output PDB file from Refmac for model 5v8g_A1_PHR_MO_s0.57_r2-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v8g_A1_PHR_MO_s0.57_r2-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 9 MR programs being used: MOLREP PHASER Best search model so far: 5v8g_A1_PHR_MO_s0.57_r2-123 using MOLREP Initial Rfree: 0.449 Final Rfree: 0.374 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v8g_A1_PHR_MO_s0.57_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v8g_A1_PHR_MO_s0.57_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v8g_A1_PHR_MO_s0.57_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v8g_A1_PHR_MO_s0.57_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 9: 5v8g_A1_PHR_MO_s0.57_r2-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_5v8g_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.57 Search model type: MOLREP Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\phaser\phaser_5v8g_A1_PHR_MO_s0.57_r2-123.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\phaser\phaser_5v8g_A1_PHR_MO_s0.57_r2-123.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\phaser\phaser_5v8g_A1_PHR_MO_s0.57_r2-123.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_HKLOUT_5v8g_A1_PHR_MO_s0.57_r2-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_5v8g_A1_PHR_MO_s0.57_r2-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\phaser\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\phaser\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '5v8g_A1_PHR_MO_s0.57_r2-123' ######################################################################### ###################################################################### ##### Results from Phaser for 5v8g_A1_PHR_MO_s0.57_r2-123: ##### ###################################################################### Template Model: 5v8g_A1_PHR_MO_s0.57_r2-123 has produced a marginal solution, final Rfree = 0.374 Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\phaser\phaser_5v8g_A1_PHR_MO_s0.57_r2-123.log Phaser PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\phaser\phaser_5v8g_A1_PHR_MO_s0.57_r2-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_5v8g_A1_PHR_MO_s0.57_r2-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_5v8g_A1_PHR_MO_s0.57_r2-123.pdb #################################################################################################### ##### Refinement results from Refmac for 5v8g_A1_PHR_MO_s0.57_r2-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 5v8g_A1_PHR_MO_s0.57_r2-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4268 0.4322 0.573 91491. 4833.9 0.0343 2.526 2.387 1.465 0.255 1 0.4083 0.4194 0.589 90752. 4804.2 0.0095 0.721 1.749 1.068 0.206 2 0.4031 0.4133 0.596 90559. 4795.0 0.0062 0.491 1.604 0.974 0.173 3 0.3995 0.4092 0.601 90370. 4785.8 0.0053 0.425 1.504 0.911 0.148 4 0.3964 0.4062 0.605 90211. 4778.4 0.0048 0.388 1.434 0.867 0.134 5 0.3934 0.4030 0.611 90048. 4770.2 0.0045 0.364 1.379 0.834 0.124 6 0.3903 0.4001 0.618 89925. 4764.7 0.0043 0.349 1.336 0.808 0.117 7 0.3872 0.3974 0.625 89813. 4760.3 0.0042 0.339 1.302 0.787 0.113 8 0.3838 0.3944 0.631 89684. 4755.4 0.0041 0.334 1.276 0.771 0.109 9 0.3824 0.3883 0.634 89475. 4744.7 0.0039 0.315 1.244 0.751 0.107 10 0.3811 0.3874 0.638 89409. 4742.4 0.0037 0.304 1.218 0.735 0.105 11 0.3797 0.3860 0.641 89365. 4740.7 0.0036 0.296 1.196 0.721 0.103 12 0.3784 0.3849 0.643 89319. 4739.1 0.0035 0.290 1.177 0.709 0.102 13 0.3773 0.3847 0.645 89288. 4738.9 0.0035 0.285 1.160 0.698 0.100 14 0.3759 0.3836 0.647 89249. 4737.6 0.0034 0.280 1.146 0.688 0.099 15 0.3746 0.3822 0.650 89212. 4736.4 0.0034 0.277 1.134 0.680 0.098 16 0.3739 0.3817 0.651 89171. 4734.5 0.0032 0.268 1.119 0.671 0.097 17 0.3732 0.3813 0.653 89140. 4733.4 0.0032 0.263 1.106 0.662 0.097 18 0.3724 0.3807 0.654 89096. 4731.6 0.0031 0.258 1.094 0.655 0.096 19 0.3717 0.3797 0.655 89052. 4729.6 0.0030 0.254 1.084 0.649 0.096 20 0.3710 0.3792 0.656 89024. 4728.7 0.0030 0.251 1.075 0.643 0.095 21 0.3703 0.3785 0.657 88998. 4727.5 0.0030 0.248 1.066 0.637 0.094 22 0.3697 0.3779 0.659 88977. 4726.9 0.0029 0.245 1.058 0.632 0.094 23 0.3692 0.3772 0.660 88960. 4726.4 0.0029 0.242 1.050 0.627 0.094 24 0.3686 0.3760 0.661 88909. 4723.6 0.0028 0.239 1.042 0.622 0.093 25 0.3680 0.3757 0.662 88889. 4722.6 0.0028 0.236 1.035 0.618 0.093 26 0.3676 0.3753 0.662 88874. 4721.9 0.0028 0.233 1.028 0.614 0.092 27 0.3672 0.3750 0.663 88837. 4720.2 0.0027 0.231 1.022 0.610 0.092 28 0.3669 0.3750 0.664 88814. 4719.3 0.0027 0.228 1.015 0.606 0.091 29 0.3666 0.3747 0.665 88788. 4717.8 0.0027 0.226 1.010 0.603 0.091 30 0.3663 0.3743 0.666 88775. 4717.4 0.0026 0.224 1.004 0.599 0.091 $$ Output MTZ file from Refmac for model 5v8g_A1_PHR_MO_s0.57_r2-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v8g_A1_PHR_MO_s0.57_r2-123.mtz Output PDB file from Refmac for model 5v8g_A1_PHR_MO_s0.57_r2-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v8g_A1_PHR_MO_s0.57_r2-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 10 MR programs being used: MOLREP PHASER Best search model so far: 5v8g_A1_PHR_MO_s0.57_r2-123 using MOLREP Initial Rfree: 0.449 Final Rfree: 0.374 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v8g_A1_PHR_MO_s0.57_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v8g_A1_PHR_MO_s0.57_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v8g_A1_PHR_MO_s0.57_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v8g_A1_PHR_MO_s0.57_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 10: 1lmq_A1_PHR_MO_s0.56_r2-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lmq_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1lmq_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.56 Search model type: MOLREP Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lmq_A1_PHR\molrep\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lmq_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1lmq_A1_PHR_MO_s0.56_r2-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lmq_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1lmq_A1_PHR_MO_s0.56_r2-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lmq_A1_PHR\molrep\mr\molrep\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lmq_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1lmq_A1_PHR_MO_s0.56_r2-123' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 1lmq_A1_PHR_MO_s0.56_r2-123: ##### ################################################################################################# Template Model: 1lmq_A1_PHR_MO_s0.56_r2-123 has produced a marginal solution, final Rfree = 0.386 Molrep log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lmq_A1_PHR\molrep\mr\molrep\molrep.log Molrep PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lmq_A1_PHR\molrep\mr\molrep\molrep_1lmq_A1_PHR_MO_s0.56_r2-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lmq_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1lmq_A1_PHR_MO_s0.56_r2-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lmq_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1lmq_A1_PHR_MO_s0.56_r2-123.pdb #################################################################################################### ##### Refinement results from Refmac for 1lmq_A1_PHR_MO_s0.56_r2-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1lmq_A1_PHR_MO_s0.56_r2-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4658 0.4639 0.492 93084. 4908.2 0.0337 2.633 3.197 1.941 0.326 1 0.4385 0.4340 0.521 91886. 4854.0 0.0087 0.705 2.242 1.348 0.191 2 0.4254 0.4185 0.545 91294. 4824.0 0.0065 0.537 1.951 1.173 0.158 3 0.4162 0.4082 0.565 90746. 4797.8 0.0058 0.474 1.797 1.079 0.142 4 0.4096 0.4033 0.578 90439. 4785.2 0.0066 0.538 1.689 1.013 0.131 5 0.4050 0.4001 0.585 90316. 4781.6 0.0050 0.410 1.609 0.963 0.124 6 0.4036 0.3993 0.590 90272. 4780.7 0.0043 0.360 1.541 0.920 0.119 7 0.4024 0.3981 0.592 90219. 4779.3 0.0041 0.340 1.485 0.885 0.115 8 0.4012 0.3975 0.595 90155. 4776.3 0.0039 0.326 1.439 0.857 0.112 9 0.3996 0.3962 0.596 90108. 4774.9 0.0038 0.316 1.403 0.835 0.109 10 0.3978 0.3946 0.600 90089. 4774.4 0.0037 0.308 1.372 0.816 0.107 11 0.3961 0.3930 0.605 90035. 4773.4 0.0036 0.302 1.347 0.800 0.105 12 0.3943 0.3915 0.608 89991. 4771.9 0.0036 0.300 1.328 0.788 0.104 13 0.3926 0.3905 0.612 89952. 4770.7 0.0036 0.297 1.309 0.777 0.102 14 0.3913 0.3897 0.616 89898. 4769.0 0.0035 0.291 1.291 0.765 0.101 15 0.3901 0.3896 0.617 89847. 4767.5 0.0034 0.285 1.273 0.755 0.100 16 0.3892 0.3891 0.618 89834. 4767.5 0.0034 0.280 1.257 0.744 0.099 17 0.3884 0.3887 0.620 89807. 4766.6 0.0033 0.275 1.241 0.735 0.098 18 0.3877 0.3884 0.622 89793. 4766.9 0.0032 0.270 1.227 0.725 0.096 19 0.3870 0.3876 0.623 89762. 4766.1 0.0032 0.266 1.213 0.717 0.096 20 0.3863 0.3874 0.625 89743. 4765.4 0.0031 0.262 1.201 0.709 0.095 21 0.3857 0.3872 0.626 89724. 4764.7 0.0031 0.258 1.189 0.702 0.094 22 0.3851 0.3870 0.627 89710. 4764.2 0.0030 0.254 1.178 0.695 0.093 23 0.3846 0.3866 0.629 89686. 4763.3 0.0030 0.250 1.168 0.688 0.093 24 0.3841 0.3865 0.629 89691. 4764.2 0.0029 0.247 1.158 0.682 0.092 25 0.3836 0.3863 0.630 89675. 4764.1 0.0029 0.243 1.150 0.675 0.091 26 0.3831 0.3864 0.631 89644. 4763.2 0.0028 0.240 1.141 0.670 0.090 27 0.3827 0.3864 0.631 89626. 4762.6 0.0028 0.237 1.133 0.664 0.090 28 0.3824 0.3865 0.632 89612. 4762.1 0.0028 0.236 1.128 0.661 0.090 29 0.3821 0.3865 0.632 89602. 4761.8 0.0028 0.235 1.124 0.659 0.089 30 0.3817 0.3864 0.634 89586. 4761.5 0.0027 0.232 1.116 0.654 0.089 $$ Output MTZ file from Refmac for model 1lmq_A1_PHR_MO_s0.56_r2-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lmq_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1lmq_A1_PHR_MO_s0.56_r2-123.mtz Output PDB file from Refmac for model 1lmq_A1_PHR_MO_s0.56_r2-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lmq_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1lmq_A1_PHR_MO_s0.56_r2-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 11 MR programs being used: MOLREP PHASER Best search model so far: 5v8g_A1_PHR_MO_s0.57_r2-123 using MOLREP Initial Rfree: 0.449 Final Rfree: 0.374 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v8g_A1_PHR_MO_s0.57_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v8g_A1_PHR_MO_s0.57_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v8g_A1_PHR_MO_s0.57_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v8g_A1_PHR_MO_s0.57_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 11: 1lmq_A1_PHR_MO_s0.56_r2-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lmq_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1lmq_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.56 Search model type: MOLREP Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lmq_A1_PHR\molrep\mr\phaser\phaser_1lmq_A1_PHR_MO_s0.56_r2-123.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lmq_A1_PHR\molrep\mr\phaser\phaser_1lmq_A1_PHR_MO_s0.56_r2-123.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lmq_A1_PHR\molrep\mr\phaser\phaser_1lmq_A1_PHR_MO_s0.56_r2-123.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lmq_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_HKLOUT_1lmq_A1_PHR_MO_s0.56_r2-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lmq_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1lmq_A1_PHR_MO_s0.56_r2-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lmq_A1_PHR\molrep\mr\phaser\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lmq_A1_PHR\molrep\mr\phaser\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1lmq_A1_PHR_MO_s0.56_r2-123' ######################################################################### ###################################################################### ##### Results from Phaser for 1lmq_A1_PHR_MO_s0.56_r2-123: ##### ###################################################################### Template Model: 1lmq_A1_PHR_MO_s0.56_r2-123 has produced a marginal solution, final Rfree = 0.386 Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lmq_A1_PHR\molrep\mr\phaser\phaser_1lmq_A1_PHR_MO_s0.56_r2-123.log Phaser PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lmq_A1_PHR\molrep\mr\phaser\phaser_1lmq_A1_PHR_MO_s0.56_r2-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lmq_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1lmq_A1_PHR_MO_s0.56_r2-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lmq_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1lmq_A1_PHR_MO_s0.56_r2-123.pdb #################################################################################################### ##### Refinement results from Refmac for 1lmq_A1_PHR_MO_s0.56_r2-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1lmq_A1_PHR_MO_s0.56_r2-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4486 0.4403 0.537 91613. 4832.4 0.0337 2.633 3.196 1.940 0.326 1 0.4443 0.4360 0.529 91729. 4841.3 0.0199 1.558 2.699 1.633 0.269 2 0.4401 0.4315 0.531 91652. 4839.9 0.0111 0.881 2.331 1.403 0.211 3 0.4359 0.4276 0.537 91478. 4831.1 0.0077 0.622 2.104 1.263 0.181 4 0.4298 0.4219 0.549 91162. 4817.0 0.0058 0.477 1.867 1.117 0.150 5 0.4244 0.4172 0.559 90941. 4805.5 0.0072 0.588 1.725 1.031 0.136 6 0.4184 0.4120 0.568 90712. 4794.2 0.0048 0.394 1.631 0.976 0.126 7 0.4120 0.4073 0.578 90548. 4788.8 0.0046 0.381 1.566 0.938 0.120 8 0.4099 0.4060 0.581 90507. 4788.1 0.0042 0.351 1.504 0.900 0.115 9 0.4075 0.4044 0.584 90365. 4781.7 0.0040 0.335 1.456 0.871 0.112 10 0.4052 0.4024 0.588 90280. 4778.5 0.0039 0.325 1.418 0.847 0.109 11 0.4029 0.4001 0.592 90203. 4775.8 0.0038 0.316 1.387 0.828 0.107 12 0.4006 0.3982 0.595 90089. 4770.8 0.0037 0.310 1.361 0.812 0.105 13 0.3983 0.3966 0.599 90010. 4768.4 0.0037 0.306 1.339 0.798 0.104 14 0.3959 0.3937 0.605 89961. 4766.7 0.0037 0.303 1.322 0.787 0.103 15 0.3947 0.3918 0.608 89982. 4768.8 0.0035 0.291 1.298 0.772 0.101 16 0.3935 0.3904 0.611 89938. 4767.1 0.0034 0.285 1.279 0.760 0.100 17 0.3924 0.3896 0.614 89890. 4765.6 0.0034 0.280 1.263 0.750 0.099 18 0.3912 0.3893 0.616 89847. 4764.3 0.0033 0.276 1.248 0.740 0.098 19 0.3901 0.3888 0.617 89811. 4763.4 0.0033 0.273 1.235 0.732 0.097 20 0.3892 0.3887 0.620 89776. 4762.3 0.0032 0.271 1.224 0.725 0.097 21 0.3882 0.3885 0.623 89732. 4761.1 0.0032 0.267 1.213 0.718 0.096 22 0.3873 0.3878 0.624 89726. 4762.0 0.0031 0.264 1.203 0.712 0.095 23 0.3865 0.3875 0.626 89708. 4762.0 0.0031 0.260 1.192 0.705 0.094 24 0.3859 0.3873 0.626 89700. 4762.1 0.0031 0.257 1.182 0.698 0.094 25 0.3853 0.3867 0.627 89683. 4761.7 0.0030 0.254 1.172 0.692 0.093 26 0.3845 0.3864 0.629 89663. 4761.6 0.0030 0.250 1.162 0.685 0.092 27 0.3841 0.3863 0.629 89657. 4762.0 0.0029 0.247 1.153 0.679 0.092 28 0.3836 0.3860 0.630 89648. 4761.8 0.0029 0.243 1.144 0.674 0.091 29 0.3831 0.3860 0.630 89635. 4761.6 0.0029 0.241 1.135 0.668 0.090 30 0.3827 0.3859 0.631 89620. 4761.0 0.0028 0.238 1.127 0.663 0.090 $$ Output MTZ file from Refmac for model 1lmq_A1_PHR_MO_s0.56_r2-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lmq_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1lmq_A1_PHR_MO_s0.56_r2-123.mtz Output PDB file from Refmac for model 1lmq_A1_PHR_MO_s0.56_r2-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lmq_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1lmq_A1_PHR_MO_s0.56_r2-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 12 MR programs being used: MOLREP PHASER Best search model so far: 5v8g_A1_PHR_MO_s0.57_r2-123 using MOLREP Initial Rfree: 0.449 Final Rfree: 0.374 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v8g_A1_PHR_MO_s0.57_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v8g_A1_PHR_MO_s0.57_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v8g_A1_PHR_MO_s0.57_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v8g_A1_PHR_MO_s0.57_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 12: 3lhm_A1_PHR_MO_s0.55_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\3lhm_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_3lhm_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.55 Search model type: MOLREP Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\3lhm_A1_PHR\molrep\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\3lhm_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_3lhm_A1_PHR_MO_s0.55_r1-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\3lhm_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_3lhm_A1_PHR_MO_s0.55_r1-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\3lhm_A1_PHR\molrep\mr\molrep\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\3lhm_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '3lhm_A1_PHR_MO_s0.55_r1-123' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 3lhm_A1_PHR_MO_s0.55_r1-123: ##### ################################################################################################# Template Model: 3lhm_A1_PHR_MO_s0.55_r1-123 has produced a marginal solution, final Rfree = 0.405 Molrep log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\3lhm_A1_PHR\molrep\mr\molrep\molrep.log Molrep PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\3lhm_A1_PHR\molrep\mr\molrep\molrep_3lhm_A1_PHR_MO_s0.55_r1-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\3lhm_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_3lhm_A1_PHR_MO_s0.55_r1-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\3lhm_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_3lhm_A1_PHR_MO_s0.55_r1-123.pdb #################################################################################################### ##### Refinement results from Refmac for 3lhm_A1_PHR_MO_s0.55_r1-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 3lhm_A1_PHR_MO_s0.55_r1-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4939 0.5070 0.406 93762. 4960.9 0.0301 2.583 3.283 2.035 0.353 1 0.4599 0.4706 0.454 92767. 4918.4 0.0092 0.745 2.234 1.368 0.281 2 0.4447 0.4528 0.492 92237. 4889.1 0.0076 0.596 1.982 1.203 0.228 3 0.4354 0.4404 0.516 91755. 4863.0 0.0063 0.496 1.833 1.105 0.183 4 0.4329 0.4375 0.523 91628. 4856.1 0.0054 0.430 1.717 1.028 0.162 5 0.4306 0.4351 0.528 91539. 4851.4 0.0050 0.398 1.635 0.974 0.144 6 0.4282 0.4330 0.536 91436. 4846.1 0.0047 0.376 1.575 0.934 0.132 7 0.4258 0.4310 0.540 91352. 4842.3 0.0045 0.360 1.529 0.903 0.125 8 0.4232 0.4287 0.544 91308. 4840.4 0.0044 0.350 1.491 0.877 0.118 9 0.4202 0.4259 0.551 91234. 4837.1 0.0043 0.345 1.467 0.859 0.116 10 0.4169 0.4226 0.557 91118. 4831.6 0.0043 0.343 1.452 0.847 0.114 11 0.4138 0.4182 0.565 91033. 4826.9 0.0043 0.340 1.442 0.838 0.112 12 0.4113 0.4161 0.573 90962. 4823.8 0.0042 0.332 1.430 0.828 0.110 13 0.4090 0.4144 0.578 90892. 4820.9 0.0041 0.325 1.417 0.818 0.109 14 0.4072 0.4137 0.583 90858. 4819.4 0.0040 0.316 1.406 0.808 0.108 15 0.4057 0.4131 0.587 90837. 4818.2 0.0038 0.308 1.393 0.799 0.107 16 0.4044 0.4124 0.590 90774. 4815.5 0.0037 0.300 1.383 0.791 0.106 17 0.4032 0.4116 0.592 90734. 4813.8 0.0036 0.294 1.372 0.783 0.105 18 0.4021 0.4108 0.594 90688. 4811.9 0.0035 0.288 1.362 0.775 0.104 19 0.4010 0.4104 0.595 90660. 4811.0 0.0035 0.282 1.353 0.768 0.103 20 0.4002 0.4097 0.597 90625. 4810.0 0.0034 0.277 1.344 0.761 0.102 21 0.3994 0.4092 0.598 90596. 4808.9 0.0033 0.272 1.335 0.755 0.102 22 0.3987 0.4087 0.599 90555. 4807.2 0.0033 0.267 1.320 0.747 0.101 23 0.3980 0.4079 0.600 90518. 4805.6 0.0032 0.263 1.310 0.740 0.101 24 0.3973 0.4077 0.601 90482. 4804.2 0.0031 0.259 1.301 0.734 0.100 25 0.3967 0.4073 0.602 90461. 4803.4 0.0031 0.255 1.293 0.729 0.100 26 0.3960 0.4069 0.605 90429. 4802.2 0.0030 0.251 1.286 0.724 0.099 27 0.3955 0.4063 0.607 90396. 4800.9 0.0030 0.248 1.279 0.719 0.099 28 0.3948 0.4058 0.608 90387. 4800.7 0.0029 0.244 1.272 0.715 0.098 29 0.3943 0.4054 0.608 90385. 4800.9 0.0029 0.241 1.266 0.711 0.098 30 0.3938 0.4051 0.609 90390. 4801.4 0.0029 0.239 1.260 0.707 0.098 $$ Output MTZ file from Refmac for model 3lhm_A1_PHR_MO_s0.55_r1-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\3lhm_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_3lhm_A1_PHR_MO_s0.55_r1-123.mtz Output PDB file from Refmac for model 3lhm_A1_PHR_MO_s0.55_r1-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\3lhm_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_3lhm_A1_PHR_MO_s0.55_r1-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 13 MR programs being used: MOLREP PHASER Best search model so far: 5v8g_A1_PHR_MO_s0.57_r2-123 using MOLREP Initial Rfree: 0.449 Final Rfree: 0.374 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v8g_A1_PHR_MO_s0.57_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v8g_A1_PHR_MO_s0.57_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v8g_A1_PHR_MO_s0.57_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v8g_A1_PHR_MO_s0.57_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 13: 3lhm_A1_PHR_MO_s0.55_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\3lhm_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_3lhm_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.55 Search model type: MOLREP Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\3lhm_A1_PHR\molrep\mr\phaser\phaser_3lhm_A1_PHR_MO_s0.55_r1-123.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\3lhm_A1_PHR\molrep\mr\phaser\phaser_3lhm_A1_PHR_MO_s0.55_r1-123.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\3lhm_A1_PHR\molrep\mr\phaser\phaser_3lhm_A1_PHR_MO_s0.55_r1-123.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\3lhm_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_HKLOUT_3lhm_A1_PHR_MO_s0.55_r1-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\3lhm_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_3lhm_A1_PHR_MO_s0.55_r1-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\3lhm_A1_PHR\molrep\mr\phaser\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\3lhm_A1_PHR\molrep\mr\phaser\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '3lhm_A1_PHR_MO_s0.55_r1-123' ######################################################################### ###################################################################### ##### Results from Phaser for 3lhm_A1_PHR_MO_s0.55_r1-123: ##### ###################################################################### Template Model: 3lhm_A1_PHR_MO_s0.55_r1-123 has produced a marginal solution, final Rfree = 0.405 Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\3lhm_A1_PHR\molrep\mr\phaser\phaser_3lhm_A1_PHR_MO_s0.55_r1-123.log Phaser PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\3lhm_A1_PHR\molrep\mr\phaser\phaser_3lhm_A1_PHR_MO_s0.55_r1-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\3lhm_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_3lhm_A1_PHR_MO_s0.55_r1-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\3lhm_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_3lhm_A1_PHR_MO_s0.55_r1-123.pdb #################################################################################################### ##### Refinement results from Refmac for 3lhm_A1_PHR_MO_s0.55_r1-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 3lhm_A1_PHR_MO_s0.55_r1-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4803 0.4826 0.468 93080. 4920.5 0.0301 2.582 3.284 2.036 0.353 1 0.4584 0.4609 0.482 92563. 4899.0 0.0093 0.762 2.188 1.340 0.282 2 0.4430 0.4450 0.510 91929. 4867.8 0.0070 0.558 1.941 1.180 0.230 3 0.4344 0.4356 0.528 91620. 4851.7 0.0061 0.480 1.805 1.089 0.187 4 0.4280 0.4288 0.538 91444. 4842.8 0.0057 0.444 1.714 1.026 0.163 5 0.4237 0.4256 0.548 91313. 4837.3 0.0054 0.421 1.646 0.980 0.144 6 0.4199 0.4222 0.555 91197. 4832.3 0.0051 0.400 1.594 0.943 0.131 7 0.4168 0.4191 0.562 91103. 4827.5 0.0049 0.382 1.551 0.912 0.122 8 0.4143 0.4166 0.568 91021. 4824.3 0.0047 0.369 1.520 0.889 0.119 9 0.4118 0.4154 0.573 90948. 4821.0 0.0045 0.357 1.494 0.870 0.116 10 0.4099 0.4139 0.578 90880. 4818.2 0.0044 0.345 1.472 0.854 0.114 11 0.4081 0.4130 0.582 90835. 4816.5 0.0042 0.335 1.452 0.839 0.112 12 0.4065 0.4121 0.586 90791. 4814.4 0.0041 0.326 1.434 0.826 0.110 13 0.4052 0.4115 0.589 90766. 4813.6 0.0039 0.316 1.417 0.815 0.108 14 0.4040 0.4106 0.591 90741. 4812.9 0.0038 0.307 1.402 0.804 0.106 15 0.4028 0.4099 0.592 90708. 4811.7 0.0037 0.300 1.388 0.795 0.105 16 0.4018 0.4094 0.594 90679. 4810.8 0.0036 0.293 1.376 0.786 0.104 17 0.4008 0.4091 0.595 90638. 4809.5 0.0035 0.287 1.359 0.776 0.103 18 0.3999 0.4090 0.596 90613. 4809.1 0.0034 0.281 1.346 0.768 0.103 19 0.3991 0.4084 0.597 90574. 4807.9 0.0034 0.276 1.336 0.760 0.102 20 0.3983 0.4077 0.599 90550. 4806.7 0.0033 0.271 1.326 0.753 0.101 21 0.3976 0.4073 0.600 90530. 4806.0 0.0032 0.266 1.316 0.746 0.101 22 0.3968 0.4071 0.602 90503. 4805.2 0.0032 0.262 1.308 0.740 0.100 23 0.3961 0.4070 0.604 90493. 4805.0 0.0031 0.258 1.300 0.735 0.100 24 0.3955 0.4068 0.605 90495. 4805.6 0.0031 0.254 1.292 0.730 0.099 25 0.3949 0.4068 0.606 90480. 4805.1 0.0030 0.251 1.285 0.725 0.099 26 0.3942 0.4064 0.607 90454. 4804.0 0.0030 0.248 1.279 0.720 0.099 27 0.3936 0.4061 0.607 90435. 4803.1 0.0029 0.245 1.273 0.716 0.098 28 0.3930 0.4059 0.608 90412. 4802.3 0.0029 0.242 1.267 0.712 0.098 29 0.3924 0.4055 0.609 90398. 4801.7 0.0029 0.240 1.261 0.708 0.098 30 0.3918 0.4050 0.610 90385. 4801.7 0.0029 0.238 1.255 0.705 0.097 $$ Output MTZ file from Refmac for model 3lhm_A1_PHR_MO_s0.55_r1-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\3lhm_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_3lhm_A1_PHR_MO_s0.55_r1-123.mtz Output PDB file from Refmac for model 3lhm_A1_PHR_MO_s0.55_r1-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\3lhm_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_3lhm_A1_PHR_MO_s0.55_r1-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 14 MR programs being used: MOLREP PHASER Best search model so far: 5v8g_A1_PHR_MO_s0.57_r2-123 using MOLREP Initial Rfree: 0.449 Final Rfree: 0.374 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v8g_A1_PHR_MO_s0.57_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v8g_A1_PHR_MO_s0.57_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v8g_A1_PHR_MO_s0.57_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v8g_A1_PHR_MO_s0.57_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 14: 5v92_B1_PHR_MO_s0.56_r2-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_5v92_B1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.56 Search model type: MOLREP Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '5v92_B1_PHR_MO_s0.56_r2-123' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 5v92_B1_PHR_MO_s0.56_r2-123: ##### ################################################################################################# Template Model: 5v92_B1_PHR_MO_s0.56_r2-123 has produced a solution, final Rfree = 0.370 and is 0.794 of initial Rfree #################################################################################################### ##### Refinement results from Refmac for 5v92_B1_PHR_MO_s0.56_r2-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 5v92_B1_PHR_MO_s0.56_r2-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4663 0.4548 0.491 92775. 4895.7 0.0346 2.540 2.385 1.435 0.242 1 0.4394 0.4285 0.527 91931. 4858.1 0.0081 0.625 1.761 1.065 0.176 2 0.4247 0.4085 0.560 91360. 4823.7 0.0060 0.480 1.607 0.966 0.138 3 0.4141 0.3945 0.588 90893. 4795.7 0.0054 0.436 1.515 0.908 0.115 4 0.4068 0.3870 0.608 90589. 4779.1 0.0050 0.408 1.449 0.867 0.105 5 0.4049 0.3852 0.616 90480. 4774.1 0.0045 0.367 1.389 0.831 0.102 6 0.4031 0.3838 0.617 90384. 4769.9 0.0042 0.347 1.346 0.804 0.101 7 0.4011 0.3830 0.622 90289. 4765.7 0.0040 0.335 1.311 0.783 0.099 8 0.3991 0.3815 0.626 90220. 4763.1 0.0039 0.326 1.284 0.766 0.098 9 0.3968 0.3802 0.632 90082. 4757.5 0.0038 0.318 1.262 0.752 0.097 10 0.3943 0.3746 0.635 89887. 4748.1 0.0037 0.314 1.244 0.741 0.096 11 0.3918 0.3724 0.639 89705. 4740.2 0.0037 0.311 1.231 0.733 0.095 12 0.3907 0.3716 0.642 89674. 4739.5 0.0035 0.299 1.211 0.720 0.094 13 0.3896 0.3712 0.645 89656. 4739.6 0.0035 0.292 1.194 0.709 0.093 14 0.3885 0.3711 0.644 89625. 4739.1 0.0034 0.287 1.180 0.700 0.092 15 0.3878 0.3710 0.646 89592. 4737.9 0.0034 0.284 1.172 0.695 0.092 16 0.3871 0.3711 0.646 89564. 4737.1 0.0033 0.282 1.165 0.691 0.091 17 0.3858 0.3709 0.648 89540. 4737.1 0.0033 0.279 1.156 0.685 0.091 18 0.3846 0.3703 0.649 89486. 4735.7 0.0033 0.277 1.148 0.679 0.090 19 0.3836 0.3703 0.650 89444. 4734.9 0.0033 0.273 1.140 0.674 0.089 20 0.3826 0.3702 0.652 89425. 4735.5 0.0032 0.269 1.130 0.668 0.089 21 0.3818 0.3702 0.652 89419. 4736.4 0.0031 0.264 1.122 0.663 0.088 22 0.3810 0.3704 0.652 89405. 4736.3 0.0031 0.260 1.114 0.657 0.088 23 0.3803 0.3705 0.654 89397. 4736.8 0.0031 0.257 1.105 0.652 0.087 24 0.3797 0.3706 0.655 89391. 4737.6 0.0030 0.253 1.098 0.647 0.087 25 0.3791 0.3705 0.656 89376. 4737.9 0.0030 0.250 1.090 0.642 0.086 26 0.3786 0.3705 0.656 89346. 4737.4 0.0029 0.246 1.083 0.638 0.086 27 0.3781 0.3704 0.656 89341. 4738.0 0.0029 0.243 1.076 0.634 0.085 28 0.3777 0.3703 0.657 89331. 4738.2 0.0029 0.240 1.070 0.630 0.085 29 0.3772 0.3702 0.658 89368. 4740.5 0.0028 0.238 1.064 0.626 0.085 30 0.3768 0.3702 0.658 89386. 4742.0 0.0028 0.236 1.057 0.622 0.084 $$ Output MTZ file from Refmac for model 5v92_B1_PHR_MO_s0.56_r2-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Output PDB file from Refmac for model 5v92_B1_PHR_MO_s0.56_r2-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 15 MR programs being used: MOLREP PHASER Best search model so far: 5v92_B1_PHR_MO_s0.56_r2-123 using MOLREP Initial Rfree: 0.466 Final Rfree: 0.370 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 15: 5v92_B1_PHR_MO_s0.56_r2-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_5v92_B1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.56 Search model type: MOLREP Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\phaser\phaser_5v92_B1_PHR_MO_s0.56_r2-123.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\phaser\phaser_5v92_B1_PHR_MO_s0.56_r2-123.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\phaser\phaser_5v92_B1_PHR_MO_s0.56_r2-123.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\phaser\refine\refmac_phaser_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\phaser\refine\refmac_phaser_5v92_B1_PHR_MO_s0.56_r2-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\phaser\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\phaser\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '5v92_B1_PHR_MO_s0.56_r2-123' ######################################################################### ###################################################################### ##### Results from Phaser for 5v92_B1_PHR_MO_s0.56_r2-123: ##### ###################################################################### Template Model: 5v92_B1_PHR_MO_s0.56_r2-123 has produced a marginal solution, final Rfree = 0.371 Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\phaser\phaser_5v92_B1_PHR_MO_s0.56_r2-123.log Phaser PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\phaser\phaser_5v92_B1_PHR_MO_s0.56_r2-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\phaser\refine\refmac_phaser_5v92_B1_PHR_MO_s0.56_r2-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\phaser\refine\refmac_phaser_5v92_B1_PHR_MO_s0.56_r2-123.pdb #################################################################################################### ##### Refinement results from Refmac for 5v92_B1_PHR_MO_s0.56_r2-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 5v92_B1_PHR_MO_s0.56_r2-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4508 0.4469 0.522 91971. 4861.6 0.0346 2.539 2.386 1.436 0.242 1 0.4429 0.4385 0.524 91691. 4847.0 0.0084 0.633 1.761 1.070 0.193 2 0.4356 0.4274 0.535 91325. 4828.6 0.0058 0.455 1.589 0.960 0.154 3 0.4303 0.4213 0.545 91072. 4815.5 0.0050 0.399 1.484 0.894 0.129 4 0.4251 0.4162 0.554 90858. 4805.1 0.0046 0.370 1.403 0.842 0.106 5 0.4200 0.4106 0.566 90605. 4791.5 0.0043 0.354 1.356 0.813 0.103 6 0.4144 0.4035 0.578 90408. 4780.6 0.0042 0.348 1.326 0.795 0.101 7 0.4077 0.3960 0.596 90222. 4770.4 0.0043 0.350 1.310 0.785 0.100 8 0.4056 0.3940 0.606 90180. 4768.7 0.0039 0.326 1.277 0.764 0.099 9 0.4031 0.3915 0.609 90099. 4764.9 0.0038 0.317 1.252 0.748 0.098 10 0.4008 0.3888 0.614 90049. 4761.9 0.0037 0.311 1.233 0.736 0.097 11 0.3983 0.3861 0.620 89997. 4759.3 0.0036 0.305 1.217 0.726 0.096 12 0.3956 0.3830 0.624 89883. 4753.3 0.0036 0.302 1.205 0.718 0.095 13 0.3929 0.3800 0.630 89761. 4747.1 0.0036 0.300 1.197 0.712 0.095 14 0.3903 0.3773 0.636 89680. 4743.4 0.0035 0.297 1.191 0.707 0.094 15 0.3890 0.3762 0.639 89624. 4741.3 0.0034 0.286 1.176 0.697 0.094 16 0.3877 0.3755 0.642 89605. 4740.9 0.0033 0.281 1.163 0.689 0.093 17 0.3864 0.3746 0.644 89569. 4739.9 0.0032 0.276 1.153 0.682 0.092 18 0.3853 0.3738 0.647 89532. 4738.7 0.0032 0.272 1.143 0.675 0.092 19 0.3842 0.3735 0.649 89520. 4739.2 0.0032 0.268 1.133 0.669 0.091 20 0.3831 0.3730 0.650 89500. 4739.2 0.0031 0.264 1.125 0.664 0.091 21 0.3820 0.3725 0.650 89474. 4738.6 0.0031 0.262 1.118 0.659 0.090 22 0.3812 0.3720 0.652 89456. 4737.9 0.0031 0.258 1.111 0.654 0.090 23 0.3804 0.3719 0.653 89428. 4737.6 0.0030 0.254 1.103 0.650 0.089 24 0.3797 0.3715 0.653 89397. 4736.7 0.0030 0.251 1.096 0.645 0.089 25 0.3791 0.3710 0.654 89378. 4736.5 0.0029 0.247 1.089 0.640 0.088 26 0.3786 0.3712 0.655 89379. 4737.0 0.0029 0.244 1.082 0.636 0.088 27 0.3781 0.3711 0.656 89360. 4736.6 0.0029 0.241 1.075 0.631 0.087 28 0.3776 0.3712 0.656 89341. 4736.2 0.0028 0.239 1.069 0.627 0.087 29 0.3771 0.3710 0.656 89319. 4735.7 0.0028 0.236 1.062 0.624 0.086 30 0.3767 0.3708 0.657 89291. 4734.6 0.0028 0.234 1.057 0.620 0.086 $$ Output MTZ file from Refmac for model 5v92_B1_PHR_MO_s0.56_r2-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Output PDB file from Refmac for model 5v92_B1_PHR_MO_s0.56_r2-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 16 MR programs being used: MOLREP PHASER Best search model so far: 5v92_B1_PHR_MO_s0.56_r2-123 using MOLREP Initial Rfree: 0.466 Final Rfree: 0.370 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 16: 6d9i_B1_PHR_MO_s0.56_r2-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6d9i_B1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_6d9i_B1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.56 Search model type: MOLREP Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6d9i_B1_PHR\molrep\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6d9i_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_6d9i_B1_PHR_MO_s0.56_r2-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6d9i_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_6d9i_B1_PHR_MO_s0.56_r2-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6d9i_B1_PHR\molrep\mr\molrep\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6d9i_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '6d9i_B1_PHR_MO_s0.56_r2-123' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 6d9i_B1_PHR_MO_s0.56_r2-123: ##### ################################################################################################# Template Model: 6d9i_B1_PHR_MO_s0.56_r2-123 has produced a marginal solution, final Rfree = 0.382 Molrep log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6d9i_B1_PHR\molrep\mr\molrep\molrep.log Molrep PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6d9i_B1_PHR\molrep\mr\molrep\molrep_6d9i_B1_PHR_MO_s0.56_r2-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6d9i_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_6d9i_B1_PHR_MO_s0.56_r2-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6d9i_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_6d9i_B1_PHR_MO_s0.56_r2-123.pdb #################################################################################################### ##### Refinement results from Refmac for 6d9i_B1_PHR_MO_s0.56_r2-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 6d9i_B1_PHR_MO_s0.56_r2-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4646 0.4639 0.491 93077. 4919.8 0.0344 2.496 2.230 1.348 0.243 1 0.4342 0.4326 0.532 91721. 4852.7 0.0090 0.669 1.666 1.008 0.195 2 0.4200 0.4156 0.565 90980. 4816.9 0.0068 0.524 1.548 0.934 0.156 3 0.4159 0.4123 0.580 90713. 4804.3 0.0056 0.438 1.475 0.886 0.130 4 0.4126 0.4100 0.586 90500. 4794.6 0.0051 0.406 1.435 0.857 0.123 5 0.4097 0.4074 0.590 90383. 4789.5 0.0048 0.390 1.409 0.837 0.123 6 0.4069 0.4048 0.597 90264. 4784.0 0.0046 0.380 1.386 0.820 0.122 7 0.4042 0.4029 0.606 90139. 4777.4 0.0045 0.373 1.373 0.809 0.123 8 0.4013 0.4005 0.613 89956. 4769.3 0.0044 0.369 1.367 0.803 0.124 9 0.3986 0.3988 0.618 89856. 4764.9 0.0043 0.365 1.368 0.801 0.126 10 0.3973 0.3976 0.622 89826. 4763.9 0.0042 0.357 1.353 0.790 0.129 11 0.3957 0.3961 0.625 89776. 4761.5 0.0041 0.346 1.343 0.782 0.129 12 0.3945 0.3950 0.626 89720. 4759.5 0.0040 0.341 1.336 0.776 0.130 13 0.3932 0.3942 0.628 89704. 4759.4 0.0039 0.338 1.332 0.772 0.131 14 0.3921 0.3933 0.629 89632. 4756.0 0.0039 0.335 1.327 0.768 0.132 15 0.3908 0.3922 0.631 89505. 4749.7 0.0039 0.333 1.325 0.766 0.131 16 0.3900 0.3916 0.633 89458. 4747.4 0.0037 0.324 1.318 0.760 0.130 17 0.3893 0.3908 0.635 89430. 4746.7 0.0037 0.319 1.311 0.755 0.130 18 0.3885 0.3899 0.637 89404. 4746.0 0.0036 0.316 1.305 0.750 0.128 19 0.3879 0.3894 0.638 89377. 4744.7 0.0036 0.314 1.299 0.746 0.127 20 0.3872 0.3885 0.639 89350. 4743.4 0.0036 0.318 1.299 0.748 0.124 21 0.3865 0.3875 0.641 89340. 4742.9 0.0037 0.328 1.303 0.752 0.123 22 0.3859 0.3867 0.642 89330. 4742.2 0.0036 0.326 1.300 0.750 0.120 23 0.3855 0.3858 0.643 89319. 4741.6 0.0035 0.318 1.290 0.743 0.119 24 0.3850 0.3849 0.644 89306. 4740.9 0.0035 0.313 1.283 0.737 0.118 25 0.3845 0.3843 0.645 89292. 4740.1 0.0035 0.310 1.276 0.732 0.117 26 0.3840 0.3837 0.645 89286. 4739.7 0.0034 0.306 1.269 0.727 0.117 27 0.3836 0.3832 0.646 89272. 4738.9 0.0034 0.302 1.263 0.722 0.116 28 0.3832 0.3827 0.647 89252. 4737.6 0.0033 0.298 1.255 0.717 0.115 29 0.3829 0.3825 0.648 89250. 4738.0 0.0033 0.295 1.247 0.711 0.114 30 0.3825 0.3820 0.648 89246. 4737.8 0.0033 0.291 1.241 0.707 0.114 $$ Output MTZ file from Refmac for model 6d9i_B1_PHR_MO_s0.56_r2-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6d9i_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_6d9i_B1_PHR_MO_s0.56_r2-123.mtz Output PDB file from Refmac for model 6d9i_B1_PHR_MO_s0.56_r2-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6d9i_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_6d9i_B1_PHR_MO_s0.56_r2-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 17 MR programs being used: MOLREP PHASER Best search model so far: 5v92_B1_PHR_MO_s0.56_r2-123 using MOLREP Initial Rfree: 0.466 Final Rfree: 0.370 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 17: 6d9i_B1_PHR_MO_s0.56_r2-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6d9i_B1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_6d9i_B1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.56 Search model type: MOLREP Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6d9i_B1_PHR\molrep\mr\phaser\phaser_6d9i_B1_PHR_MO_s0.56_r2-123.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6d9i_B1_PHR\molrep\mr\phaser\phaser_6d9i_B1_PHR_MO_s0.56_r2-123.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6d9i_B1_PHR\molrep\mr\phaser\phaser_6d9i_B1_PHR_MO_s0.56_r2-123.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6d9i_B1_PHR\molrep\mr\phaser\refine\refmac_phaser_HKLOUT_6d9i_B1_PHR_MO_s0.56_r2-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6d9i_B1_PHR\molrep\mr\phaser\refine\refmac_phaser_6d9i_B1_PHR_MO_s0.56_r2-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6d9i_B1_PHR\molrep\mr\phaser\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6d9i_B1_PHR\molrep\mr\phaser\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '6d9i_B1_PHR_MO_s0.56_r2-123' ######################################################################### ###################################################################### ##### Results from Phaser for 6d9i_B1_PHR_MO_s0.56_r2-123: ##### ###################################################################### Template Model: 6d9i_B1_PHR_MO_s0.56_r2-123 has produced a marginal solution, final Rfree = 0.383 Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6d9i_B1_PHR\molrep\mr\phaser\phaser_6d9i_B1_PHR_MO_s0.56_r2-123.log Phaser PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6d9i_B1_PHR\molrep\mr\phaser\phaser_6d9i_B1_PHR_MO_s0.56_r2-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6d9i_B1_PHR\molrep\mr\phaser\refine\refmac_phaser_6d9i_B1_PHR_MO_s0.56_r2-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6d9i_B1_PHR\molrep\mr\phaser\refine\refmac_phaser_6d9i_B1_PHR_MO_s0.56_r2-123.pdb #################################################################################################### ##### Refinement results from Refmac for 6d9i_B1_PHR_MO_s0.56_r2-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 6d9i_B1_PHR_MO_s0.56_r2-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4524 0.4529 0.519 92138. 4874.2 0.0344 2.496 2.229 1.348 0.243 1 0.4300 0.4279 0.545 91257. 4830.0 0.0091 0.677 1.663 1.002 0.202 2 0.4236 0.4217 0.563 90979. 4816.0 0.0063 0.489 1.545 0.928 0.170 3 0.4192 0.4170 0.576 90734. 4803.9 0.0054 0.430 1.473 0.879 0.136 4 0.4153 0.4129 0.584 90551. 4794.9 0.0050 0.407 1.432 0.850 0.126 5 0.4119 0.4092 0.591 90402. 4788.5 0.0048 0.395 1.409 0.831 0.124 6 0.4085 0.4057 0.599 90283. 4782.9 0.0047 0.388 1.398 0.822 0.125 7 0.4051 0.4030 0.607 90137. 4777.0 0.0046 0.386 1.391 0.815 0.126 8 0.4034 0.4010 0.609 90056. 4773.2 0.0043 0.369 1.365 0.799 0.126 9 0.4017 0.3997 0.612 89997. 4770.7 0.0042 0.362 1.353 0.789 0.128 10 0.4001 0.3985 0.615 89961. 4770.0 0.0041 0.357 1.346 0.782 0.130 11 0.3985 0.3973 0.618 89890. 4767.3 0.0041 0.353 1.343 0.777 0.132 12 0.3969 0.3962 0.621 89795. 4763.7 0.0041 0.352 1.342 0.774 0.133 13 0.3953 0.3955 0.623 89741. 4761.7 0.0041 0.352 1.343 0.773 0.135 14 0.3936 0.3939 0.626 89605. 4755.5 0.0041 0.353 1.344 0.773 0.133 15 0.3925 0.3936 0.628 89560. 4754.0 0.0039 0.345 1.338 0.768 0.133 16 0.3913 0.3923 0.630 89516. 4751.8 0.0040 0.346 1.331 0.763 0.134 17 0.3902 0.3912 0.632 89486. 4750.7 0.0039 0.337 1.327 0.759 0.133 18 0.3893 0.3904 0.633 89461. 4749.6 0.0038 0.333 1.323 0.756 0.133 19 0.3884 0.3894 0.636 89424. 4747.0 0.0038 0.331 1.319 0.753 0.132 20 0.3874 0.3888 0.640 89368. 4743.7 0.0037 0.328 1.313 0.749 0.130 21 0.3868 0.3880 0.642 89333. 4742.6 0.0036 0.323 1.305 0.744 0.129 22 0.3862 0.3874 0.643 89323. 4742.1 0.0036 0.319 1.297 0.739 0.127 23 0.3857 0.3866 0.645 89338. 4742.6 0.0035 0.316 1.289 0.734 0.125 24 0.3852 0.3859 0.646 89327. 4741.8 0.0035 0.314 1.282 0.730 0.124 25 0.3847 0.3853 0.647 89315. 4741.0 0.0035 0.313 1.275 0.726 0.122 26 0.3841 0.3846 0.648 89298. 4739.9 0.0035 0.312 1.267 0.722 0.119 27 0.3837 0.3841 0.649 89280. 4738.9 0.0035 0.311 1.258 0.716 0.117 28 0.3834 0.3838 0.649 89268. 4738.0 0.0034 0.309 1.250 0.711 0.116 29 0.3830 0.3833 0.650 89248. 4736.8 0.0034 0.308 1.242 0.707 0.115 30 0.3827 0.3829 0.651 89236. 4736.3 0.0034 0.306 1.235 0.703 0.114 $$ Output MTZ file from Refmac for model 6d9i_B1_PHR_MO_s0.56_r2-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6d9i_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_6d9i_B1_PHR_MO_s0.56_r2-123.mtz Output PDB file from Refmac for model 6d9i_B1_PHR_MO_s0.56_r2-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6d9i_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_6d9i_B1_PHR_MO_s0.56_r2-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 18 MR programs being used: MOLREP PHASER Best search model so far: 5v92_B1_PHR_MO_s0.56_r2-123 using MOLREP Initial Rfree: 0.466 Final Rfree: 0.370 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 18: 1i20_A1_PHR_MO_s0.54_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i20_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1i20_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.54 Search model type: MOLREP Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i20_A1_PHR\molrep\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i20_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1i20_A1_PHR_MO_s0.54_r1-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i20_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1i20_A1_PHR_MO_s0.54_r1-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i20_A1_PHR\molrep\mr\molrep\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i20_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1i20_A1_PHR_MO_s0.54_r1-123' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 1i20_A1_PHR_MO_s0.54_r1-123: ##### ################################################################################################# Template Model: 1i20_A1_PHR_MO_s0.54_r1-123 has produced a marginal solution, final Rfree = 0.399 Molrep log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i20_A1_PHR\molrep\mr\molrep\molrep.log Molrep PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i20_A1_PHR\molrep\mr\molrep\molrep_1i20_A1_PHR_MO_s0.54_r1-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i20_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1i20_A1_PHR_MO_s0.54_r1-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i20_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1i20_A1_PHR_MO_s0.54_r1-123.pdb #################################################################################################### ##### Refinement results from Refmac for 1i20_A1_PHR_MO_s0.54_r1-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1i20_A1_PHR_MO_s0.54_r1-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4899 0.5001 0.415 93878. 4963.1 0.0307 2.530 3.322 2.039 0.390 1 0.4582 0.4764 0.452 92887. 4921.8 0.0108 0.866 2.498 1.530 0.292 2 0.4428 0.4557 0.488 92201. 4886.4 0.0085 0.676 2.222 1.346 0.217 3 0.4319 0.4404 0.517 91626. 4856.0 0.0074 0.593 2.051 1.233 0.172 4 0.4249 0.4313 0.534 91327. 4839.7 0.0068 0.540 1.920 1.146 0.142 5 0.4197 0.4256 0.547 91169. 4832.7 0.0062 0.499 1.826 1.083 0.131 6 0.4158 0.4217 0.556 91067. 4827.6 0.0058 0.469 1.757 1.036 0.124 7 0.4125 0.4177 0.563 90991. 4824.5 0.0055 0.441 1.703 0.998 0.119 8 0.4100 0.4149 0.569 90898. 4819.4 0.0052 0.420 1.657 0.965 0.115 9 0.4079 0.4122 0.574 90880. 4820.4 0.0050 0.400 1.618 0.938 0.112 10 0.4060 0.4104 0.577 90835. 4819.0 0.0047 0.382 1.582 0.912 0.109 11 0.4043 0.4091 0.578 90822. 4819.0 0.0045 0.365 1.552 0.891 0.107 12 0.4027 0.4080 0.581 90749. 4815.8 0.0043 0.352 1.525 0.871 0.106 13 0.4016 0.4078 0.584 90661. 4812.2 0.0042 0.339 1.502 0.854 0.104 14 0.4004 0.4073 0.587 90610. 4810.0 0.0040 0.328 1.480 0.839 0.103 15 0.3994 0.4067 0.589 90594. 4810.0 0.0039 0.317 1.461 0.824 0.102 16 0.3982 0.4057 0.589 90567. 4808.8 0.0038 0.308 1.444 0.812 0.101 17 0.3975 0.4053 0.592 90551. 4808.0 0.0037 0.303 1.436 0.805 0.101 18 0.3969 0.4051 0.593 90537. 4807.8 0.0036 0.298 1.420 0.796 0.100 19 0.3960 0.4048 0.594 90511. 4806.9 0.0035 0.292 1.396 0.783 0.100 20 0.3952 0.4042 0.595 90489. 4806.0 0.0035 0.285 1.379 0.773 0.099 21 0.3943 0.4037 0.596 90453. 4804.5 0.0034 0.279 1.365 0.763 0.099 22 0.3936 0.4032 0.598 90398. 4801.7 0.0033 0.273 1.352 0.755 0.098 23 0.3928 0.4027 0.599 90347. 4799.3 0.0032 0.268 1.340 0.747 0.098 24 0.3921 0.4023 0.601 90321. 4798.4 0.0032 0.263 1.329 0.740 0.097 25 0.3914 0.4017 0.604 90289. 4796.8 0.0031 0.259 1.319 0.733 0.097 26 0.3908 0.4014 0.605 90274. 4796.5 0.0031 0.254 1.309 0.726 0.096 27 0.3901 0.4006 0.606 90246. 4795.0 0.0030 0.251 1.296 0.718 0.096 28 0.3895 0.3999 0.607 90222. 4793.7 0.0030 0.247 1.288 0.713 0.095 29 0.3889 0.3996 0.607 90205. 4793.1 0.0029 0.244 1.280 0.707 0.095 30 0.3886 0.3992 0.608 90206. 4793.3 0.0029 0.243 1.275 0.704 0.094 $$ Output MTZ file from Refmac for model 1i20_A1_PHR_MO_s0.54_r1-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i20_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1i20_A1_PHR_MO_s0.54_r1-123.mtz Output PDB file from Refmac for model 1i20_A1_PHR_MO_s0.54_r1-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i20_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1i20_A1_PHR_MO_s0.54_r1-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 19 MR programs being used: MOLREP PHASER Best search model so far: 5v92_B1_PHR_MO_s0.56_r2-123 using MOLREP Initial Rfree: 0.466 Final Rfree: 0.370 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 19: 1i20_A1_PHR_MO_s0.54_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i20_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1i20_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.54 Search model type: MOLREP Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i20_A1_PHR\molrep\mr\phaser\phaser_1i20_A1_PHR_MO_s0.54_r1-123.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i20_A1_PHR\molrep\mr\phaser\phaser_1i20_A1_PHR_MO_s0.54_r1-123.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i20_A1_PHR\molrep\mr\phaser\phaser_1i20_A1_PHR_MO_s0.54_r1-123.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i20_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_HKLOUT_1i20_A1_PHR_MO_s0.54_r1-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i20_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1i20_A1_PHR_MO_s0.54_r1-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i20_A1_PHR\molrep\mr\phaser\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i20_A1_PHR\molrep\mr\phaser\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1i20_A1_PHR_MO_s0.54_r1-123' ######################################################################### ###################################################################### ##### Results from Phaser for 1i20_A1_PHR_MO_s0.54_r1-123: ##### ###################################################################### Template Model: 1i20_A1_PHR_MO_s0.54_r1-123 has produced a marginal solution, final Rfree = 0.398 Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i20_A1_PHR\molrep\mr\phaser\phaser_1i20_A1_PHR_MO_s0.54_r1-123.log Phaser PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i20_A1_PHR\molrep\mr\phaser\phaser_1i20_A1_PHR_MO_s0.54_r1-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i20_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1i20_A1_PHR_MO_s0.54_r1-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i20_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1i20_A1_PHR_MO_s0.54_r1-123.pdb #################################################################################################### ##### Refinement results from Refmac for 1i20_A1_PHR_MO_s0.54_r1-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1i20_A1_PHR_MO_s0.54_r1-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4767 0.4837 0.471 93127. 4918.7 0.0307 2.533 3.322 2.039 0.391 1 0.4549 0.4648 0.483 92351. 4885.2 0.0110 0.889 2.470 1.509 0.293 2 0.4396 0.4480 0.511 91696. 4854.4 0.0082 0.660 2.196 1.327 0.217 3 0.4314 0.4387 0.530 91361. 4837.9 0.0072 0.577 2.025 1.211 0.172 4 0.4250 0.4308 0.540 91221. 4831.4 0.0066 0.529 1.902 1.130 0.144 5 0.4203 0.4257 0.550 91087. 4824.9 0.0062 0.494 1.815 1.072 0.134 6 0.4167 0.4212 0.557 90992. 4821.4 0.0058 0.465 1.750 1.027 0.127 7 0.4135 0.4173 0.564 90922. 4818.4 0.0055 0.443 1.700 0.992 0.122 8 0.4110 0.4142 0.571 90897. 4818.0 0.0052 0.420 1.657 0.962 0.118 9 0.4086 0.4118 0.575 90822. 4815.0 0.0050 0.400 1.619 0.934 0.114 10 0.4067 0.4099 0.580 90803. 4814.5 0.0048 0.383 1.584 0.910 0.111 11 0.4049 0.4087 0.584 90746. 4813.1 0.0045 0.366 1.553 0.888 0.109 12 0.4033 0.4078 0.586 90722. 4812.6 0.0044 0.352 1.525 0.869 0.107 13 0.4020 0.4078 0.588 90714. 4813.1 0.0042 0.340 1.500 0.851 0.105 14 0.4008 0.4072 0.589 90682. 4811.8 0.0040 0.328 1.479 0.836 0.104 15 0.3997 0.4064 0.593 90618. 4808.8 0.0039 0.318 1.460 0.822 0.102 16 0.3985 0.4050 0.595 90553. 4805.8 0.0038 0.309 1.433 0.807 0.102 17 0.3975 0.4044 0.596 90522. 4804.7 0.0037 0.301 1.411 0.794 0.101 18 0.3965 0.4038 0.598 90489. 4803.6 0.0036 0.293 1.395 0.783 0.100 19 0.3956 0.4031 0.598 90466. 4802.8 0.0035 0.286 1.380 0.773 0.100 20 0.3947 0.4022 0.599 90430. 4801.4 0.0034 0.280 1.366 0.764 0.099 21 0.3939 0.4016 0.601 90383. 4799.1 0.0033 0.274 1.354 0.756 0.099 22 0.3932 0.4011 0.603 90348. 4797.2 0.0032 0.269 1.343 0.748 0.098 23 0.3925 0.4007 0.606 90318. 4795.8 0.0032 0.264 1.332 0.741 0.098 24 0.3918 0.4001 0.608 90300. 4795.3 0.0031 0.259 1.322 0.734 0.097 25 0.3911 0.3997 0.609 90287. 4794.7 0.0031 0.255 1.313 0.727 0.097 26 0.3905 0.3993 0.610 90265. 4793.9 0.0030 0.251 1.305 0.721 0.096 27 0.3899 0.3988 0.610 90270. 4794.2 0.0030 0.248 1.298 0.716 0.096 28 0.3893 0.3985 0.611 90251. 4793.7 0.0029 0.245 1.291 0.711 0.096 29 0.3888 0.3982 0.611 90256. 4794.1 0.0029 0.242 1.283 0.706 0.095 30 0.3882 0.3977 0.612 90250. 4793.7 0.0029 0.239 1.277 0.702 0.095 $$ Output MTZ file from Refmac for model 1i20_A1_PHR_MO_s0.54_r1-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i20_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1i20_A1_PHR_MO_s0.54_r1-123.mtz Output PDB file from Refmac for model 1i20_A1_PHR_MO_s0.54_r1-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i20_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1i20_A1_PHR_MO_s0.54_r1-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 20 MR programs being used: MOLREP PHASER Best search model so far: 5v92_B1_PHR_MO_s0.56_r2-123 using MOLREP Initial Rfree: 0.466 Final Rfree: 0.370 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 20: 1d6q_A1_PHR_MO_s0.54_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1d6q_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1d6q_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.54 Search model type: MOLREP Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1d6q_A1_PHR\molrep\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1d6q_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1d6q_A1_PHR_MO_s0.54_r1-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1d6q_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1d6q_A1_PHR_MO_s0.54_r1-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1d6q_A1_PHR\molrep\mr\molrep\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1d6q_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1d6q_A1_PHR_MO_s0.54_r1-123' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 1d6q_A1_PHR_MO_s0.54_r1-123: ##### ################################################################################################# Template Model: 1d6q_A1_PHR_MO_s0.54_r1-123 has produced a marginal solution, final Rfree = 0.388 Molrep log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1d6q_A1_PHR\molrep\mr\molrep\molrep.log Molrep PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1d6q_A1_PHR\molrep\mr\molrep\molrep_1d6q_A1_PHR_MO_s0.54_r1-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1d6q_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1d6q_A1_PHR_MO_s0.54_r1-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1d6q_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1d6q_A1_PHR_MO_s0.54_r1-123.pdb #################################################################################################### ##### Refinement results from Refmac for 1d6q_A1_PHR_MO_s0.54_r1-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1d6q_A1_PHR_MO_s0.54_r1-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4824 0.4864 0.430 93363. 4933.5 0.0268 2.175 2.589 1.560 0.346 1 0.4508 0.4588 0.471 92353. 4887.9 0.0083 0.680 1.987 1.186 0.246 2 0.4362 0.4484 0.504 91935. 4867.7 0.0065 0.529 1.804 1.069 0.183 3 0.4262 0.4378 0.529 91547. 4849.2 0.0058 0.474 1.704 1.005 0.150 4 0.4202 0.4313 0.543 91284. 4836.5 0.0053 0.437 1.623 0.954 0.133 5 0.4156 0.4268 0.556 91087. 4827.5 0.0049 0.410 1.558 0.914 0.123 6 0.4141 0.4239 0.562 91039. 4825.5 0.0044 0.370 1.488 0.871 0.117 7 0.4125 0.4220 0.566 90959. 4821.7 0.0041 0.347 1.434 0.838 0.111 8 0.4109 0.4202 0.571 90939. 4820.8 0.0039 0.330 1.391 0.811 0.107 9 0.4092 0.4177 0.574 90896. 4818.6 0.0038 0.318 1.355 0.788 0.105 10 0.4071 0.4140 0.579 90683. 4807.1 0.0037 0.310 1.326 0.770 0.103 11 0.4052 0.4096 0.583 90569. 4802.2 0.0036 0.303 1.302 0.755 0.101 12 0.4033 0.4068 0.588 90500. 4797.9 0.0035 0.298 1.283 0.743 0.100 13 0.4017 0.4047 0.592 90447. 4795.9 0.0035 0.291 1.266 0.731 0.099 14 0.4003 0.4026 0.596 90422. 4794.8 0.0034 0.284 1.248 0.720 0.098 15 0.3990 0.4009 0.597 90392. 4793.1 0.0033 0.277 1.231 0.710 0.096 16 0.3979 0.3995 0.600 90354. 4791.3 0.0032 0.271 1.216 0.700 0.095 17 0.3969 0.3982 0.603 90315. 4789.4 0.0031 0.266 1.201 0.691 0.095 18 0.3961 0.3967 0.605 90257. 4786.3 0.0031 0.261 1.187 0.682 0.094 19 0.3953 0.3957 0.606 90235. 4785.3 0.0030 0.257 1.175 0.675 0.093 20 0.3944 0.3946 0.608 90211. 4784.2 0.0030 0.253 1.164 0.668 0.092 21 0.3937 0.3937 0.610 90195. 4783.6 0.0029 0.250 1.153 0.661 0.092 22 0.3930 0.3926 0.611 90176. 4783.1 0.0029 0.246 1.143 0.655 0.091 23 0.3924 0.3918 0.612 90146. 4781.8 0.0029 0.244 1.132 0.649 0.090 24 0.3918 0.3910 0.613 90130. 4781.1 0.0028 0.241 1.122 0.643 0.090 25 0.3913 0.3903 0.613 90117. 4780.4 0.0028 0.238 1.114 0.639 0.089 26 0.3909 0.3897 0.614 90089. 4779.3 0.0028 0.236 1.107 0.634 0.088 27 0.3904 0.3893 0.615 90060. 4777.9 0.0027 0.234 1.100 0.630 0.088 28 0.3899 0.3889 0.615 90034. 4776.9 0.0027 0.232 1.093 0.626 0.087 29 0.3894 0.3887 0.616 90017. 4776.4 0.0027 0.231 1.086 0.622 0.087 30 0.3890 0.3883 0.617 89993. 4775.7 0.0027 0.229 1.080 0.619 0.086 $$ Output MTZ file from Refmac for model 1d6q_A1_PHR_MO_s0.54_r1-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1d6q_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1d6q_A1_PHR_MO_s0.54_r1-123.mtz Output PDB file from Refmac for model 1d6q_A1_PHR_MO_s0.54_r1-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1d6q_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1d6q_A1_PHR_MO_s0.54_r1-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 21 MR programs being used: MOLREP PHASER Best search model so far: 5v92_B1_PHR_MO_s0.56_r2-123 using MOLREP Initial Rfree: 0.466 Final Rfree: 0.370 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 21: 1d6q_A1_PHR_MO_s0.54_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1d6q_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1d6q_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.54 Search model type: MOLREP Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1d6q_A1_PHR\molrep\mr\phaser\phaser_1d6q_A1_PHR_MO_s0.54_r1-123.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1d6q_A1_PHR\molrep\mr\phaser\phaser_1d6q_A1_PHR_MO_s0.54_r1-123.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1d6q_A1_PHR\molrep\mr\phaser\phaser_1d6q_A1_PHR_MO_s0.54_r1-123.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1d6q_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_HKLOUT_1d6q_A1_PHR_MO_s0.54_r1-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1d6q_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1d6q_A1_PHR_MO_s0.54_r1-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1d6q_A1_PHR\molrep\mr\phaser\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1d6q_A1_PHR\molrep\mr\phaser\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1d6q_A1_PHR_MO_s0.54_r1-123' ######################################################################### ###################################################################### ##### Results from Phaser for 1d6q_A1_PHR_MO_s0.54_r1-123: ##### ###################################################################### Template Model: 1d6q_A1_PHR_MO_s0.54_r1-123 has produced a marginal solution, final Rfree = 0.390 Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1d6q_A1_PHR\molrep\mr\phaser\phaser_1d6q_A1_PHR_MO_s0.54_r1-123.log Phaser PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1d6q_A1_PHR\molrep\mr\phaser\phaser_1d6q_A1_PHR_MO_s0.54_r1-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1d6q_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1d6q_A1_PHR_MO_s0.54_r1-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1d6q_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1d6q_A1_PHR_MO_s0.54_r1-123.pdb #################################################################################################### ##### Refinement results from Refmac for 1d6q_A1_PHR_MO_s0.54_r1-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1d6q_A1_PHR_MO_s0.54_r1-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4654 0.4553 0.492 92553. 4893.9 0.0268 2.180 2.590 1.561 0.346 1 0.4564 0.4523 0.494 92300. 4880.7 0.0077 0.640 1.981 1.187 0.260 2 0.4486 0.4481 0.504 91856. 4858.9 0.0058 0.489 1.764 1.050 0.195 3 0.4432 0.4449 0.511 91699. 4852.2 0.0052 0.435 1.638 0.972 0.156 4 0.4374 0.4407 0.520 91462. 4841.5 0.0048 0.404 1.559 0.922 0.135 5 0.4318 0.4368 0.529 91345. 4836.5 0.0046 0.384 1.503 0.888 0.124 6 0.4257 0.4319 0.542 91242. 4832.6 0.0045 0.372 1.465 0.864 0.118 7 0.4200 0.4277 0.555 91087. 4825.8 0.0044 0.365 1.435 0.843 0.113 8 0.4177 0.4253 0.561 91035. 4824.2 0.0040 0.337 1.391 0.816 0.109 9 0.4156 0.4227 0.566 91001. 4823.1 0.0038 0.323 1.359 0.795 0.107 10 0.4132 0.4199 0.572 90956. 4821.1 0.0037 0.313 1.332 0.777 0.105 11 0.4109 0.4171 0.576 90910. 4818.7 0.0036 0.305 1.309 0.762 0.103 12 0.4087 0.4141 0.581 90879. 4817.2 0.0036 0.300 1.291 0.749 0.102 13 0.4067 0.4118 0.586 90819. 4814.4 0.0035 0.295 1.274 0.738 0.101 14 0.4047 0.4102 0.588 90636. 4804.3 0.0035 0.291 1.261 0.729 0.100 15 0.4035 0.4048 0.593 90507. 4797.5 0.0033 0.280 1.239 0.716 0.098 16 0.4022 0.4035 0.596 90483. 4796.8 0.0032 0.273 1.222 0.705 0.097 17 0.4010 0.4020 0.598 90435. 4794.7 0.0032 0.267 1.206 0.696 0.096 18 0.3999 0.4008 0.600 90407. 4793.4 0.0031 0.262 1.193 0.687 0.095 19 0.3989 0.3993 0.603 90359. 4790.7 0.0030 0.258 1.182 0.680 0.094 20 0.3979 0.3979 0.605 90318. 4788.8 0.0030 0.255 1.172 0.673 0.094 21 0.3969 0.3965 0.607 90291. 4787.6 0.0030 0.252 1.163 0.668 0.093 22 0.3959 0.3951 0.609 90252. 4785.7 0.0029 0.249 1.154 0.662 0.092 23 0.3950 0.3940 0.610 90233. 4784.9 0.0029 0.246 1.145 0.656 0.092 24 0.3942 0.3930 0.611 90212. 4784.0 0.0029 0.244 1.136 0.651 0.091 25 0.3934 0.3925 0.612 90189. 4783.2 0.0028 0.242 1.127 0.646 0.090 26 0.3928 0.3917 0.613 90162. 4781.9 0.0028 0.240 1.118 0.641 0.089 27 0.3922 0.3913 0.614 90125. 4780.3 0.0028 0.237 1.110 0.636 0.089 28 0.3916 0.3906 0.615 90111. 4779.8 0.0027 0.236 1.102 0.631 0.088 29 0.3911 0.3900 0.616 90090. 4779.0 0.0027 0.234 1.094 0.627 0.088 30 0.3907 0.3895 0.617 90075. 4778.1 0.0027 0.232 1.087 0.623 0.087 $$ Output MTZ file from Refmac for model 1d6q_A1_PHR_MO_s0.54_r1-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1d6q_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1d6q_A1_PHR_MO_s0.54_r1-123.mtz Output PDB file from Refmac for model 1d6q_A1_PHR_MO_s0.54_r1-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1d6q_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1d6q_A1_PHR_MO_s0.54_r1-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 22 MR programs being used: MOLREP PHASER Best search model so far: 5v92_B1_PHR_MO_s0.56_r2-123 using MOLREP Initial Rfree: 0.466 Final Rfree: 0.370 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 22: 1i1z_A1_PHR_MO_s0.54_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i1z_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1i1z_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.54 Search model type: MOLREP Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i1z_A1_PHR\molrep\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i1z_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1i1z_A1_PHR_MO_s0.54_r1-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i1z_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1i1z_A1_PHR_MO_s0.54_r1-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i1z_A1_PHR\molrep\mr\molrep\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i1z_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1i1z_A1_PHR_MO_s0.54_r1-123' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 1i1z_A1_PHR_MO_s0.54_r1-123: ##### ################################################################################################# Template Model: 1i1z_A1_PHR_MO_s0.54_r1-123 has produced a solution, final Rfree = 0.390 and is 0.792 of initial Rfree #################################################################################################### ##### Refinement results from Refmac for 1i1z_A1_PHR_MO_s0.54_r1-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1i1z_A1_PHR_MO_s0.54_r1-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4922 0.5024 0.400 93558. 4944.5 0.0307 2.621 3.292 2.001 0.385 1 0.4586 0.4713 0.442 92635. 4907.5 0.0100 0.842 2.355 1.426 0.275 2 0.4408 0.4535 0.485 92013. 4877.4 0.0084 0.668 2.067 1.248 0.218 3 0.4299 0.4383 0.515 91662. 4857.4 0.0074 0.586 1.888 1.139 0.185 4 0.4232 0.4290 0.536 91349. 4839.7 0.0067 0.534 1.765 1.061 0.161 5 0.4185 0.4216 0.549 91215. 4833.0 0.0062 0.493 1.674 1.004 0.145 6 0.4151 0.4158 0.558 91159. 4830.3 0.0058 0.460 1.608 0.959 0.131 7 0.4121 0.4117 0.568 91065. 4825.0 0.0054 0.433 1.565 0.925 0.123 8 0.4096 0.4089 0.574 91009. 4822.6 0.0051 0.408 1.519 0.893 0.117 9 0.4073 0.4078 0.580 90937. 4818.8 0.0048 0.390 1.484 0.868 0.113 10 0.4053 0.4063 0.587 90898. 4816.9 0.0045 0.368 1.448 0.845 0.111 11 0.4035 0.4043 0.592 90837. 4813.3 0.0043 0.350 1.416 0.824 0.109 12 0.4019 0.4028 0.595 90791. 4811.0 0.0040 0.332 1.388 0.805 0.107 13 0.4005 0.4012 0.598 90738. 4808.1 0.0038 0.317 1.363 0.789 0.106 14 0.3993 0.3997 0.600 90692. 4805.9 0.0037 0.305 1.341 0.774 0.105 15 0.3981 0.3986 0.603 90637. 4803.0 0.0035 0.293 1.323 0.762 0.104 16 0.3970 0.3974 0.605 90601. 4801.3 0.0034 0.283 1.305 0.750 0.104 17 0.3959 0.3965 0.607 90565. 4799.8 0.0033 0.273 1.289 0.739 0.103 18 0.3948 0.3957 0.610 90532. 4798.9 0.0031 0.265 1.275 0.730 0.102 19 0.3938 0.3948 0.612 90520. 4798.5 0.0030 0.257 1.261 0.721 0.102 20 0.3929 0.3941 0.612 90502. 4797.9 0.0030 0.251 1.248 0.712 0.101 21 0.3920 0.3936 0.614 90467. 4796.0 0.0029 0.245 1.237 0.705 0.100 22 0.3912 0.3932 0.616 90427. 4794.3 0.0028 0.241 1.228 0.698 0.100 23 0.3904 0.3928 0.617 90402. 4793.4 0.0028 0.236 1.220 0.693 0.100 24 0.3897 0.3923 0.619 90399. 4793.5 0.0027 0.232 1.212 0.687 0.099 25 0.3890 0.3916 0.619 90384. 4793.0 0.0027 0.229 1.206 0.682 0.099 26 0.3884 0.3910 0.620 90358. 4791.6 0.0026 0.226 1.200 0.677 0.098 27 0.3878 0.3905 0.622 90330. 4790.5 0.0026 0.223 1.195 0.673 0.098 28 0.3871 0.3902 0.622 90279. 4788.0 0.0026 0.221 1.190 0.669 0.098 29 0.3867 0.3898 0.623 90248. 4786.1 0.0025 0.219 1.186 0.666 0.097 30 0.3861 0.3896 0.625 90198. 4783.8 0.0025 0.217 1.181 0.662 0.097 $$ Output MTZ file from Refmac for model 1i1z_A1_PHR_MO_s0.54_r1-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i1z_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1i1z_A1_PHR_MO_s0.54_r1-123.mtz Output PDB file from Refmac for model 1i1z_A1_PHR_MO_s0.54_r1-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i1z_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1i1z_A1_PHR_MO_s0.54_r1-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 23 MR programs being used: MOLREP PHASER Best search model so far: 5v92_B1_PHR_MO_s0.56_r2-123 using MOLREP Initial Rfree: 0.466 Final Rfree: 0.370 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 23: 1i1z_A1_PHR_MO_s0.54_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i1z_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1i1z_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.54 Search model type: MOLREP Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i1z_A1_PHR\molrep\mr\phaser\phaser_1i1z_A1_PHR_MO_s0.54_r1-123.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i1z_A1_PHR\molrep\mr\phaser\phaser_1i1z_A1_PHR_MO_s0.54_r1-123.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i1z_A1_PHR\molrep\mr\phaser\phaser_1i1z_A1_PHR_MO_s0.54_r1-123.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i1z_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_HKLOUT_1i1z_A1_PHR_MO_s0.54_r1-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i1z_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1i1z_A1_PHR_MO_s0.54_r1-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i1z_A1_PHR\molrep\mr\phaser\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i1z_A1_PHR\molrep\mr\phaser\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1i1z_A1_PHR_MO_s0.54_r1-123' ######################################################################### ###################################################################### ##### Results from Phaser for 1i1z_A1_PHR_MO_s0.54_r1-123: ##### ###################################################################### Template Model: 1i1z_A1_PHR_MO_s0.54_r1-123 has produced a marginal solution, final Rfree = 0.390 Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i1z_A1_PHR\molrep\mr\phaser\phaser_1i1z_A1_PHR_MO_s0.54_r1-123.log Phaser PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i1z_A1_PHR\molrep\mr\phaser\phaser_1i1z_A1_PHR_MO_s0.54_r1-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i1z_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1i1z_A1_PHR_MO_s0.54_r1-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i1z_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1i1z_A1_PHR_MO_s0.54_r1-123.pdb #################################################################################################### ##### Refinement results from Refmac for 1i1z_A1_PHR_MO_s0.54_r1-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1i1z_A1_PHR_MO_s0.54_r1-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4740 0.4764 0.472 92678. 4898.5 0.0307 2.621 3.292 2.000 0.385 1 0.4620 0.4652 0.473 92601. 4898.5 0.0182 1.563 2.698 1.645 0.331 2 0.4420 0.4480 0.500 91919. 4866.7 0.0098 0.833 2.162 1.312 0.251 3 0.4319 0.4372 0.525 91543. 4848.6 0.0083 0.663 1.949 1.181 0.207 4 0.4256 0.4294 0.540 91287. 4835.0 0.0070 0.559 1.816 1.093 0.175 5 0.4211 0.4232 0.550 91168. 4829.1 0.0064 0.507 1.720 1.030 0.154 6 0.4174 0.4176 0.561 91162. 4829.1 0.0059 0.470 1.642 0.978 0.135 7 0.4144 0.4146 0.568 91060. 4823.6 0.0055 0.441 1.585 0.940 0.126 8 0.4118 0.4117 0.573 90995. 4820.8 0.0052 0.415 1.535 0.906 0.119 9 0.4094 0.4095 0.577 90972. 4819.7 0.0049 0.393 1.493 0.878 0.116 10 0.4074 0.4074 0.583 90924. 4818.0 0.0046 0.372 1.459 0.855 0.114 11 0.4055 0.4058 0.588 90907. 4816.8 0.0044 0.355 1.428 0.834 0.112 12 0.4039 0.4037 0.593 90867. 4814.0 0.0041 0.339 1.400 0.815 0.110 13 0.4024 0.4025 0.598 90819. 4812.0 0.0039 0.323 1.376 0.798 0.108 14 0.4010 0.4007 0.601 90747. 4808.5 0.0037 0.309 1.354 0.783 0.107 15 0.3998 0.3997 0.602 90718. 4807.6 0.0035 0.295 1.332 0.769 0.106 16 0.3986 0.3982 0.603 90682. 4806.0 0.0034 0.285 1.314 0.757 0.105 17 0.3976 0.3969 0.607 90645. 4803.7 0.0033 0.276 1.299 0.746 0.104 18 0.3965 0.3957 0.609 90601. 4801.8 0.0032 0.268 1.284 0.735 0.103 19 0.3954 0.3948 0.611 90570. 4800.6 0.0031 0.261 1.271 0.726 0.103 20 0.3945 0.3943 0.612 90534. 4799.6 0.0030 0.254 1.259 0.718 0.102 21 0.3936 0.3936 0.613 90526. 4799.5 0.0029 0.248 1.248 0.710 0.101 22 0.3927 0.3930 0.614 90517. 4799.3 0.0029 0.243 1.238 0.703 0.101 23 0.3919 0.3926 0.616 90518. 4799.7 0.0028 0.239 1.228 0.696 0.100 24 0.3911 0.3924 0.616 90469. 4797.3 0.0027 0.235 1.219 0.690 0.100 25 0.3904 0.3920 0.618 90437. 4795.9 0.0027 0.231 1.212 0.685 0.099 26 0.3898 0.3915 0.619 90400. 4794.2 0.0027 0.228 1.205 0.679 0.098 27 0.3891 0.3913 0.619 90347. 4791.6 0.0026 0.225 1.199 0.675 0.098 28 0.3884 0.3906 0.620 90313. 4789.9 0.0026 0.223 1.194 0.671 0.098 29 0.3879 0.3903 0.621 90277. 4788.1 0.0026 0.220 1.189 0.667 0.098 30 0.3874 0.3898 0.622 90237. 4785.7 0.0025 0.218 1.185 0.664 0.097 $$ Output MTZ file from Refmac for model 1i1z_A1_PHR_MO_s0.54_r1-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i1z_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1i1z_A1_PHR_MO_s0.54_r1-123.mtz Output PDB file from Refmac for model 1i1z_A1_PHR_MO_s0.54_r1-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i1z_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1i1z_A1_PHR_MO_s0.54_r1-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 24 MR programs being used: MOLREP PHASER Best search model so far: 5v92_B1_PHR_MO_s0.56_r2-123 using MOLREP Initial Rfree: 0.466 Final Rfree: 0.370 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 24: 1i22_D1_PHR_SC_s0.56_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\sculptor Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\sculpt_1i22_D1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.56 Search model type: SCLPTR Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\sculptor\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: refmac failed to complete successfully Log file can be found here: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\sculptor\mr\molrep\refine\refmac_molrep_1i22_D1_PHR_SC_s0.56_r1-123.log Finished job, checking results.... ######################################################################### Job has completed for model '1i22_D1_PHR_SC_s0.56_r1-123' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 1i22_D1_PHR_SC_s0.56_r1-123: ##### ################################################################################################# Template Model: 1i22_D1_PHR_SC_s0.56_r1-123 produced a poor solution (Final Rfree = 1.000) Molrep log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\sculptor\mr\molrep\molrep.log Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\sculptor\mr\molrep\refine\refmac_molrep_1i22_D1_PHR_SC_s0.56_r1-123.log $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 25 MR programs being used: MOLREP PHASER Best search model so far: 5v92_B1_PHR_MO_s0.56_r2-123 using MOLREP Initial Rfree: 0.466 Final Rfree: 0.370 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 25: 1i22_D1_PHR_SC_s0.56_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\sculptor Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\sculpt_1i22_D1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.56 Search model type: SCLPTR Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\sculptor\mr\phaser\phaser_1i22_D1_PHR_SC_s0.56_r1-123.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\sculptor\mr\phaser\phaser_1i22_D1_PHR_SC_s0.56_r1-123.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\sculptor\mr\phaser\phaser_1i22_D1_PHR_SC_s0.56_r1-123.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: refmac failed to complete successfully Log file can be found here: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\sculptor\mr\phaser\refine\refmac_phaser_1i22_D1_PHR_SC_s0.56_r1-123.log Error: Could not find output PDB from Refmac, can't continue Finished job, checking results.... ######################################################################### Job has completed for model '1i22_D1_PHR_SC_s0.56_r1-123' ######################################################################### ###################################################################### ##### Results from Phaser for 1i22_D1_PHR_SC_s0.56_r1-123: ##### ###################################################################### Template Model: 1i22_D1_PHR_SC_s0.56_r1-123 produced a poor solution (Final Rfree = 1.000) Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\sculptor\mr\phaser\phaser_1i22_D1_PHR_SC_s0.56_r1-123.log Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\sculptor\mr\phaser\refine\refmac_phaser_1i22_D1_PHR_SC_s0.56_r1-123.log $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 26 MR programs being used: MOLREP PHASER Best search model so far: 5v92_B1_PHR_MO_s0.56_r2-123 using MOLREP Initial Rfree: 0.466 Final Rfree: 0.370 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 26: 1wqm_A1_PHR_MO_s0.54_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1wqm_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1wqm_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.54 Search model type: MOLREP Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1wqm_A1_PHR\molrep\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1wqm_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1wqm_A1_PHR_MO_s0.54_r1-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1wqm_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1wqm_A1_PHR_MO_s0.54_r1-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1wqm_A1_PHR\molrep\mr\molrep\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1wqm_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1wqm_A1_PHR_MO_s0.54_r1-123' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 1wqm_A1_PHR_MO_s0.54_r1-123: ##### ################################################################################################# Template Model: 1wqm_A1_PHR_MO_s0.54_r1-123 has produced a marginal solution, final Rfree = 0.398 Molrep log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1wqm_A1_PHR\molrep\mr\molrep\molrep.log Molrep PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1wqm_A1_PHR\molrep\mr\molrep\molrep_1wqm_A1_PHR_MO_s0.54_r1-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1wqm_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1wqm_A1_PHR_MO_s0.54_r1-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1wqm_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1wqm_A1_PHR_MO_s0.54_r1-123.pdb #################################################################################################### ##### Refinement results from Refmac for 1wqm_A1_PHR_MO_s0.54_r1-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1wqm_A1_PHR_MO_s0.54_r1-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4832 0.4863 0.433 93371. 4933.1 0.0277 2.275 2.503 1.542 0.344 1 0.4547 0.4630 0.463 92630. 4907.2 0.0084 0.652 1.854 1.145 0.261 2 0.4404 0.4488 0.492 92051. 4880.8 0.0070 0.539 1.683 1.036 0.204 3 0.4297 0.4387 0.516 91624. 4859.6 0.0064 0.489 1.603 0.982 0.166 4 0.4229 0.4331 0.531 91299. 4844.3 0.0060 0.456 1.543 0.940 0.143 5 0.4173 0.4262 0.540 91031. 4831.8 0.0058 0.441 1.490 0.902 0.127 6 0.4129 0.4220 0.549 90870. 4824.7 0.0055 0.424 1.462 0.878 0.118 7 0.4098 0.4188 0.556 90760. 4819.5 0.0052 0.403 1.434 0.854 0.112 8 0.4067 0.4165 0.562 90691. 4816.6 0.0050 0.387 1.413 0.834 0.107 9 0.4046 0.4152 0.567 90639. 4813.7 0.0047 0.372 1.398 0.819 0.105 10 0.4026 0.4137 0.571 90620. 4812.9 0.0045 0.359 1.386 0.806 0.103 11 0.4008 0.4122 0.576 90568. 4810.0 0.0043 0.347 1.376 0.794 0.102 12 0.3993 0.4109 0.581 90524. 4808.2 0.0042 0.335 1.363 0.781 0.101 13 0.3978 0.4093 0.584 90487. 4806.6 0.0040 0.324 1.350 0.770 0.100 14 0.3966 0.4077 0.586 90433. 4803.9 0.0039 0.315 1.339 0.760 0.099 15 0.3955 0.4064 0.588 90397. 4802.5 0.0037 0.305 1.327 0.751 0.098 16 0.3944 0.4053 0.589 90356. 4800.7 0.0036 0.298 1.308 0.740 0.097 17 0.3934 0.4039 0.591 90320. 4799.1 0.0035 0.291 1.292 0.731 0.096 18 0.3925 0.4033 0.592 90292. 4797.8 0.0034 0.283 1.275 0.722 0.095 19 0.3918 0.4025 0.594 90280. 4797.6 0.0033 0.277 1.261 0.714 0.095 20 0.3911 0.4015 0.595 90256. 4796.5 0.0032 0.272 1.254 0.708 0.094 21 0.3905 0.4008 0.597 90222. 4795.4 0.0032 0.268 1.246 0.703 0.094 22 0.3903 0.4015 0.598 90201. 4794.9 0.0032 0.264 1.237 0.697 0.094 23 0.3896 0.4009 0.599 90160. 4793.2 0.0031 0.261 1.229 0.692 0.093 24 0.3890 0.4008 0.599 90140. 4792.6 0.0031 0.258 1.220 0.687 0.093 25 0.3885 0.4005 0.601 90126. 4791.9 0.0030 0.255 1.212 0.682 0.093 26 0.3879 0.3997 0.603 90127. 4792.5 0.0030 0.252 1.204 0.677 0.093 27 0.3875 0.3993 0.603 90125. 4792.8 0.0029 0.249 1.197 0.673 0.092 28 0.3871 0.3989 0.604 90105. 4792.3 0.0029 0.247 1.190 0.669 0.092 29 0.3866 0.3986 0.604 90088. 4791.7 0.0029 0.244 1.184 0.665 0.092 30 0.3863 0.3983 0.604 90079. 4791.4 0.0028 0.243 1.181 0.663 0.092 $$ Output MTZ file from Refmac for model 1wqm_A1_PHR_MO_s0.54_r1-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1wqm_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1wqm_A1_PHR_MO_s0.54_r1-123.mtz Output PDB file from Refmac for model 1wqm_A1_PHR_MO_s0.54_r1-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1wqm_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1wqm_A1_PHR_MO_s0.54_r1-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 27 MR programs being used: MOLREP PHASER Best search model so far: 5v92_B1_PHR_MO_s0.56_r2-123 using MOLREP Initial Rfree: 0.466 Final Rfree: 0.370 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 27: 1wqm_A1_PHR_MO_s0.54_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1wqm_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1wqm_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.54 Search model type: MOLREP Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1wqm_A1_PHR\molrep\mr\phaser\phaser_1wqm_A1_PHR_MO_s0.54_r1-123.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1wqm_A1_PHR\molrep\mr\phaser\phaser_1wqm_A1_PHR_MO_s0.54_r1-123.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1wqm_A1_PHR\molrep\mr\phaser\phaser_1wqm_A1_PHR_MO_s0.54_r1-123.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1wqm_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_HKLOUT_1wqm_A1_PHR_MO_s0.54_r1-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1wqm_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1wqm_A1_PHR_MO_s0.54_r1-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1wqm_A1_PHR\molrep\mr\phaser\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1wqm_A1_PHR\molrep\mr\phaser\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1wqm_A1_PHR_MO_s0.54_r1-123' ######################################################################### ###################################################################### ##### Results from Phaser for 1wqm_A1_PHR_MO_s0.54_r1-123: ##### ###################################################################### Template Model: 1wqm_A1_PHR_MO_s0.54_r1-123 has produced a marginal solution, final Rfree = 0.401 Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1wqm_A1_PHR\molrep\mr\phaser\phaser_1wqm_A1_PHR_MO_s0.54_r1-123.log Phaser PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1wqm_A1_PHR\molrep\mr\phaser\phaser_1wqm_A1_PHR_MO_s0.54_r1-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1wqm_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1wqm_A1_PHR_MO_s0.54_r1-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1wqm_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1wqm_A1_PHR_MO_s0.54_r1-123.pdb #################################################################################################### ##### Refinement results from Refmac for 1wqm_A1_PHR_MO_s0.54_r1-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1wqm_A1_PHR_MO_s0.54_r1-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4719 0.4714 0.457 92614. 4899.4 0.0277 2.273 2.502 1.541 0.344 1 0.4504 0.4574 0.478 92196. 4883.5 0.0129 0.819 1.838 1.136 0.267 2 0.4348 0.4441 0.506 91616. 4857.7 0.0076 0.557 1.674 1.033 0.212 3 0.4268 0.4373 0.524 91337. 4844.1 0.0064 0.484 1.591 0.976 0.174 4 0.4210 0.4330 0.534 91241. 4841.0 0.0060 0.456 1.527 0.931 0.150 5 0.4163 0.4285 0.544 91136. 4837.2 0.0057 0.437 1.491 0.901 0.133 6 0.4123 0.4251 0.552 91066. 4834.0 0.0055 0.420 1.464 0.877 0.122 7 0.4092 0.4225 0.558 90993. 4831.0 0.0052 0.403 1.439 0.855 0.116 8 0.4067 0.4202 0.565 90911. 4827.2 0.0050 0.388 1.419 0.836 0.109 9 0.4046 0.4184 0.571 90874. 4825.9 0.0047 0.373 1.398 0.818 0.106 10 0.4026 0.4170 0.574 90824. 4823.5 0.0045 0.360 1.383 0.803 0.104 11 0.4010 0.4156 0.576 90765. 4820.4 0.0043 0.347 1.371 0.790 0.103 12 0.3993 0.4143 0.579 90715. 4817.9 0.0042 0.337 1.358 0.779 0.102 13 0.3980 0.4131 0.582 90670. 4816.2 0.0040 0.326 1.344 0.767 0.101 14 0.3966 0.4117 0.585 90628. 4813.4 0.0039 0.317 1.331 0.757 0.100 15 0.3955 0.4104 0.589 90580. 4812.0 0.0038 0.307 1.319 0.748 0.099 16 0.3944 0.4092 0.591 90566. 4811.7 0.0036 0.299 1.300 0.738 0.098 17 0.3934 0.4083 0.592 90508. 4809.0 0.0035 0.289 1.279 0.727 0.097 18 0.3926 0.4075 0.594 90445. 4806.1 0.0034 0.283 1.263 0.719 0.096 19 0.3918 0.4067 0.596 90396. 4803.8 0.0033 0.277 1.251 0.711 0.095 20 0.3912 0.4062 0.597 90378. 4803.6 0.0032 0.272 1.240 0.704 0.095 21 0.3905 0.4055 0.598 90380. 4804.1 0.0032 0.267 1.232 0.699 0.094 22 0.3899 0.4044 0.599 90374. 4803.8 0.0031 0.264 1.224 0.693 0.094 23 0.3895 0.4048 0.599 90362. 4803.8 0.0031 0.260 1.215 0.688 0.093 24 0.3890 0.4043 0.600 90336. 4802.5 0.0030 0.257 1.208 0.683 0.093 25 0.3884 0.4038 0.601 90294. 4800.5 0.0030 0.254 1.201 0.678 0.093 26 0.3878 0.4032 0.602 90271. 4799.7 0.0030 0.252 1.195 0.674 0.093 27 0.3874 0.4025 0.603 90234. 4797.6 0.0029 0.249 1.188 0.670 0.093 28 0.3869 0.4021 0.605 90203. 4796.4 0.0029 0.247 1.182 0.666 0.092 29 0.3864 0.4017 0.605 90186. 4795.9 0.0029 0.244 1.176 0.663 0.092 30 0.3860 0.4013 0.607 90169. 4795.5 0.0028 0.242 1.171 0.660 0.092 $$ Output MTZ file from Refmac for model 1wqm_A1_PHR_MO_s0.54_r1-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1wqm_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1wqm_A1_PHR_MO_s0.54_r1-123.mtz Output PDB file from Refmac for model 1wqm_A1_PHR_MO_s0.54_r1-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1wqm_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1wqm_A1_PHR_MO_s0.54_r1-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 28 MR programs being used: MOLREP PHASER Best search model so far: 5v92_B1_PHR_MO_s0.56_r2-123 using MOLREP Initial Rfree: 0.466 Final Rfree: 0.370 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 28: 1oub_A1_PHR_MO_s0.54_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1oub_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1oub_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.54 Search model type: MOLREP Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1oub_A1_PHR\molrep\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1oub_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1oub_A1_PHR_MO_s0.54_r1-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1oub_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1oub_A1_PHR_MO_s0.54_r1-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1oub_A1_PHR\molrep\mr\molrep\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1oub_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1oub_A1_PHR_MO_s0.54_r1-123' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 1oub_A1_PHR_MO_s0.54_r1-123: ##### ################################################################################################# Template Model: 1oub_A1_PHR_MO_s0.54_r1-123 has produced a solution, final Rfree = 0.390 and is 0.798 of initial Rfree #################################################################################################### ##### Refinement results from Refmac for 1oub_A1_PHR_MO_s0.54_r1-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1oub_A1_PHR_MO_s0.54_r1-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4887 0.4977 0.417 93669. 4952.5 0.0275 2.239 2.479 1.525 0.343 1 0.4581 0.4677 0.453 92881. 4922.2 0.0082 0.643 1.824 1.126 0.259 2 0.4419 0.4510 0.491 92098. 4883.9 0.0069 0.529 1.664 1.021 0.194 3 0.4309 0.4385 0.518 91604. 4859.6 0.0061 0.470 1.562 0.951 0.156 4 0.4227 0.4240 0.535 91158. 4835.8 0.0057 0.439 1.499 0.905 0.133 5 0.4208 0.4216 0.540 91070. 4832.1 0.0049 0.384 1.427 0.856 0.119 6 0.4189 0.4195 0.544 91016. 4830.3 0.0045 0.358 1.377 0.822 0.109 7 0.4167 0.4175 0.548 90947. 4826.8 0.0043 0.342 1.346 0.799 0.106 8 0.4144 0.4154 0.556 90878. 4823.4 0.0042 0.332 1.325 0.782 0.103 9 0.4120 0.4131 0.561 90844. 4821.8 0.0041 0.325 1.310 0.769 0.101 10 0.4093 0.4103 0.564 90776. 4818.7 0.0040 0.321 1.303 0.761 0.100 11 0.4066 0.4074 0.571 90690. 4814.1 0.0041 0.322 1.300 0.755 0.099 12 0.4041 0.4050 0.577 90724. 4816.5 0.0040 0.318 1.296 0.748 0.098 13 0.4019 0.4031 0.582 90674. 4814.3 0.0039 0.309 1.291 0.741 0.098 14 0.4002 0.4018 0.584 90614. 4811.3 0.0038 0.300 1.286 0.734 0.097 15 0.3988 0.4004 0.589 90562. 4808.4 0.0036 0.290 1.279 0.727 0.097 16 0.3976 0.3990 0.594 90496. 4805.6 0.0034 0.280 1.273 0.720 0.097 17 0.3963 0.3976 0.597 90451. 4803.7 0.0033 0.273 1.265 0.714 0.097 18 0.3952 0.3965 0.599 90391. 4800.4 0.0032 0.266 1.258 0.707 0.096 19 0.3943 0.3958 0.602 90362. 4799.1 0.0031 0.260 1.250 0.701 0.096 20 0.3933 0.3952 0.604 90325. 4797.6 0.0031 0.255 1.245 0.696 0.096 21 0.3925 0.3944 0.605 90285. 4795.7 0.0030 0.251 1.239 0.692 0.096 22 0.3917 0.3939 0.606 90267. 4795.2 0.0030 0.247 1.234 0.688 0.096 23 0.3909 0.3932 0.606 90250. 4794.7 0.0029 0.244 1.228 0.683 0.096 24 0.3902 0.3925 0.607 90231. 4794.1 0.0029 0.241 1.220 0.678 0.096 25 0.3896 0.3920 0.610 90215. 4793.0 0.0028 0.238 1.213 0.674 0.096 26 0.3890 0.3915 0.612 90198. 4792.8 0.0028 0.234 1.206 0.670 0.096 27 0.3885 0.3910 0.613 90169. 4791.8 0.0027 0.231 1.200 0.666 0.096 28 0.3880 0.3908 0.614 90134. 4790.6 0.0027 0.228 1.194 0.662 0.096 29 0.3874 0.3904 0.615 90121. 4790.2 0.0027 0.226 1.188 0.658 0.096 30 0.3870 0.3900 0.615 90108. 4790.1 0.0026 0.224 1.183 0.655 0.096 $$ Output MTZ file from Refmac for model 1oub_A1_PHR_MO_s0.54_r1-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1oub_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1oub_A1_PHR_MO_s0.54_r1-123.mtz Output PDB file from Refmac for model 1oub_A1_PHR_MO_s0.54_r1-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1oub_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1oub_A1_PHR_MO_s0.54_r1-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 29 MR programs being used: MOLREP PHASER Best search model so far: 5v92_B1_PHR_MO_s0.56_r2-123 using MOLREP Initial Rfree: 0.466 Final Rfree: 0.370 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 29: 1oub_A1_PHR_MO_s0.54_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1oub_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1oub_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.54 Search model type: MOLREP Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1oub_A1_PHR\molrep\mr\phaser\phaser_1oub_A1_PHR_MO_s0.54_r1-123.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1oub_A1_PHR\molrep\mr\phaser\phaser_1oub_A1_PHR_MO_s0.54_r1-123.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1oub_A1_PHR\molrep\mr\phaser\phaser_1oub_A1_PHR_MO_s0.54_r1-123.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1oub_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_HKLOUT_1oub_A1_PHR_MO_s0.54_r1-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1oub_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1oub_A1_PHR_MO_s0.54_r1-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1oub_A1_PHR\molrep\mr\phaser\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1oub_A1_PHR\molrep\mr\phaser\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1oub_A1_PHR_MO_s0.54_r1-123' ######################################################################### ###################################################################### ##### Results from Phaser for 1oub_A1_PHR_MO_s0.54_r1-123: ##### ###################################################################### Template Model: 1oub_A1_PHR_MO_s0.54_r1-123 has produced a marginal solution, final Rfree = 0.388 Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1oub_A1_PHR\molrep\mr\phaser\phaser_1oub_A1_PHR_MO_s0.54_r1-123.log Phaser PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1oub_A1_PHR\molrep\mr\phaser\phaser_1oub_A1_PHR_MO_s0.54_r1-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1oub_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1oub_A1_PHR_MO_s0.54_r1-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1oub_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1oub_A1_PHR_MO_s0.54_r1-123.pdb #################################################################################################### ##### Refinement results from Refmac for 1oub_A1_PHR_MO_s0.54_r1-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1oub_A1_PHR_MO_s0.54_r1-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4760 0.4722 0.462 92883. 4909.5 0.0275 2.240 2.479 1.525 0.343 1 0.4548 0.4537 0.477 92457. 4895.4 0.0112 0.760 1.796 1.110 0.264 2 0.4376 0.4378 0.508 91842. 4867.7 0.0071 0.534 1.642 1.009 0.199 3 0.4288 0.4295 0.528 91501. 4850.0 0.0063 0.477 1.547 0.943 0.157 4 0.4219 0.4181 0.540 91153. 4833.0 0.0058 0.442 1.496 0.902 0.132 5 0.4170 0.4131 0.552 90997. 4825.1 0.0055 0.419 1.460 0.870 0.120 6 0.4130 0.4095 0.560 90841. 4818.3 0.0051 0.398 1.429 0.844 0.108 7 0.4096 0.4061 0.568 90755. 4814.4 0.0049 0.382 1.401 0.822 0.104 8 0.4068 0.4038 0.574 90735. 4814.5 0.0047 0.366 1.378 0.805 0.102 9 0.4042 0.4021 0.576 90683. 4812.9 0.0045 0.351 1.357 0.789 0.100 10 0.4023 0.4007 0.581 90631. 4811.0 0.0043 0.338 1.340 0.775 0.099 11 0.4008 0.3996 0.585 90582. 4809.4 0.0041 0.324 1.323 0.762 0.098 12 0.3992 0.3986 0.586 90532. 4807.6 0.0039 0.312 1.309 0.751 0.097 13 0.3980 0.3980 0.589 90506. 4806.2 0.0038 0.302 1.296 0.741 0.097 14 0.3967 0.3971 0.592 90453. 4804.1 0.0036 0.293 1.284 0.731 0.096 15 0.3957 0.3963 0.594 90410. 4802.7 0.0035 0.284 1.271 0.722 0.096 16 0.3948 0.3953 0.596 90396. 4802.2 0.0034 0.276 1.260 0.714 0.096 17 0.3938 0.3945 0.597 90351. 4800.2 0.0033 0.268 1.250 0.707 0.096 18 0.3929 0.3940 0.598 90308. 4797.9 0.0032 0.261 1.248 0.701 0.095 19 0.3921 0.3934 0.602 90290. 4796.5 0.0031 0.256 1.243 0.696 0.095 20 0.3914 0.3930 0.604 90262. 4795.9 0.0030 0.250 1.236 0.690 0.094 21 0.3907 0.3925 0.605 90245. 4795.5 0.0029 0.246 1.229 0.684 0.094 22 0.3900 0.3919 0.606 90244. 4796.0 0.0029 0.242 1.222 0.679 0.094 23 0.3894 0.3916 0.607 90218. 4795.0 0.0028 0.238 1.217 0.675 0.094 24 0.3889 0.3912 0.608 90201. 4794.4 0.0028 0.235 1.211 0.671 0.093 25 0.3883 0.3906 0.609 90190. 4794.4 0.0028 0.232 1.205 0.667 0.093 26 0.3877 0.3899 0.610 90154. 4792.7 0.0027 0.230 1.199 0.664 0.093 27 0.3872 0.3893 0.612 90130. 4791.2 0.0027 0.228 1.193 0.660 0.093 28 0.3867 0.3887 0.614 90093. 4789.6 0.0027 0.225 1.186 0.656 0.092 29 0.3862 0.3882 0.616 90074. 4788.8 0.0026 0.223 1.176 0.651 0.092 30 0.3858 0.3879 0.618 90060. 4788.7 0.0026 0.221 1.168 0.647 0.092 $$ Output MTZ file from Refmac for model 1oub_A1_PHR_MO_s0.54_r1-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1oub_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1oub_A1_PHR_MO_s0.54_r1-123.mtz Output PDB file from Refmac for model 1oub_A1_PHR_MO_s0.54_r1-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1oub_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1oub_A1_PHR_MO_s0.54_r1-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 30 MR programs being used: MOLREP PHASER Best search model so far: 5v92_B1_PHR_MO_s0.56_r2-123 using MOLREP Initial Rfree: 0.466 Final Rfree: 0.370 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 30: 1ge3_A1_PHR_MO_s0.54_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1ge3_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1ge3_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.54 Search model type: MOLREP Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1ge3_A1_PHR\molrep\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1ge3_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1ge3_A1_PHR_MO_s0.54_r1-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1ge3_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1ge3_A1_PHR_MO_s0.54_r1-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1ge3_A1_PHR\molrep\mr\molrep\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1ge3_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1ge3_A1_PHR_MO_s0.54_r1-123' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 1ge3_A1_PHR_MO_s0.54_r1-123: ##### ################################################################################################# Template Model: 1ge3_A1_PHR_MO_s0.54_r1-123 has produced a marginal solution, final Rfree = 0.399 Molrep log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1ge3_A1_PHR\molrep\mr\molrep\molrep.log Molrep PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1ge3_A1_PHR\molrep\mr\molrep\molrep_1ge3_A1_PHR_MO_s0.54_r1-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1ge3_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1ge3_A1_PHR_MO_s0.54_r1-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1ge3_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1ge3_A1_PHR_MO_s0.54_r1-123.pdb #################################################################################################### ##### Refinement results from Refmac for 1ge3_A1_PHR_MO_s0.54_r1-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1ge3_A1_PHR_MO_s0.54_r1-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4796 0.4795 0.439 93276. 4930.8 0.0280 2.286 2.540 1.558 0.335 1 0.4492 0.4514 0.470 92478. 4902.1 0.0085 0.660 1.892 1.166 0.260 2 0.4358 0.4380 0.498 91977. 4878.1 0.0070 0.534 1.711 1.050 0.199 3 0.4271 0.4294 0.522 91636. 4861.4 0.0062 0.476 1.606 0.982 0.163 4 0.4210 0.4237 0.536 91264. 4843.6 0.0057 0.438 1.533 0.930 0.132 5 0.4162 0.4165 0.547 91038. 4832.8 0.0053 0.411 1.484 0.894 0.121 6 0.4126 0.4131 0.556 90927. 4828.1 0.0050 0.389 1.443 0.864 0.116 7 0.4097 0.4102 0.563 90850. 4825.6 0.0048 0.370 1.406 0.837 0.113 8 0.4074 0.4081 0.569 90774. 4822.1 0.0045 0.351 1.377 0.817 0.110 9 0.4055 0.4065 0.572 90694. 4819.0 0.0042 0.333 1.352 0.798 0.109 10 0.4038 0.4055 0.576 90649. 4817.7 0.0040 0.320 1.334 0.784 0.108 11 0.4025 0.4045 0.579 90623. 4816.9 0.0039 0.308 1.316 0.770 0.107 12 0.4010 0.4036 0.581 90579. 4814.7 0.0037 0.299 1.300 0.758 0.107 13 0.4000 0.4028 0.586 90507. 4810.9 0.0036 0.291 1.287 0.747 0.106 14 0.3989 0.4023 0.588 90489. 4810.7 0.0035 0.282 1.275 0.738 0.106 15 0.3979 0.4019 0.590 90468. 4810.2 0.0034 0.275 1.265 0.729 0.105 16 0.3970 0.4017 0.590 90451. 4809.7 0.0033 0.269 1.252 0.721 0.105 17 0.3961 0.4013 0.591 90436. 4809.5 0.0032 0.263 1.243 0.714 0.105 18 0.3952 0.4013 0.593 90437. 4810.0 0.0031 0.257 1.237 0.708 0.105 19 0.3945 0.4009 0.595 90417. 4809.7 0.0030 0.252 1.230 0.702 0.104 20 0.3938 0.4002 0.598 90376. 4807.6 0.0030 0.248 1.223 0.696 0.104 21 0.3931 0.3998 0.599 90346. 4806.6 0.0029 0.243 1.216 0.691 0.104 22 0.3924 0.3994 0.600 90319. 4805.4 0.0029 0.240 1.210 0.686 0.103 23 0.3918 0.3993 0.600 90298. 4804.6 0.0028 0.238 1.204 0.682 0.103 24 0.3911 0.3990 0.601 90272. 4803.7 0.0028 0.235 1.199 0.677 0.103 25 0.3905 0.3989 0.602 90252. 4803.2 0.0027 0.233 1.193 0.673 0.102 26 0.3899 0.3988 0.604 90239. 4802.6 0.0027 0.231 1.187 0.669 0.102 27 0.3895 0.3988 0.604 90244. 4803.3 0.0027 0.228 1.182 0.665 0.102 28 0.3889 0.3985 0.605 90233. 4803.1 0.0027 0.227 1.177 0.662 0.101 29 0.3884 0.3985 0.605 90217. 4802.6 0.0027 0.225 1.172 0.658 0.101 30 0.3880 0.3985 0.606 90195. 4801.7 0.0026 0.224 1.168 0.655 0.101 $$ Output MTZ file from Refmac for model 1ge3_A1_PHR_MO_s0.54_r1-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1ge3_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1ge3_A1_PHR_MO_s0.54_r1-123.mtz Output PDB file from Refmac for model 1ge3_A1_PHR_MO_s0.54_r1-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1ge3_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1ge3_A1_PHR_MO_s0.54_r1-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 31 MR programs being used: MOLREP PHASER Best search model so far: 5v92_B1_PHR_MO_s0.56_r2-123 using MOLREP Initial Rfree: 0.466 Final Rfree: 0.370 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 31: 1ge3_A1_PHR_MO_s0.54_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1ge3_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1ge3_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.54 Search model type: MOLREP Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1ge3_A1_PHR\molrep\mr\phaser\phaser_1ge3_A1_PHR_MO_s0.54_r1-123.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1ge3_A1_PHR\molrep\mr\phaser\phaser_1ge3_A1_PHR_MO_s0.54_r1-123.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1ge3_A1_PHR\molrep\mr\phaser\phaser_1ge3_A1_PHR_MO_s0.54_r1-123.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1ge3_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_HKLOUT_1ge3_A1_PHR_MO_s0.54_r1-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1ge3_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1ge3_A1_PHR_MO_s0.54_r1-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1ge3_A1_PHR\molrep\mr\phaser\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1ge3_A1_PHR\molrep\mr\phaser\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1ge3_A1_PHR_MO_s0.54_r1-123' ######################################################################### ###################################################################### ##### Results from Phaser for 1ge3_A1_PHR_MO_s0.54_r1-123: ##### ###################################################################### Template Model: 1ge3_A1_PHR_MO_s0.54_r1-123 has produced a marginal solution, final Rfree = 0.404 Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1ge3_A1_PHR\molrep\mr\phaser\phaser_1ge3_A1_PHR_MO_s0.54_r1-123.log Phaser PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1ge3_A1_PHR\molrep\mr\phaser\phaser_1ge3_A1_PHR_MO_s0.54_r1-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1ge3_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1ge3_A1_PHR_MO_s0.54_r1-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1ge3_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1ge3_A1_PHR_MO_s0.54_r1-123.pdb #################################################################################################### ##### Refinement results from Refmac for 1ge3_A1_PHR_MO_s0.54_r1-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1ge3_A1_PHR_MO_s0.54_r1-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4684 0.4646 0.473 92673. 4901.9 0.0280 2.286 2.541 1.558 0.336 1 0.4473 0.4459 0.490 92152. 4883.0 0.0087 0.685 1.876 1.154 0.262 2 0.4336 0.4331 0.514 91760. 4866.3 0.0068 0.529 1.702 1.042 0.203 3 0.4260 0.4263 0.530 91520. 4855.1 0.0061 0.472 1.604 0.977 0.167 4 0.4202 0.4214 0.544 91261. 4843.2 0.0056 0.436 1.535 0.928 0.134 5 0.4161 0.4194 0.554 91154. 4838.9 0.0053 0.409 1.485 0.892 0.123 6 0.4124 0.4165 0.560 91083. 4836.5 0.0050 0.389 1.442 0.862 0.117 7 0.4097 0.4137 0.567 90983. 4832.2 0.0047 0.369 1.407 0.837 0.115 8 0.4075 0.4124 0.572 90880. 4828.0 0.0045 0.351 1.377 0.816 0.112 9 0.4054 0.4107 0.575 90814. 4825.0 0.0043 0.336 1.354 0.799 0.111 10 0.4037 0.4092 0.578 90756. 4823.1 0.0041 0.323 1.333 0.783 0.110 11 0.4022 0.4083 0.582 90730. 4823.0 0.0039 0.311 1.316 0.770 0.109 12 0.4008 0.4078 0.584 90730. 4823.3 0.0037 0.301 1.300 0.758 0.108 13 0.3996 0.4078 0.587 90720. 4823.5 0.0036 0.292 1.287 0.747 0.108 14 0.3986 0.4073 0.588 90712. 4823.7 0.0035 0.284 1.275 0.738 0.107 15 0.3975 0.4067 0.590 90695. 4823.3 0.0034 0.276 1.262 0.729 0.107 16 0.3965 0.4067 0.592 90683. 4823.0 0.0033 0.269 1.252 0.721 0.107 17 0.3956 0.4063 0.594 90674. 4823.2 0.0032 0.262 1.244 0.714 0.107 18 0.3948 0.4059 0.594 90677. 4824.0 0.0031 0.257 1.236 0.708 0.106 19 0.3941 0.4055 0.595 90646. 4822.7 0.0030 0.252 1.229 0.702 0.106 20 0.3934 0.4051 0.597 90592. 4820.2 0.0030 0.248 1.223 0.697 0.106 21 0.3927 0.4051 0.599 90544. 4817.9 0.0029 0.245 1.217 0.692 0.106 22 0.3920 0.4049 0.601 90512. 4816.7 0.0029 0.241 1.210 0.687 0.105 23 0.3914 0.4047 0.602 90499. 4816.5 0.0028 0.238 1.204 0.682 0.105 24 0.3907 0.4046 0.603 90481. 4816.0 0.0028 0.235 1.198 0.677 0.104 25 0.3901 0.4047 0.603 90458. 4815.1 0.0027 0.233 1.193 0.673 0.104 26 0.3896 0.4045 0.604 90446. 4814.7 0.0027 0.231 1.187 0.669 0.104 27 0.3891 0.4044 0.604 90428. 4814.1 0.0027 0.229 1.182 0.666 0.103 28 0.3886 0.4041 0.605 90404. 4813.1 0.0027 0.227 1.177 0.662 0.103 29 0.3882 0.4040 0.605 90380. 4812.1 0.0026 0.226 1.173 0.659 0.103 30 0.3877 0.4039 0.606 90359. 4811.3 0.0026 0.225 1.168 0.656 0.102 $$ Output MTZ file from Refmac for model 1ge3_A1_PHR_MO_s0.54_r1-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1ge3_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1ge3_A1_PHR_MO_s0.54_r1-123.mtz Output PDB file from Refmac for model 1ge3_A1_PHR_MO_s0.54_r1-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1ge3_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1ge3_A1_PHR_MO_s0.54_r1-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 32 MR programs being used: MOLREP PHASER Best search model so far: 5v92_B1_PHR_MO_s0.56_r2-123 using MOLREP Initial Rfree: 0.466 Final Rfree: 0.370 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 32: 1di3_A1_PHR_MO_s0.54_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1di3_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1di3_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.54 Search model type: MOLREP Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1di3_A1_PHR\molrep\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1di3_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1di3_A1_PHR_MO_s0.54_r1-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1di3_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1di3_A1_PHR_MO_s0.54_r1-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1di3_A1_PHR\molrep\mr\molrep\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1di3_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1di3_A1_PHR_MO_s0.54_r1-123' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 1di3_A1_PHR_MO_s0.54_r1-123: ##### ################################################################################################# Template Model: 1di3_A1_PHR_MO_s0.54_r1-123 has produced a marginal solution, final Rfree = 0.407 Molrep log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1di3_A1_PHR\molrep\mr\molrep\molrep.log Molrep PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1di3_A1_PHR\molrep\mr\molrep\molrep_1di3_A1_PHR_MO_s0.54_r1-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1di3_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1di3_A1_PHR_MO_s0.54_r1-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1di3_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1di3_A1_PHR_MO_s0.54_r1-123.pdb #################################################################################################### ##### Refinement results from Refmac for 1di3_A1_PHR_MO_s0.54_r1-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1di3_A1_PHR_MO_s0.54_r1-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4830 0.4996 0.425 93589. 4954.5 0.0279 2.275 2.587 1.593 0.343 1 0.4541 0.4699 0.455 92822. 4920.6 0.0081 0.637 1.895 1.174 0.264 2 0.4385 0.4518 0.488 92233. 4891.5 0.0066 0.513 1.733 1.069 0.208 3 0.4279 0.4395 0.511 91731. 4866.4 0.0060 0.465 1.631 1.001 0.164 4 0.4211 0.4317 0.528 91448. 4853.7 0.0056 0.432 1.563 0.955 0.142 5 0.4194 0.4302 0.534 91397. 4852.1 0.0048 0.378 1.488 0.906 0.126 6 0.4176 0.4286 0.540 91390. 4851.7 0.0044 0.352 1.432 0.870 0.118 7 0.4157 0.4270 0.544 91344. 4850.2 0.0042 0.335 1.389 0.841 0.111 8 0.4135 0.4252 0.549 91281. 4846.8 0.0040 0.323 1.358 0.820 0.108 9 0.4114 0.4236 0.553 91224. 4845.2 0.0039 0.314 1.335 0.803 0.106 10 0.4090 0.4219 0.558 91183. 4843.4 0.0038 0.307 1.321 0.790 0.104 11 0.4067 0.4206 0.565 91120. 4840.8 0.0037 0.305 1.313 0.781 0.103 12 0.4046 0.4197 0.572 91004. 4834.1 0.0037 0.302 1.305 0.772 0.102 13 0.4031 0.4187 0.578 90945. 4831.8 0.0037 0.297 1.295 0.762 0.101 14 0.4015 0.4178 0.581 90926. 4831.2 0.0036 0.291 1.284 0.752 0.101 15 0.4002 0.4175 0.585 90909. 4830.3 0.0035 0.285 1.271 0.742 0.101 16 0.3989 0.4164 0.589 90867. 4828.0 0.0034 0.278 1.257 0.732 0.100 17 0.3979 0.4157 0.592 90829. 4826.8 0.0033 0.272 1.244 0.723 0.100 18 0.3969 0.4147 0.593 90802. 4825.3 0.0032 0.266 1.232 0.715 0.100 19 0.3958 0.4136 0.594 90767. 4823.5 0.0031 0.262 1.221 0.708 0.100 20 0.3948 0.4136 0.596 90668. 4818.3 0.0031 0.258 1.211 0.701 0.100 21 0.3941 0.4127 0.600 90630. 4817.0 0.0030 0.254 1.202 0.694 0.100 22 0.3933 0.4115 0.603 90559. 4813.8 0.0029 0.249 1.192 0.688 0.100 23 0.3926 0.4103 0.605 90496. 4810.7 0.0029 0.245 1.184 0.682 0.100 24 0.3919 0.4097 0.605 90456. 4808.8 0.0028 0.242 1.177 0.677 0.100 25 0.3912 0.4089 0.606 90414. 4806.8 0.0028 0.239 1.171 0.673 0.100 26 0.3906 0.4086 0.608 90385. 4805.1 0.0028 0.236 1.164 0.668 0.100 27 0.3901 0.4085 0.610 90333. 4802.8 0.0027 0.234 1.157 0.664 0.099 28 0.3895 0.4080 0.611 90303. 4801.5 0.0027 0.231 1.152 0.660 0.099 29 0.3891 0.4076 0.612 90292. 4801.2 0.0027 0.229 1.146 0.656 0.099 30 0.3887 0.4072 0.613 90277. 4800.8 0.0026 0.227 1.141 0.652 0.099 $$ Output MTZ file from Refmac for model 1di3_A1_PHR_MO_s0.54_r1-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1di3_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1di3_A1_PHR_MO_s0.54_r1-123.mtz Output PDB file from Refmac for model 1di3_A1_PHR_MO_s0.54_r1-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1di3_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1di3_A1_PHR_MO_s0.54_r1-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 33 MR programs being used: MOLREP PHASER Best search model so far: 5v92_B1_PHR_MO_s0.56_r2-123 using MOLREP Initial Rfree: 0.466 Final Rfree: 0.370 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 33: 1di3_A1_PHR_MO_s0.54_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1di3_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1di3_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.54 Search model type: MOLREP Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1di3_A1_PHR\molrep\mr\phaser\phaser_1di3_A1_PHR_MO_s0.54_r1-123.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1di3_A1_PHR\molrep\mr\phaser\phaser_1di3_A1_PHR_MO_s0.54_r1-123.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1di3_A1_PHR\molrep\mr\phaser\phaser_1di3_A1_PHR_MO_s0.54_r1-123.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1di3_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_HKLOUT_1di3_A1_PHR_MO_s0.54_r1-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1di3_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1di3_A1_PHR_MO_s0.54_r1-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1di3_A1_PHR\molrep\mr\phaser\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1di3_A1_PHR\molrep\mr\phaser\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1di3_A1_PHR_MO_s0.54_r1-123' ######################################################################### ###################################################################### ##### Results from Phaser for 1di3_A1_PHR_MO_s0.54_r1-123: ##### ###################################################################### Template Model: 1di3_A1_PHR_MO_s0.54_r1-123 has produced a marginal solution, final Rfree = 0.408 Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1di3_A1_PHR\molrep\mr\phaser\phaser_1di3_A1_PHR_MO_s0.54_r1-123.log Phaser PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1di3_A1_PHR\molrep\mr\phaser\phaser_1di3_A1_PHR_MO_s0.54_r1-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1di3_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1di3_A1_PHR_MO_s0.54_r1-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1di3_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1di3_A1_PHR_MO_s0.54_r1-123.pdb #################################################################################################### ##### Refinement results from Refmac for 1di3_A1_PHR_MO_s0.54_r1-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1di3_A1_PHR_MO_s0.54_r1-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4686 0.4811 0.461 92900. 4921.5 0.0279 2.274 2.587 1.593 0.344 1 0.4484 0.4585 0.479 92296. 4892.2 0.0084 0.662 1.882 1.165 0.263 2 0.4413 0.4492 0.491 91940. 4874.6 0.0058 0.466 1.712 1.057 0.212 3 0.4372 0.4440 0.499 91763. 4865.4 0.0052 0.415 1.595 0.981 0.170 4 0.4332 0.4389 0.508 91573. 4856.7 0.0048 0.387 1.516 0.930 0.146 5 0.4294 0.4356 0.515 91482. 4852.2 0.0046 0.369 1.461 0.894 0.133 6 0.4252 0.4312 0.522 91421. 4849.9 0.0045 0.358 1.421 0.866 0.122 7 0.4210 0.4273 0.533 91373. 4848.6 0.0044 0.352 1.394 0.846 0.116 8 0.4166 0.4247 0.543 91325. 4847.8 0.0044 0.348 1.378 0.832 0.111 9 0.4148 0.4237 0.547 91294. 4847.2 0.0041 0.323 1.344 0.808 0.108 10 0.4129 0.4229 0.551 91260. 4845.7 0.0039 0.312 1.320 0.791 0.106 11 0.4109 0.4220 0.555 91208. 4844.0 0.0037 0.303 1.301 0.777 0.105 12 0.4089 0.4210 0.559 91137. 4840.3 0.0036 0.297 1.287 0.766 0.104 13 0.4071 0.4205 0.563 91100. 4839.7 0.0036 0.292 1.276 0.757 0.103 14 0.4050 0.4195 0.568 91051. 4837.4 0.0035 0.290 1.268 0.749 0.102 15 0.4031 0.4187 0.572 90997. 4834.7 0.0035 0.289 1.262 0.743 0.101 16 0.4015 0.4181 0.577 90944. 4832.8 0.0035 0.286 1.256 0.736 0.101 17 0.4001 0.4175 0.581 90901. 4830.1 0.0034 0.281 1.246 0.729 0.100 18 0.3990 0.4166 0.587 90832. 4826.8 0.0033 0.275 1.235 0.721 0.100 19 0.3978 0.4160 0.590 90763. 4823.0 0.0033 0.270 1.224 0.714 0.100 20 0.3966 0.4151 0.592 90699. 4820.1 0.0032 0.266 1.215 0.707 0.100 21 0.3955 0.4143 0.596 90653. 4817.8 0.0031 0.261 1.206 0.701 0.099 22 0.3947 0.4135 0.598 90631. 4817.0 0.0030 0.255 1.196 0.694 0.099 23 0.3937 0.4126 0.600 90598. 4815.1 0.0030 0.251 1.188 0.689 0.099 24 0.3929 0.4124 0.602 90542. 4812.8 0.0029 0.247 1.181 0.684 0.099 25 0.3921 0.4115 0.604 90479. 4809.8 0.0029 0.243 1.174 0.678 0.099 26 0.3914 0.4108 0.605 90453. 4808.7 0.0028 0.241 1.167 0.673 0.099 27 0.3906 0.4101 0.606 90446. 4808.2 0.0028 0.238 1.161 0.669 0.098 28 0.3901 0.4096 0.608 90425. 4807.7 0.0027 0.235 1.156 0.665 0.098 29 0.3896 0.4088 0.609 90402. 4806.9 0.0027 0.233 1.151 0.661 0.098 30 0.3891 0.4082 0.610 90391. 4806.4 0.0027 0.230 1.146 0.657 0.098 $$ Output MTZ file from Refmac for model 1di3_A1_PHR_MO_s0.54_r1-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1di3_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1di3_A1_PHR_MO_s0.54_r1-123.mtz Output PDB file from Refmac for model 1di3_A1_PHR_MO_s0.54_r1-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1di3_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1di3_A1_PHR_MO_s0.54_r1-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 34 MR programs being used: MOLREP PHASER Best search model so far: 5v92_B1_PHR_MO_s0.56_r2-123 using MOLREP Initial Rfree: 0.466 Final Rfree: 0.370 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 662.00 28.50 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 34: 5v8g_A1_PHR_SC_s0.57_r2-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\sculptor Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\sculpt_5v8g_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.57 Search model type: SCLPTR Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\sculptor\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\sculptor\mr\molrep\refine\refmac_molrep_HKLOUT_5v8g_A1_PHR_SC_s0.57_r2-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\sculptor\mr\molrep\refine\refmac_molrep_5v8g_A1_PHR_SC_s0.57_r2-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\sculptor\mr\molrep\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\sculptor\mr\molrep\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '5v8g_A1_PHR_SC_s0.57_r2-123' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 5v8g_A1_PHR_SC_s0.57_r2-123: ##### ################################################################################################# Template Model: 5v8g_A1_PHR_SC_s0.57_r2-123 has produced a marginal solution, final Rfree = 0.372 Molrep log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\sculptor\mr\molrep\molrep.log Molrep PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\sculptor\mr\molrep\molrep_5v8g_A1_PHR_SC_s0.57_r2-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\sculptor\mr\molrep\refine\refmac_molrep_5v8g_A1_PHR_SC_s0.57_r2-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\sculptor\mr\molrep\refine\refmac_molrep_5v8g_A1_PHR_SC_s0.57_r2-123.pdb #################################################################################################### ##### Refinement results from Refmac for 5v8g_A1_PHR_SC_s0.57_r2-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 5v8g_A1_PHR_SC_s0.57_r2-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4513 0.4437 0.538 92012. 4846.3 0.0184 1.600 1.924 1.207 0.124 1 0.4242 0.4240 0.565 91044. 4805.0 0.0061 0.539 1.602 0.988 0.106 2 0.4102 0.4081 0.587 90601. 4784.1 0.0050 0.435 1.470 0.902 0.104 3 0.4069 0.4042 0.597 90386. 4773.2 0.0044 0.378 1.382 0.847 0.101 4 0.4040 0.4025 0.602 90139. 4761.2 0.0040 0.348 1.320 0.808 0.100 5 0.4012 0.4003 0.607 89979. 4753.3 0.0038 0.329 1.275 0.779 0.099 6 0.3985 0.3981 0.612 89854. 4748.4 0.0037 0.315 1.239 0.757 0.098 7 0.3956 0.3952 0.617 89736. 4743.9 0.0036 0.307 1.213 0.740 0.098 8 0.3923 0.3896 0.624 89468. 4731.2 0.0036 0.302 1.192 0.726 0.098 9 0.3888 0.3843 0.629 89289. 4724.5 0.0036 0.301 1.177 0.715 0.098 10 0.3878 0.3832 0.631 89253. 4723.7 0.0034 0.288 1.153 0.700 0.097 11 0.3868 0.3818 0.634 89179. 4720.3 0.0033 0.281 1.135 0.687 0.097 12 0.3855 0.3808 0.636 89142. 4719.2 0.0032 0.275 1.118 0.677 0.096 13 0.3841 0.3795 0.638 89087. 4717.1 0.0032 0.271 1.105 0.668 0.096 14 0.3828 0.3783 0.641 89033. 4715.5 0.0031 0.268 1.094 0.660 0.095 15 0.3814 0.3769 0.644 88979. 4713.8 0.0031 0.265 1.084 0.653 0.095 16 0.3810 0.3774 0.644 88988. 4715.7 0.0030 0.258 1.072 0.645 0.095 17 0.3802 0.3770 0.645 88966. 4715.0 0.0030 0.254 1.062 0.638 0.094 18 0.3795 0.3765 0.646 88940. 4714.4 0.0029 0.251 1.053 0.632 0.094 19 0.3787 0.3760 0.647 88892. 4712.4 0.0029 0.248 1.045 0.627 0.093 20 0.3779 0.3754 0.648 88858. 4711.0 0.0029 0.245 1.037 0.622 0.093 21 0.3770 0.3740 0.651 88806. 4708.1 0.0028 0.243 1.030 0.617 0.093 22 0.3763 0.3736 0.653 88744. 4705.5 0.0028 0.241 1.022 0.613 0.092 23 0.3758 0.3734 0.653 88728. 4705.1 0.0028 0.237 1.014 0.608 0.092 24 0.3754 0.3730 0.654 88708. 4704.4 0.0027 0.234 1.007 0.603 0.091 25 0.3749 0.3727 0.654 88694. 4704.2 0.0027 0.231 1.000 0.599 0.091 26 0.3745 0.3724 0.655 88685. 4704.0 0.0026 0.229 0.994 0.596 0.090 27 0.3741 0.3723 0.655 88671. 4703.9 0.0026 0.227 0.988 0.592 0.090 28 0.3737 0.3721 0.656 88672. 4704.5 0.0026 0.225 0.981 0.588 0.089 29 0.3734 0.3719 0.656 88657. 4704.1 0.0026 0.223 0.976 0.585 0.089 30 0.3730 0.3717 0.657 88635. 4703.4 0.0025 0.221 0.970 0.582 0.089 $$ Output MTZ file from Refmac for model 5v8g_A1_PHR_SC_s0.57_r2-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\sculptor\mr\molrep\refine\refmac_molrep_HKLOUT_5v8g_A1_PHR_SC_s0.57_r2-123.mtz Output PDB file from Refmac for model 5v8g_A1_PHR_SC_s0.57_r2-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\sculptor\mr\molrep\refine\refmac_molrep_5v8g_A1_PHR_SC_s0.57_r2-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 35 MR programs being used: MOLREP PHASER Best search model so far: 5v92_B1_PHR_MO_s0.56_r2-123 using MOLREP Initial Rfree: 0.466 Final Rfree: 0.370 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 662.00 28.50 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 35: 5v8g_A1_PHR_SC_s0.57_r2-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\sculptor Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\sculpt_5v8g_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.57 Search model type: SCLPTR Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\sculptor\mr\phaser\phaser_5v8g_A1_PHR_SC_s0.57_r2-123.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\sculptor\mr\phaser\phaser_5v8g_A1_PHR_SC_s0.57_r2-123.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\sculptor\mr\phaser\phaser_5v8g_A1_PHR_SC_s0.57_r2-123.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\sculptor\mr\phaser\refine\refmac_phaser_HKLOUT_5v8g_A1_PHR_SC_s0.57_r2-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\sculptor\mr\phaser\refine\refmac_phaser_5v8g_A1_PHR_SC_s0.57_r2-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\sculptor\mr\phaser\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\sculptor\mr\phaser\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '5v8g_A1_PHR_SC_s0.57_r2-123' ######################################################################### ###################################################################### ##### Results from Phaser for 5v8g_A1_PHR_SC_s0.57_r2-123: ##### ###################################################################### Template Model: 5v8g_A1_PHR_SC_s0.57_r2-123 has produced a marginal solution, final Rfree = 0.372 Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\sculptor\mr\phaser\phaser_5v8g_A1_PHR_SC_s0.57_r2-123.log Phaser PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\sculptor\mr\phaser\phaser_5v8g_A1_PHR_SC_s0.57_r2-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\sculptor\mr\phaser\refine\refmac_phaser_5v8g_A1_PHR_SC_s0.57_r2-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\sculptor\mr\phaser\refine\refmac_phaser_5v8g_A1_PHR_SC_s0.57_r2-123.pdb #################################################################################################### ##### Refinement results from Refmac for 5v8g_A1_PHR_SC_s0.57_r2-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 5v8g_A1_PHR_SC_s0.57_r2-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4303 0.4304 0.573 91183. 4812.7 0.0183 1.588 1.922 1.205 0.123 1 0.4230 0.4251 0.570 90928. 4803.0 0.0059 0.535 1.623 1.003 0.105 2 0.4189 0.4206 0.574 90801. 4797.9 0.0051 0.460 1.524 0.940 0.102 3 0.4152 0.4156 0.579 90606. 4788.6 0.0046 0.413 1.450 0.893 0.100 4 0.4097 0.4080 0.587 90367. 4776.9 0.0042 0.369 1.361 0.837 0.099 5 0.4046 0.4023 0.597 90188. 4767.9 0.0040 0.345 1.303 0.801 0.099 6 0.3995 0.3968 0.608 89922. 4755.2 0.0039 0.333 1.263 0.775 0.099 7 0.3974 0.3950 0.613 89835. 4751.1 0.0037 0.316 1.225 0.751 0.098 8 0.3953 0.3932 0.617 89701. 4745.0 0.0036 0.305 1.196 0.733 0.098 9 0.3929 0.3881 0.622 89439. 4731.6 0.0035 0.297 1.173 0.718 0.097 10 0.3907 0.3852 0.627 89350. 4727.2 0.0034 0.291 1.155 0.705 0.097 11 0.3886 0.3833 0.632 89254. 4722.8 0.0034 0.287 1.139 0.695 0.097 12 0.3865 0.3816 0.636 89163. 4719.6 0.0034 0.285 1.126 0.686 0.097 13 0.3844 0.3797 0.639 89077. 4716.5 0.0034 0.284 1.114 0.677 0.096 14 0.3835 0.3787 0.640 89051. 4715.9 0.0033 0.276 1.098 0.666 0.096 15 0.3824 0.3778 0.641 89023. 4715.3 0.0032 0.271 1.085 0.657 0.095 16 0.3814 0.3769 0.643 88971. 4713.5 0.0031 0.267 1.074 0.650 0.095 17 0.3804 0.3763 0.644 88920. 4711.7 0.0031 0.263 1.065 0.644 0.095 18 0.3793 0.3752 0.645 88867. 4709.5 0.0031 0.260 1.057 0.638 0.094 19 0.3783 0.3746 0.647 88792. 4706.2 0.0030 0.258 1.050 0.633 0.094 20 0.3774 0.3741 0.650 88756. 4705.4 0.0030 0.256 1.043 0.629 0.094 21 0.3768 0.3737 0.651 88732. 4704.6 0.0029 0.250 1.034 0.623 0.093 22 0.3764 0.3741 0.652 88737. 4705.8 0.0029 0.246 1.025 0.617 0.093 23 0.3759 0.3738 0.654 88724. 4705.7 0.0028 0.242 1.018 0.612 0.092 24 0.3753 0.3724 0.655 88698. 4703.6 0.0028 0.239 1.011 0.608 0.092 25 0.3748 0.3721 0.656 88681. 4702.7 0.0027 0.236 1.005 0.604 0.091 26 0.3743 0.3722 0.656 88668. 4702.9 0.0027 0.234 0.999 0.600 0.091 27 0.3739 0.3719 0.657 88673. 4703.5 0.0027 0.231 0.993 0.596 0.090 28 0.3735 0.3718 0.658 88659. 4703.2 0.0026 0.229 0.987 0.592 0.090 29 0.3732 0.3716 0.658 88648. 4703.0 0.0026 0.227 0.981 0.589 0.089 30 0.3729 0.3716 0.658 88634. 4702.7 0.0026 0.224 0.975 0.585 0.089 $$ Output MTZ file from Refmac for model 5v8g_A1_PHR_SC_s0.57_r2-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\sculptor\mr\molrep\refine\refmac_molrep_HKLOUT_5v8g_A1_PHR_SC_s0.57_r2-123.mtz Output PDB file from Refmac for model 5v8g_A1_PHR_SC_s0.57_r2-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\sculptor\mr\molrep\refine\refmac_molrep_5v8g_A1_PHR_SC_s0.57_r2-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 36 MR programs being used: MOLREP PHASER Best search model so far: 5v92_B1_PHR_MO_s0.56_r2-123 using MOLREP Initial Rfree: 0.466 Final Rfree: 0.370 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 PHASER MARGINAL 1567.00 41.40 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 662.00 28.50 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 36: 5v8g_A1_PHR_CH_s0.57_r2-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\chainsaw Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\CHAINSAW_5v8g_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.57 Search model type: CHNSAW Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\chainsaw\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\chainsaw\mr\molrep\refine\refmac_molrep_HKLOUT_5v8g_A1_PHR_CH_s0.57_r2-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\chainsaw\mr\molrep\refine\refmac_molrep_5v8g_A1_PHR_CH_s0.57_r2-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\chainsaw\mr\molrep\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\chainsaw\mr\molrep\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '5v8g_A1_PHR_CH_s0.57_r2-123' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 5v8g_A1_PHR_CH_s0.57_r2-123: ##### ################################################################################################# Template Model: 5v8g_A1_PHR_CH_s0.57_r2-123 has produced a marginal solution, final Rfree = 0.371 Molrep log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\chainsaw\mr\molrep\molrep.log Molrep PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\chainsaw\mr\molrep\molrep_5v8g_A1_PHR_CH_s0.57_r2-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\chainsaw\mr\molrep\refine\refmac_molrep_5v8g_A1_PHR_CH_s0.57_r2-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\chainsaw\mr\molrep\refine\refmac_molrep_5v8g_A1_PHR_CH_s0.57_r2-123.pdb #################################################################################################### ##### Refinement results from Refmac for 5v8g_A1_PHR_CH_s0.57_r2-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 5v8g_A1_PHR_CH_s0.57_r2-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4508 0.4432 0.539 91971. 4844.2 0.0198 1.724 1.933 1.211 0.125 1 0.4239 0.4240 0.565 91026. 4804.0 0.0061 0.544 1.623 0.993 0.106 2 0.4099 0.4090 0.587 90538. 4781.2 0.0050 0.436 1.480 0.905 0.103 3 0.4066 0.4051 0.598 90302. 4769.0 0.0044 0.379 1.386 0.847 0.100 4 0.4037 0.4025 0.603 90107. 4759.7 0.0040 0.349 1.319 0.806 0.098 5 0.4010 0.4000 0.607 89989. 4753.9 0.0038 0.328 1.271 0.776 0.097 6 0.3983 0.3980 0.613 89863. 4749.4 0.0037 0.315 1.234 0.754 0.097 7 0.3952 0.3920 0.620 89604. 4736.8 0.0036 0.306 1.206 0.737 0.096 8 0.3922 0.3882 0.624 89470. 4731.8 0.0036 0.301 1.184 0.722 0.096 9 0.3888 0.3842 0.629 89307. 4725.4 0.0036 0.300 1.168 0.711 0.096 10 0.3878 0.3831 0.633 89256. 4723.4 0.0034 0.288 1.145 0.696 0.096 11 0.3867 0.3820 0.635 89196. 4721.2 0.0033 0.280 1.126 0.684 0.095 12 0.3855 0.3806 0.637 89130. 4718.5 0.0032 0.275 1.111 0.673 0.095 13 0.3841 0.3796 0.639 89080. 4716.8 0.0032 0.271 1.098 0.664 0.095 14 0.3829 0.3784 0.641 89040. 4715.8 0.0032 0.268 1.087 0.657 0.094 15 0.3815 0.3772 0.642 88999. 4714.7 0.0031 0.265 1.078 0.650 0.094 16 0.3811 0.3777 0.642 88984. 4715.4 0.0030 0.259 1.067 0.643 0.094 17 0.3804 0.3772 0.644 88956. 4714.6 0.0030 0.255 1.058 0.636 0.093 18 0.3796 0.3767 0.646 88919. 4713.4 0.0029 0.251 1.049 0.631 0.093 19 0.3788 0.3761 0.648 88855. 4710.7 0.0029 0.248 1.042 0.626 0.093 20 0.3778 0.3746 0.650 88801. 4707.5 0.0029 0.246 1.035 0.621 0.092 21 0.3771 0.3739 0.653 88766. 4706.0 0.0028 0.243 1.027 0.616 0.092 22 0.3764 0.3736 0.654 88721. 4704.2 0.0028 0.241 1.020 0.612 0.092 23 0.3760 0.3733 0.654 88696. 4703.2 0.0028 0.237 1.012 0.607 0.091 24 0.3755 0.3730 0.655 88675. 4702.6 0.0027 0.234 1.006 0.603 0.091 25 0.3751 0.3727 0.655 88668. 4702.6 0.0027 0.232 0.999 0.599 0.090 26 0.3747 0.3722 0.656 88671. 4703.1 0.0027 0.229 0.994 0.596 0.090 27 0.3742 0.3720 0.656 88671. 4703.6 0.0026 0.227 0.988 0.592 0.090 28 0.3738 0.3719 0.656 88659. 4703.4 0.0026 0.225 0.982 0.589 0.089 29 0.3735 0.3717 0.657 88646. 4703.2 0.0026 0.224 0.977 0.586 0.089 30 0.3732 0.3714 0.657 88634. 4702.9 0.0025 0.222 0.972 0.582 0.088 $$ Output MTZ file from Refmac for model 5v8g_A1_PHR_CH_s0.57_r2-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\chainsaw\mr\molrep\refine\refmac_molrep_HKLOUT_5v8g_A1_PHR_CH_s0.57_r2-123.mtz Output PDB file from Refmac for model 5v8g_A1_PHR_CH_s0.57_r2-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\chainsaw\mr\molrep\refine\refmac_molrep_5v8g_A1_PHR_CH_s0.57_r2-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 37 MR programs being used: MOLREP PHASER Best search model so far: 5v92_B1_PHR_MO_s0.56_r2-123 using MOLREP Initial Rfree: 0.466 Final Rfree: 0.370 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 PHASER MARGINAL 1567.00 41.40 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 662.00 28.50 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 37: 5v8g_A1_PHR_CH_s0.57_r2-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\chainsaw Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\CHAINSAW_5v8g_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.57 Search model type: CHNSAW Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\chainsaw\mr\phaser\phaser_5v8g_A1_PHR_CH_s0.57_r2-123.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\chainsaw\mr\phaser\phaser_5v8g_A1_PHR_CH_s0.57_r2-123.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\chainsaw\mr\phaser\phaser_5v8g_A1_PHR_CH_s0.57_r2-123.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\chainsaw\mr\phaser\refine\refmac_phaser_HKLOUT_5v8g_A1_PHR_CH_s0.57_r2-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\chainsaw\mr\phaser\refine\refmac_phaser_5v8g_A1_PHR_CH_s0.57_r2-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\chainsaw\mr\phaser\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\chainsaw\mr\phaser\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '5v8g_A1_PHR_CH_s0.57_r2-123' ######################################################################### ###################################################################### ##### Results from Phaser for 5v8g_A1_PHR_CH_s0.57_r2-123: ##### ###################################################################### Template Model: 5v8g_A1_PHR_CH_s0.57_r2-123 has produced a marginal solution, final Rfree = 0.371 Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\chainsaw\mr\phaser\phaser_5v8g_A1_PHR_CH_s0.57_r2-123.log Phaser PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\chainsaw\mr\phaser\phaser_5v8g_A1_PHR_CH_s0.57_r2-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\chainsaw\mr\phaser\refine\refmac_phaser_5v8g_A1_PHR_CH_s0.57_r2-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\chainsaw\mr\phaser\refine\refmac_phaser_5v8g_A1_PHR_CH_s0.57_r2-123.pdb #################################################################################################### ##### Refinement results from Refmac for 5v8g_A1_PHR_CH_s0.57_r2-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 5v8g_A1_PHR_CH_s0.57_r2-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4303 0.4304 0.574 91179. 4811.8 0.0198 1.723 1.932 1.211 0.126 1 0.4231 0.4250 0.570 90952. 4804.2 0.0060 0.542 1.649 1.010 0.105 2 0.4190 0.4205 0.574 90814. 4798.4 0.0052 0.464 1.545 0.944 0.101 3 0.4154 0.4154 0.579 90621. 4789.1 0.0047 0.416 1.466 0.896 0.099 4 0.4099 0.4076 0.587 90372. 4777.1 0.0042 0.369 1.371 0.838 0.098 5 0.4048 0.4018 0.597 90181. 4767.5 0.0040 0.344 1.310 0.800 0.097 6 0.3998 0.3968 0.608 89932. 4755.5 0.0039 0.332 1.266 0.774 0.097 7 0.3978 0.3948 0.612 89856. 4752.3 0.0037 0.314 1.226 0.750 0.097 8 0.3957 0.3931 0.616 89733. 4746.5 0.0036 0.303 1.195 0.731 0.096 9 0.3933 0.3891 0.621 89531. 4736.1 0.0035 0.296 1.171 0.716 0.096 10 0.3912 0.3852 0.627 89375. 4728.6 0.0034 0.290 1.152 0.704 0.096 11 0.3890 0.3831 0.632 89255. 4722.9 0.0034 0.286 1.136 0.693 0.096 12 0.3869 0.3815 0.635 89186. 4720.4 0.0034 0.284 1.123 0.684 0.096 13 0.3848 0.3797 0.639 89070. 4716.0 0.0034 0.284 1.111 0.675 0.096 14 0.3839 0.3789 0.640 89033. 4715.0 0.0033 0.275 1.094 0.664 0.095 15 0.3828 0.3778 0.642 89016. 4715.1 0.0032 0.270 1.081 0.655 0.095 16 0.3818 0.3773 0.643 88990. 4714.7 0.0031 0.266 1.071 0.648 0.095 17 0.3810 0.3774 0.643 88966. 4715.1 0.0031 0.262 1.061 0.642 0.094 18 0.3799 0.3763 0.644 88928. 4713.8 0.0030 0.259 1.054 0.636 0.094 19 0.3790 0.3756 0.647 88857. 4710.8 0.0030 0.257 1.047 0.631 0.094 20 0.3780 0.3749 0.650 88815. 4709.5 0.0030 0.255 1.040 0.627 0.093 21 0.3774 0.3747 0.651 88802. 4709.2 0.0029 0.248 1.030 0.620 0.093 22 0.3768 0.3743 0.652 88787. 4708.9 0.0028 0.244 1.022 0.615 0.093 23 0.3763 0.3740 0.654 88772. 4708.3 0.0028 0.241 1.015 0.610 0.092 24 0.3758 0.3736 0.654 88753. 4707.7 0.0028 0.238 1.008 0.606 0.092 25 0.3752 0.3723 0.655 88730. 4705.7 0.0027 0.235 1.002 0.602 0.091 26 0.3748 0.3723 0.656 88723. 4706.0 0.0027 0.233 0.996 0.598 0.091 27 0.3743 0.3720 0.657 88708. 4705.5 0.0027 0.230 0.990 0.594 0.090 28 0.3739 0.3718 0.657 88689. 4705.0 0.0026 0.228 0.984 0.591 0.090 29 0.3736 0.3718 0.657 88678. 4704.8 0.0026 0.226 0.979 0.587 0.089 30 0.3733 0.3715 0.658 88669. 4704.5 0.0026 0.223 0.973 0.584 0.089 $$ Output MTZ file from Refmac for model 5v8g_A1_PHR_CH_s0.57_r2-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\chainsaw\mr\molrep\refine\refmac_molrep_HKLOUT_5v8g_A1_PHR_CH_s0.57_r2-123.mtz Output PDB file from Refmac for model 5v8g_A1_PHR_CH_s0.57_r2-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v8g_A1_PHR\chainsaw\mr\molrep\refine\refmac_molrep_5v8g_A1_PHR_CH_s0.57_r2-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 38 MR programs being used: MOLREP PHASER Best search model so far: 5v92_B1_PHR_MO_s0.56_r2-123 using MOLREP Initial Rfree: 0.466 Final Rfree: 0.370 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 PHASER MARGINAL 1571.00 42.20 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 PHASER MARGINAL 1567.00 41.40 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 662.00 28.50 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 38: 1i22_D1_PHR_CH_s0.56_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\chainsaw Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\CHAINSAW_1i22_D1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.56 Search model type: CHNSAW Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\chainsaw\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\chainsaw\mr\molrep\refine\refmac_molrep_HKLOUT_1i22_D1_PHR_CH_s0.56_r1-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\chainsaw\mr\molrep\refine\refmac_molrep_1i22_D1_PHR_CH_s0.56_r1-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\chainsaw\mr\molrep\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\chainsaw\mr\molrep\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1i22_D1_PHR_CH_s0.56_r1-123' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 1i22_D1_PHR_CH_s0.56_r1-123: ##### ################################################################################################# Template Model: 1i22_D1_PHR_CH_s0.56_r1-123 has produced a marginal solution, final Rfree = 0.397 Molrep log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\chainsaw\mr\molrep\molrep.log Molrep PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\chainsaw\mr\molrep\molrep_1i22_D1_PHR_CH_s0.56_r1-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\chainsaw\mr\molrep\refine\refmac_molrep_1i22_D1_PHR_CH_s0.56_r1-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\chainsaw\mr\molrep\refine\refmac_molrep_1i22_D1_PHR_CH_s0.56_r1-123.pdb #################################################################################################### ##### Refinement results from Refmac for 1i22_D1_PHR_CH_s0.56_r1-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1i22_D1_PHR_CH_s0.56_r1-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4927 0.4844 0.422 93483. 4941.8 0.0246 2.156 3.348 2.075 0.226 1 0.4661 0.4574 0.449 92627. 4905.3 0.0105 0.926 2.611 1.558 0.162 2 0.4515 0.4435 0.483 91811. 4863.6 0.0086 0.737 2.321 1.363 0.143 3 0.4417 0.4326 0.508 91335. 4838.8 0.0076 0.643 2.133 1.242 0.131 4 0.4391 0.4290 0.517 91115. 4827.4 0.0066 0.554 1.994 1.150 0.124 5 0.4358 0.4265 0.525 90959. 4819.8 0.0059 0.502 1.884 1.079 0.119 6 0.4330 0.4247 0.530 90872. 4815.3 0.0055 0.463 1.797 1.024 0.115 7 0.4307 0.4230 0.535 90807. 4813.1 0.0051 0.433 1.727 0.980 0.112 8 0.4278 0.4209 0.540 90783. 4811.8 0.0049 0.411 1.667 0.944 0.110 9 0.4246 0.4194 0.548 90773. 4811.8 0.0047 0.395 1.621 0.915 0.108 10 0.4212 0.4153 0.556 90638. 4804.9 0.0046 0.384 1.587 0.895 0.108 11 0.4198 0.4142 0.560 90589. 4802.4 0.0043 0.358 1.545 0.868 0.107 12 0.4183 0.4129 0.563 90530. 4800.3 0.0041 0.343 1.508 0.845 0.106 13 0.4167 0.4111 0.565 90483. 4797.6 0.0039 0.329 1.476 0.826 0.105 14 0.4152 0.4093 0.570 90447. 4795.8 0.0038 0.319 1.448 0.809 0.105 15 0.4136 0.4076 0.573 90436. 4796.0 0.0037 0.312 1.424 0.795 0.104 16 0.4120 0.4057 0.578 90391. 4793.2 0.0037 0.309 1.402 0.783 0.104 17 0.4106 0.4038 0.582 90370. 4792.1 0.0037 0.305 1.383 0.772 0.103 18 0.4097 0.4030 0.585 90345. 4790.9 0.0035 0.295 1.360 0.759 0.102 19 0.4089 0.4021 0.588 90313. 4789.2 0.0035 0.288 1.341 0.747 0.101 20 0.4080 0.4012 0.590 90319. 4789.9 0.0034 0.283 1.324 0.738 0.101 21 0.4070 0.4002 0.592 90290. 4788.7 0.0033 0.278 1.310 0.729 0.100 22 0.4062 0.3997 0.595 90285. 4788.6 0.0033 0.274 1.296 0.721 0.100 23 0.4052 0.3988 0.597 90257. 4787.0 0.0032 0.271 1.284 0.714 0.099 24 0.4043 0.3982 0.599 90218. 4785.4 0.0032 0.267 1.273 0.708 0.098 25 0.4037 0.3979 0.600 90194. 4784.2 0.0031 0.262 1.260 0.700 0.098 26 0.4030 0.3975 0.602 90173. 4783.3 0.0031 0.258 1.249 0.692 0.097 27 0.4023 0.3976 0.603 90169. 4783.8 0.0030 0.255 1.238 0.686 0.097 28 0.4017 0.3975 0.605 90163. 4783.8 0.0030 0.252 1.228 0.680 0.096 29 0.4010 0.3973 0.606 90145. 4783.1 0.0030 0.249 1.219 0.674 0.096 30 0.4004 0.3969 0.606 90121. 4782.0 0.0029 0.246 1.212 0.670 0.095 $$ Output MTZ file from Refmac for model 1i22_D1_PHR_CH_s0.56_r1-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\chainsaw\mr\molrep\refine\refmac_molrep_HKLOUT_1i22_D1_PHR_CH_s0.56_r1-123.mtz Output PDB file from Refmac for model 1i22_D1_PHR_CH_s0.56_r1-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\chainsaw\mr\molrep\refine\refmac_molrep_1i22_D1_PHR_CH_s0.56_r1-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 39 MR programs being used: MOLREP PHASER Best search model so far: 5v92_B1_PHR_MO_s0.56_r2-123 using MOLREP Initial Rfree: 0.466 Final Rfree: 0.370 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 PHASER MARGINAL 1571.00 42.20 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 PHASER MARGINAL 1567.00 41.40 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 MOLREP MARGINAL -- -- 0.40 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 662.00 28.50 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 39: 1i22_D1_PHR_CH_s0.56_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\chainsaw Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\CHAINSAW_1i22_D1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.56 Search model type: CHNSAW Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\chainsaw\mr\phaser\phaser_1i22_D1_PHR_CH_s0.56_r1-123.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\chainsaw\mr\phaser\phaser_1i22_D1_PHR_CH_s0.56_r1-123.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\chainsaw\mr\phaser\phaser_1i22_D1_PHR_CH_s0.56_r1-123.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\chainsaw\mr\phaser\refine\refmac_phaser_HKLOUT_1i22_D1_PHR_CH_s0.56_r1-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\chainsaw\mr\phaser\refine\refmac_phaser_1i22_D1_PHR_CH_s0.56_r1-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\chainsaw\mr\phaser\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\chainsaw\mr\phaser\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1i22_D1_PHR_CH_s0.56_r1-123' ######################################################################### ###################################################################### ##### Results from Phaser for 1i22_D1_PHR_CH_s0.56_r1-123: ##### ###################################################################### Template Model: 1i22_D1_PHR_CH_s0.56_r1-123 has produced a marginal solution, final Rfree = 0.398 Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\chainsaw\mr\phaser\phaser_1i22_D1_PHR_CH_s0.56_r1-123.log Phaser PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\chainsaw\mr\phaser\phaser_1i22_D1_PHR_CH_s0.56_r1-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\chainsaw\mr\phaser\refine\refmac_phaser_1i22_D1_PHR_CH_s0.56_r1-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\chainsaw\mr\phaser\refine\refmac_phaser_1i22_D1_PHR_CH_s0.56_r1-123.pdb #################################################################################################### ##### Refinement results from Refmac for 1i22_D1_PHR_CH_s0.56_r1-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1i22_D1_PHR_CH_s0.56_r1-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4832 0.4689 0.460 92379. 4880.2 0.0246 2.154 3.349 2.076 0.226 1 0.4758 0.4639 0.452 92475. 4887.1 0.0162 1.444 2.957 1.808 0.189 2 0.4689 0.4563 0.457 92432. 4887.9 0.0111 0.995 2.639 1.591 0.161 3 0.4631 0.4506 0.467 92186. 4876.5 0.0090 0.800 2.427 1.448 0.146 4 0.4552 0.4419 0.483 91727. 4854.5 0.0076 0.657 2.187 1.288 0.131 5 0.4490 0.4362 0.495 91461. 4841.5 0.0069 0.585 2.019 1.179 0.122 6 0.4418 0.4301 0.507 91127. 4824.5 0.0064 0.536 1.903 1.104 0.117 7 0.4353 0.4247 0.522 90833. 4810.0 0.0061 0.506 1.825 1.054 0.113 8 0.4328 0.4229 0.527 90895. 4814.4 0.0055 0.458 1.743 1.001 0.109 9 0.4301 0.4209 0.534 90833. 4811.2 0.0051 0.426 1.677 0.959 0.108 10 0.4277 0.4191 0.543 90782. 4809.0 0.0048 0.403 1.624 0.926 0.106 11 0.4249 0.4165 0.548 90671. 4803.3 0.0046 0.384 1.580 0.899 0.105 12 0.4221 0.4144 0.554 90595. 4799.8 0.0045 0.371 1.545 0.876 0.105 13 0.4195 0.4122 0.560 90524. 4797.4 0.0043 0.359 1.517 0.859 0.104 14 0.4186 0.4109 0.565 90512. 4797.1 0.0041 0.342 1.478 0.836 0.103 15 0.4171 0.4095 0.569 90532. 4798.7 0.0040 0.329 1.444 0.816 0.102 16 0.4157 0.4081 0.572 90498. 4797.1 0.0039 0.319 1.417 0.800 0.102 17 0.4142 0.4065 0.576 90460. 4795.2 0.0038 0.312 1.391 0.786 0.101 18 0.4128 0.4049 0.580 90433. 4794.5 0.0037 0.305 1.369 0.774 0.101 19 0.4113 0.4037 0.582 90400. 4793.1 0.0036 0.299 1.350 0.763 0.100 20 0.4100 0.4029 0.585 90367. 4791.3 0.0036 0.295 1.333 0.754 0.099 21 0.4091 0.4021 0.588 90394. 4793.2 0.0035 0.288 1.313 0.742 0.099 22 0.4081 0.4012 0.589 90375. 4792.4 0.0034 0.282 1.297 0.732 0.098 23 0.4071 0.4006 0.590 90347. 4791.2 0.0033 0.278 1.282 0.724 0.097 24 0.4062 0.4000 0.592 90336. 4791.0 0.0033 0.275 1.270 0.716 0.097 25 0.4053 0.3994 0.596 90324. 4790.1 0.0032 0.271 1.259 0.710 0.096 26 0.4045 0.3991 0.599 90314. 4790.3 0.0032 0.267 1.247 0.702 0.096 27 0.4035 0.3985 0.600 90270. 4788.5 0.0032 0.264 1.237 0.696 0.095 28 0.4028 0.3982 0.601 90240. 4787.2 0.0031 0.259 1.225 0.689 0.095 29 0.4021 0.3980 0.602 90217. 4786.4 0.0030 0.255 1.215 0.682 0.094 30 0.4013 0.3977 0.603 90192. 4785.8 0.0030 0.252 1.206 0.677 0.094 $$ Output MTZ file from Refmac for model 1i22_D1_PHR_CH_s0.56_r1-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\chainsaw\mr\molrep\refine\refmac_molrep_HKLOUT_1i22_D1_PHR_CH_s0.56_r1-123.mtz Output PDB file from Refmac for model 1i22_D1_PHR_CH_s0.56_r1-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1i22_D1_PHR\chainsaw\mr\molrep\refine\refmac_molrep_1i22_D1_PHR_CH_s0.56_r1-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 40 MR programs being used: MOLREP PHASER Best search model so far: 5v92_B1_PHR_MO_s0.56_r2-123 using MOLREP Initial Rfree: 0.466 Final Rfree: 0.370 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 PHASER MARGINAL 1571.00 42.20 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 PHASER MARGINAL 1567.00 41.40 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 MOLREP MARGINAL -- -- 0.40 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 PHASER MARGINAL 558.00 27.80 0.40 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 662.00 28.50 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 40: 2ihl_A1_PHR_MO_s0.56_r4-121 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2ihl_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_2ihl_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.56 Search model type: MOLREP Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2ihl_A1_PHR\molrep\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2ihl_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_2ihl_A1_PHR_MO_s0.56_r4-121.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2ihl_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_2ihl_A1_PHR_MO_s0.56_r4-121.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2ihl_A1_PHR\molrep\mr\molrep\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2ihl_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '2ihl_A1_PHR_MO_s0.56_r4-121' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 2ihl_A1_PHR_MO_s0.56_r4-121: ##### ################################################################################################# Template Model: 2ihl_A1_PHR_MO_s0.56_r4-121 has produced a marginal solution, final Rfree = 0.382 Molrep log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2ihl_A1_PHR\molrep\mr\molrep\molrep.log Molrep PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2ihl_A1_PHR\molrep\mr\molrep\molrep_2ihl_A1_PHR_MO_s0.56_r4-121.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2ihl_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_2ihl_A1_PHR_MO_s0.56_r4-121.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2ihl_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_2ihl_A1_PHR_MO_s0.56_r4-121.pdb #################################################################################################### ##### Refinement results from Refmac for 2ihl_A1_PHR_MO_s0.56_r4-121: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 2ihl_A1_PHR_MO_s0.56_r4-121: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4581 0.4630 0.493 92022. 4857.7 0.0388 3.105 3.217 1.962 0.139 1 0.4283 0.4433 0.525 91098. 4823.5 0.0101 0.775 1.952 1.166 0.104 2 0.4143 0.4285 0.556 90458. 4792.0 0.0069 0.544 1.710 1.007 0.104 3 0.4061 0.4202 0.579 90086. 4772.2 0.0059 0.456 1.600 0.938 0.102 4 0.4011 0.4155 0.593 89898. 4762.7 0.0053 0.415 1.521 0.891 0.099 5 0.3977 0.4114 0.603 89746. 4754.7 0.0049 0.387 1.462 0.856 0.096 6 0.3949 0.4084 0.609 89653. 4749.7 0.0046 0.366 1.415 0.829 0.094 7 0.3927 0.4049 0.616 89597. 4746.2 0.0044 0.348 1.375 0.805 0.093 8 0.3908 0.4023 0.622 89523. 4742.6 0.0042 0.333 1.340 0.784 0.092 9 0.3893 0.4001 0.625 89445. 4738.8 0.0040 0.320 1.311 0.767 0.091 10 0.3879 0.3984 0.627 89431. 4738.2 0.0038 0.310 1.285 0.751 0.090 11 0.3868 0.3968 0.630 89461. 4740.3 0.0037 0.300 1.261 0.736 0.089 12 0.3866 0.3952 0.632 89485. 4741.9 0.0036 0.291 1.238 0.722 0.088 13 0.3858 0.3937 0.634 89471. 4741.8 0.0035 0.285 1.218 0.710 0.087 14 0.3850 0.3927 0.635 89470. 4742.3 0.0034 0.278 1.202 0.700 0.086 15 0.3841 0.3912 0.637 89450. 4741.9 0.0034 0.274 1.187 0.691 0.086 16 0.3833 0.3900 0.638 89424. 4740.6 0.0033 0.267 1.175 0.682 0.085 17 0.3827 0.3890 0.640 89414. 4740.5 0.0032 0.262 1.162 0.674 0.085 18 0.3821 0.3882 0.640 89416. 4741.1 0.0032 0.257 1.150 0.667 0.084 19 0.3816 0.3875 0.641 89406. 4741.0 0.0031 0.253 1.137 0.659 0.084 20 0.3812 0.3869 0.642 89397. 4740.9 0.0031 0.250 1.126 0.652 0.083 21 0.3808 0.3861 0.642 89372. 4740.1 0.0030 0.247 1.116 0.646 0.083 22 0.3803 0.3855 0.642 89347. 4739.3 0.0030 0.244 1.106 0.641 0.082 23 0.3799 0.3848 0.643 89328. 4738.6 0.0029 0.242 1.098 0.635 0.082 24 0.3795 0.3842 0.643 89301. 4737.9 0.0029 0.239 1.090 0.630 0.081 25 0.3791 0.3838 0.643 89281. 4737.3 0.0029 0.237 1.083 0.626 0.081 26 0.3788 0.3832 0.644 89254. 4736.2 0.0028 0.234 1.076 0.622 0.081 27 0.3785 0.3829 0.645 89236. 4735.7 0.0028 0.233 1.070 0.617 0.080 28 0.3781 0.3824 0.646 89207. 4734.4 0.0028 0.231 1.064 0.613 0.080 29 0.3779 0.3821 0.646 89192. 4733.9 0.0028 0.229 1.058 0.610 0.080 30 0.3777 0.3819 0.646 89167. 4732.7 0.0028 0.228 1.054 0.607 0.080 $$ Output MTZ file from Refmac for model 2ihl_A1_PHR_MO_s0.56_r4-121 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2ihl_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_2ihl_A1_PHR_MO_s0.56_r4-121.mtz Output PDB file from Refmac for model 2ihl_A1_PHR_MO_s0.56_r4-121: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2ihl_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_2ihl_A1_PHR_MO_s0.56_r4-121.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 41 MR programs being used: MOLREP PHASER Best search model so far: 5v92_B1_PHR_MO_s0.56_r2-123 using MOLREP Initial Rfree: 0.466 Final Rfree: 0.370 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 PHASER MARGINAL 1571.00 42.20 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 PHASER MARGINAL 1567.00 41.40 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 MOLREP MARGINAL -- -- 0.40 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 PHASER MARGINAL 558.00 27.80 0.40 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 662.00 28.50 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 41: 2ihl_A1_PHR_MO_s0.56_r4-121 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2ihl_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_2ihl_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.56 Search model type: MOLREP Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2ihl_A1_PHR\molrep\mr\phaser\phaser_2ihl_A1_PHR_MO_s0.56_r4-121.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2ihl_A1_PHR\molrep\mr\phaser\phaser_2ihl_A1_PHR_MO_s0.56_r4-121.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2ihl_A1_PHR\molrep\mr\phaser\phaser_2ihl_A1_PHR_MO_s0.56_r4-121.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2ihl_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_HKLOUT_2ihl_A1_PHR_MO_s0.56_r4-121.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2ihl_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_2ihl_A1_PHR_MO_s0.56_r4-121.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2ihl_A1_PHR\molrep\mr\phaser\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2ihl_A1_PHR\molrep\mr\phaser\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '2ihl_A1_PHR_MO_s0.56_r4-121' ######################################################################### ###################################################################### ##### Results from Phaser for 2ihl_A1_PHR_MO_s0.56_r4-121: ##### ###################################################################### Template Model: 2ihl_A1_PHR_MO_s0.56_r4-121 has produced a marginal solution, final Rfree = 0.382 Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2ihl_A1_PHR\molrep\mr\phaser\phaser_2ihl_A1_PHR_MO_s0.56_r4-121.log Phaser PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2ihl_A1_PHR\molrep\mr\phaser\phaser_2ihl_A1_PHR_MO_s0.56_r4-121.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2ihl_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_2ihl_A1_PHR_MO_s0.56_r4-121.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2ihl_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_2ihl_A1_PHR_MO_s0.56_r4-121.pdb #################################################################################################### ##### Refinement results from Refmac for 2ihl_A1_PHR_MO_s0.56_r4-121: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 2ihl_A1_PHR_MO_s0.56_r4-121: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4506 0.4530 0.515 91604. 4840.7 0.0387 3.103 3.218 1.962 0.139 1 0.4283 0.4387 0.535 91073. 4822.1 0.0103 0.788 1.935 1.158 0.104 2 0.4129 0.4269 0.561 90406. 4790.7 0.0068 0.529 1.694 1.000 0.104 3 0.4052 0.4202 0.578 90115. 4774.8 0.0058 0.453 1.583 0.929 0.102 4 0.4005 0.4154 0.594 89909. 4763.8 0.0053 0.414 1.508 0.885 0.098 5 0.3973 0.4124 0.606 89720. 4753.3 0.0049 0.386 1.452 0.852 0.096 6 0.3947 0.4095 0.612 89620. 4748.0 0.0046 0.363 1.405 0.824 0.094 7 0.3925 0.4063 0.617 89511. 4742.0 0.0043 0.346 1.366 0.800 0.093 8 0.3908 0.4038 0.622 89450. 4738.6 0.0041 0.332 1.333 0.780 0.091 9 0.3892 0.4017 0.624 89424. 4737.5 0.0040 0.320 1.304 0.763 0.090 10 0.3879 0.4002 0.627 89387. 4736.0 0.0038 0.309 1.279 0.747 0.089 11 0.3869 0.3985 0.629 89403. 4736.5 0.0037 0.300 1.257 0.734 0.088 12 0.3860 0.3972 0.631 89430. 4738.4 0.0036 0.292 1.236 0.721 0.087 13 0.3851 0.3959 0.633 89414. 4738.3 0.0035 0.284 1.216 0.709 0.086 14 0.3842 0.3941 0.635 89414. 4738.6 0.0034 0.279 1.198 0.698 0.085 15 0.3840 0.3919 0.636 89419. 4739.0 0.0034 0.274 1.185 0.689 0.085 16 0.3833 0.3909 0.638 89407. 4739.1 0.0033 0.268 1.172 0.681 0.084 17 0.3827 0.3900 0.639 89409. 4739.7 0.0032 0.262 1.159 0.673 0.083 18 0.3821 0.3890 0.640 89389. 4738.7 0.0032 0.258 1.146 0.665 0.083 19 0.3816 0.3883 0.641 89415. 4741.0 0.0031 0.254 1.134 0.658 0.082 20 0.3812 0.3877 0.642 89408. 4741.1 0.0031 0.250 1.122 0.651 0.082 21 0.3807 0.3869 0.642 89390. 4740.7 0.0030 0.247 1.112 0.645 0.082 22 0.3803 0.3863 0.643 89371. 4740.1 0.0030 0.244 1.103 0.639 0.081 23 0.3799 0.3857 0.643 89348. 4739.3 0.0029 0.241 1.094 0.634 0.081 24 0.3796 0.3851 0.644 89329. 4739.0 0.0029 0.239 1.086 0.629 0.080 25 0.3792 0.3843 0.645 89301. 4737.8 0.0029 0.237 1.080 0.624 0.080 26 0.3788 0.3838 0.645 89278. 4737.1 0.0028 0.235 1.073 0.620 0.080 27 0.3785 0.3832 0.645 89262. 4736.6 0.0028 0.233 1.067 0.616 0.079 28 0.3783 0.3827 0.647 89222. 4734.7 0.0028 0.231 1.060 0.612 0.079 29 0.3779 0.3822 0.647 89194. 4733.7 0.0028 0.230 1.054 0.608 0.079 30 0.3777 0.3820 0.647 89187. 4733.8 0.0028 0.228 1.049 0.605 0.078 $$ Output MTZ file from Refmac for model 2ihl_A1_PHR_MO_s0.56_r4-121 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2ihl_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_2ihl_A1_PHR_MO_s0.56_r4-121.mtz Output PDB file from Refmac for model 2ihl_A1_PHR_MO_s0.56_r4-121: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2ihl_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_2ihl_A1_PHR_MO_s0.56_r4-121.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 42 MR programs being used: MOLREP PHASER Best search model so far: 5v92_B1_PHR_MO_s0.56_r2-123 using MOLREP Initial Rfree: 0.466 Final Rfree: 0.370 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_5v92_B1_PHR_MO_s0.56_r2-123.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\refine\refmac_molrep_5v92_B1_PHR_MO_s0.56_r2-123.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\5v92_B1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_5v92_B1_PHR_MO_s0.56_r2-123.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 PHASER MARGINAL 1571.00 42.20 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 PHASER MARGINAL 1567.00 41.40 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 PHASER MARGINAL 1083.00 38.10 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 MOLREP MARGINAL -- -- 0.40 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 PHASER MARGINAL 558.00 27.80 0.40 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 662.00 28.50 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 42: 1lze_A1_PHR_MO_s0.55_r2-121 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1lze_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.55 Search model type: MOLREP Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1lze_A1_PHR_MO_s0.55_r2-121.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1lze_A1_PHR_MO_s0.55_r2-121.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1lze_A1_PHR_MO_s0.55_r2-121' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 1lze_A1_PHR_MO_s0.55_r2-121: ##### ################################################################################################# Template Model: 1lze_A1_PHR_MO_s0.55_r2-121 has produced a marginal solution, final Rfree = 0.366 Molrep log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\molrep.log Molrep PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\molrep_1lze_A1_PHR_MO_s0.55_r2-121.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1lze_A1_PHR_MO_s0.55_r2-121.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1lze_A1_PHR_MO_s0.55_r2-121.pdb #################################################################################################### ##### Refinement results from Refmac for 1lze_A1_PHR_MO_s0.55_r2-121: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1lze_A1_PHR_MO_s0.55_r2-121: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4010 0.4051 0.608 90378. 4787.5 0.0377 2.930 3.225 1.985 0.283 1 0.3791 0.3866 0.635 89420. 4744.0 0.0093 0.718 2.177 1.332 0.207 2 0.3719 0.3792 0.650 89084. 4724.8 0.0065 0.518 1.889 1.146 0.175 3 0.3675 0.3761 0.660 88842. 4712.6 0.0055 0.447 1.727 1.043 0.151 4 0.3648 0.3736 0.667 88676. 4705.2 0.0049 0.403 1.614 0.971 0.135 5 0.3629 0.3721 0.671 88593. 4701.8 0.0045 0.371 1.523 0.914 0.120 6 0.3614 0.3714 0.673 88532. 4700.0 0.0042 0.346 1.451 0.869 0.109 7 0.3603 0.3708 0.674 88493. 4698.7 0.0039 0.326 1.394 0.834 0.104 8 0.3593 0.3703 0.675 88447. 4697.4 0.0037 0.309 1.347 0.804 0.101 9 0.3584 0.3699 0.677 88403. 4696.0 0.0035 0.295 1.306 0.778 0.098 10 0.3577 0.3693 0.677 88380. 4695.7 0.0034 0.283 1.269 0.756 0.096 11 0.3571 0.3688 0.678 88357. 4695.2 0.0033 0.273 1.238 0.736 0.094 12 0.3565 0.3682 0.678 88333. 4694.7 0.0032 0.264 1.210 0.720 0.093 13 0.3560 0.3679 0.679 88310. 4694.3 0.0030 0.256 1.187 0.705 0.092 14 0.3555 0.3675 0.680 88293. 4693.7 0.0030 0.249 1.165 0.692 0.091 15 0.3551 0.3675 0.681 88276. 4693.4 0.0029 0.243 1.146 0.679 0.090 16 0.3546 0.3671 0.682 88250. 4692.5 0.0028 0.237 1.129 0.669 0.089 17 0.3542 0.3669 0.683 88234. 4692.1 0.0027 0.233 1.114 0.659 0.088 18 0.3538 0.3667 0.684 88212. 4691.4 0.0027 0.229 1.100 0.650 0.088 19 0.3534 0.3665 0.684 88200. 4691.1 0.0027 0.225 1.087 0.642 0.087 20 0.3532 0.3665 0.684 88191. 4690.8 0.0026 0.223 1.080 0.637 0.087 21 0.3530 0.3665 0.685 88175. 4690.4 0.0026 0.221 1.073 0.633 0.086 22 0.3527 0.3663 0.685 88157. 4689.7 0.0026 0.218 1.062 0.626 0.086 23 0.3524 0.3661 0.685 88133. 4688.7 0.0025 0.216 1.052 0.620 0.085 24 0.3522 0.3660 0.686 88106. 4687.6 0.0025 0.213 1.043 0.614 0.085 25 0.3519 0.3661 0.686 88095. 4687.5 0.0025 0.211 1.034 0.609 0.084 26 0.3518 0.3661 0.686 88095. 4687.8 0.0024 0.210 1.029 0.605 0.084 27 0.3516 0.3660 0.686 88088. 4687.7 0.0024 0.208 1.024 0.602 0.084 28 0.3514 0.3659 0.686 88079. 4687.5 0.0024 0.207 1.017 0.598 0.083 29 0.3513 0.3658 0.686 88076. 4687.5 0.0024 0.206 1.012 0.595 0.083 30 0.3512 0.3657 0.687 88069. 4687.3 0.0024 0.205 1.008 0.592 0.083 $$ Output MTZ file from Refmac for model 1lze_A1_PHR_MO_s0.55_r2-121 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1lze_A1_PHR_MO_s0.55_r2-121.mtz Output PDB file from Refmac for model 1lze_A1_PHR_MO_s0.55_r2-121: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1lze_A1_PHR_MO_s0.55_r2-121.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 43 MR programs being used: MOLREP PHASER Best search model so far: 1lze_A1_PHR_MO_s0.55_r2-121 using MOLREP Initial Rfree: 0.401 Final Rfree: 0.366 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1lze_A1_PHR_MO_s0.55_r2-121.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1lze_A1_PHR_MO_s0.55_r2-121.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1lze_A1_PHR_MO_s0.55_r2-121.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_1lze_A1_PHR_MO_s0.55_r2-121.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 1lze_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 PHASER MARGINAL 1571.00 42.20 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 PHASER MARGINAL 1567.00 41.40 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 PHASER MARGINAL 1083.00 38.10 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 MOLREP MARGINAL -- -- 0.40 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 PHASER MARGINAL 558.00 27.80 0.40 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 662.00 28.50 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 43: 1lze_A1_PHR_MO_s0.55_r2-121 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1lze_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.55 Search model type: MOLREP Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\phaser\phaser_1lze_A1_PHR_MO_s0.55_r2-121.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\phaser\phaser_1lze_A1_PHR_MO_s0.55_r2-121.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\phaser\phaser_1lze_A1_PHR_MO_s0.55_r2-121.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_HKLOUT_1lze_A1_PHR_MO_s0.55_r2-121.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1lze_A1_PHR_MO_s0.55_r2-121.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\phaser\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\phaser\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1lze_A1_PHR_MO_s0.55_r2-121' ######################################################################### ###################################################################### ##### Results from Phaser for 1lze_A1_PHR_MO_s0.55_r2-121: ##### ###################################################################### Template Model: 1lze_A1_PHR_MO_s0.55_r2-121 has produced a marginal solution, final Rfree = 0.366 Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\phaser\phaser_1lze_A1_PHR_MO_s0.55_r2-121.log Phaser PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\phaser\phaser_1lze_A1_PHR_MO_s0.55_r2-121.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1lze_A1_PHR_MO_s0.55_r2-121.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1lze_A1_PHR_MO_s0.55_r2-121.pdb #################################################################################################### ##### Refinement results from Refmac for 1lze_A1_PHR_MO_s0.55_r2-121: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1lze_A1_PHR_MO_s0.55_r2-121: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.3893 0.3992 0.638 89563. 4738.0 0.0377 2.931 3.224 1.984 0.282 1 0.3850 0.3947 0.640 89531. 4743.5 0.0099 0.748 2.235 1.374 0.225 2 0.3805 0.3865 0.644 89303. 4732.8 0.0066 0.525 1.936 1.182 0.193 3 0.3776 0.3843 0.647 89189. 4728.0 0.0056 0.451 1.761 1.070 0.167 4 0.3746 0.3821 0.651 89051. 4721.8 0.0050 0.407 1.639 0.993 0.148 5 0.3717 0.3796 0.657 88922. 4715.8 0.0046 0.375 1.544 0.932 0.128 6 0.3688 0.3777 0.662 88786. 4710.3 0.0042 0.351 1.467 0.883 0.112 7 0.3655 0.3752 0.666 88638. 4703.9 0.0040 0.333 1.408 0.846 0.106 8 0.3629 0.3733 0.670 88538. 4699.9 0.0038 0.319 1.360 0.816 0.102 9 0.3611 0.3719 0.674 88440. 4695.9 0.0036 0.304 1.319 0.790 0.100 10 0.3597 0.3707 0.676 88383. 4694.5 0.0035 0.291 1.283 0.767 0.097 11 0.3586 0.3703 0.677 88357. 4694.2 0.0034 0.280 1.250 0.746 0.095 12 0.3578 0.3697 0.679 88326. 4693.7 0.0032 0.270 1.221 0.728 0.094 13 0.3570 0.3694 0.680 88311. 4693.7 0.0031 0.261 1.196 0.712 0.093 14 0.3564 0.3687 0.681 88302. 4693.8 0.0030 0.254 1.173 0.698 0.091 15 0.3559 0.3682 0.681 88276. 4693.1 0.0029 0.247 1.153 0.686 0.090 16 0.3553 0.3678 0.681 88247. 4692.1 0.0029 0.241 1.135 0.674 0.089 17 0.3549 0.3677 0.682 88235. 4691.7 0.0028 0.236 1.118 0.664 0.089 18 0.3544 0.3676 0.683 88225. 4691.9 0.0027 0.231 1.103 0.654 0.088 19 0.3540 0.3672 0.684 88198. 4690.9 0.0027 0.227 1.089 0.646 0.087 20 0.3537 0.3671 0.684 88176. 4690.5 0.0026 0.223 1.076 0.638 0.087 21 0.3533 0.3668 0.685 88149. 4689.5 0.0026 0.220 1.065 0.631 0.086 22 0.3530 0.3664 0.686 88127. 4688.7 0.0026 0.217 1.055 0.624 0.085 23 0.3526 0.3662 0.686 88107. 4688.1 0.0025 0.215 1.045 0.618 0.085 24 0.3523 0.3659 0.686 88101. 4688.1 0.0025 0.213 1.035 0.612 0.084 25 0.3522 0.3660 0.686 88095. 4688.2 0.0025 0.211 1.030 0.608 0.084 26 0.3520 0.3660 0.686 88093. 4688.3 0.0025 0.210 1.024 0.605 0.084 27 0.3518 0.3660 0.687 88076. 4687.7 0.0024 0.208 1.017 0.600 0.083 28 0.3515 0.3659 0.687 88063. 4687.4 0.0024 0.206 1.009 0.595 0.083 29 0.3513 0.3658 0.687 88039. 4686.4 0.0024 0.204 1.002 0.591 0.083 30 0.3511 0.3657 0.687 88025. 4685.9 0.0024 0.203 0.996 0.587 0.082 $$ Output MTZ file from Refmac for model 1lze_A1_PHR_MO_s0.55_r2-121 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1lze_A1_PHR_MO_s0.55_r2-121.mtz Output PDB file from Refmac for model 1lze_A1_PHR_MO_s0.55_r2-121: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1lze_A1_PHR_MO_s0.55_r2-121.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 44 MR programs being used: MOLREP PHASER Best search model so far: 1lze_A1_PHR_MO_s0.55_r2-121 using MOLREP Initial Rfree: 0.401 Final Rfree: 0.366 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1lze_A1_PHR_MO_s0.55_r2-121.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1lze_A1_PHR_MO_s0.55_r2-121.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1lze_A1_PHR_MO_s0.55_r2-121.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_1lze_A1_PHR_MO_s0.55_r2-121.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 1lze_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.37 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2663.00 56.60 0.35 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 PHASER MARGINAL 1571.00 42.20 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 PHASER MARGINAL 1567.00 41.40 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 PHASER MARGINAL 1083.00 38.10 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 MOLREP MARGINAL -- -- 0.40 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 PHASER MARGINAL 558.00 27.80 0.40 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 662.00 28.50 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 44: 1gfr_A1_PHR_MO_s0.53_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfr_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1gfr_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.53 Search model type: MOLREP Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfr_A1_PHR\molrep\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfr_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1gfr_A1_PHR_MO_s0.53_r1-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfr_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1gfr_A1_PHR_MO_s0.53_r1-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfr_A1_PHR\molrep\mr\molrep\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfr_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1gfr_A1_PHR_MO_s0.53_r1-123' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 1gfr_A1_PHR_MO_s0.53_r1-123: ##### ################################################################################################# Template Model: 1gfr_A1_PHR_MO_s0.53_r1-123 has produced a marginal solution, final Rfree = 0.396 Molrep log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfr_A1_PHR\molrep\mr\molrep\molrep.log Molrep PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfr_A1_PHR\molrep\mr\molrep\molrep_1gfr_A1_PHR_MO_s0.53_r1-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfr_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1gfr_A1_PHR_MO_s0.53_r1-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfr_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1gfr_A1_PHR_MO_s0.53_r1-123.pdb #################################################################################################### ##### Refinement results from Refmac for 1gfr_A1_PHR_MO_s0.53_r1-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1gfr_A1_PHR_MO_s0.53_r1-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4794 0.4862 0.436 93429. 4939.3 0.0282 2.296 2.561 1.569 0.344 1 0.4504 0.4597 0.468 92398. 4895.5 0.0084 0.656 1.885 1.157 0.265 2 0.4370 0.4454 0.498 91838. 4868.8 0.0069 0.535 1.692 1.040 0.212 3 0.4276 0.4336 0.520 91451. 4852.6 0.0061 0.470 1.581 0.970 0.170 4 0.4210 0.4254 0.536 91177. 4839.9 0.0057 0.437 1.515 0.922 0.147 5 0.4163 0.4201 0.547 91096. 4836.3 0.0053 0.409 1.465 0.884 0.131 6 0.4123 0.4153 0.558 90995. 4831.6 0.0050 0.387 1.424 0.852 0.118 7 0.4095 0.4133 0.566 90930. 4829.3 0.0047 0.367 1.389 0.824 0.111 8 0.4069 0.4117 0.571 90873. 4826.1 0.0045 0.349 1.355 0.798 0.103 9 0.4048 0.4107 0.575 90828. 4824.3 0.0043 0.334 1.324 0.777 0.099 10 0.4029 0.4095 0.578 90783. 4822.6 0.0041 0.321 1.296 0.758 0.097 11 0.4014 0.4085 0.582 90745. 4820.8 0.0039 0.310 1.273 0.742 0.095 12 0.4000 0.4075 0.585 90708. 4819.0 0.0037 0.299 1.254 0.729 0.093 13 0.3985 0.4063 0.587 90667. 4816.9 0.0036 0.290 1.240 0.718 0.093 14 0.3973 0.4052 0.589 90652. 4816.5 0.0035 0.282 1.226 0.708 0.092 15 0.3961 0.4041 0.591 90617. 4814.8 0.0034 0.275 1.213 0.699 0.091 16 0.3952 0.4033 0.592 90564. 4812.5 0.0033 0.269 1.202 0.691 0.091 17 0.3942 0.4022 0.595 90531. 4811.0 0.0032 0.263 1.194 0.684 0.090 18 0.3933 0.4014 0.598 90480. 4808.6 0.0031 0.257 1.185 0.678 0.090 19 0.3925 0.4006 0.600 90438. 4806.5 0.0031 0.253 1.178 0.672 0.089 20 0.3918 0.3999 0.603 90405. 4805.4 0.0030 0.249 1.170 0.666 0.089 21 0.3911 0.3993 0.606 90364. 4803.7 0.0029 0.245 1.163 0.661 0.088 22 0.3905 0.3987 0.608 90360. 4804.1 0.0029 0.241 1.155 0.656 0.087 23 0.3898 0.3981 0.608 90341. 4803.4 0.0028 0.238 1.147 0.651 0.087 24 0.3892 0.3974 0.609 90304. 4801.7 0.0028 0.235 1.140 0.646 0.086 25 0.3886 0.3969 0.610 90282. 4800.6 0.0027 0.232 1.134 0.642 0.086 26 0.3880 0.3964 0.611 90267. 4800.0 0.0027 0.229 1.128 0.637 0.085 27 0.3875 0.3959 0.612 90266. 4800.1 0.0027 0.227 1.121 0.633 0.085 28 0.3870 0.3959 0.613 90254. 4799.7 0.0026 0.224 1.116 0.629 0.085 29 0.3864 0.3957 0.613 90249. 4799.7 0.0026 0.223 1.111 0.626 0.084 30 0.3859 0.3957 0.614 90242. 4799.7 0.0026 0.221 1.106 0.623 0.084 $$ Output MTZ file from Refmac for model 1gfr_A1_PHR_MO_s0.53_r1-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfr_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1gfr_A1_PHR_MO_s0.53_r1-123.mtz Output PDB file from Refmac for model 1gfr_A1_PHR_MO_s0.53_r1-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfr_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1gfr_A1_PHR_MO_s0.53_r1-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 45 MR programs being used: MOLREP PHASER Best search model so far: 1lze_A1_PHR_MO_s0.55_r2-121 using MOLREP Initial Rfree: 0.401 Final Rfree: 0.366 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1lze_A1_PHR_MO_s0.55_r2-121.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1lze_A1_PHR_MO_s0.55_r2-121.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1lze_A1_PHR_MO_s0.55_r2-121.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_1lze_A1_PHR_MO_s0.55_r2-121.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 1lze_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.37 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2663.00 56.60 0.35 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 PHASER MARGINAL 1571.00 42.20 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 PHASER MARGINAL 1567.00 41.40 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 PHASER MARGINAL 1083.00 38.10 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 MOLREP MARGINAL -- -- 0.40 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 PHASER MARGINAL 558.00 27.80 0.40 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 662.00 28.50 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 45: 1gfr_A1_PHR_MO_s0.53_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfr_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1gfr_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.53 Search model type: MOLREP Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfr_A1_PHR\molrep\mr\phaser\phaser_1gfr_A1_PHR_MO_s0.53_r1-123.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfr_A1_PHR\molrep\mr\phaser\phaser_1gfr_A1_PHR_MO_s0.53_r1-123.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfr_A1_PHR\molrep\mr\phaser\phaser_1gfr_A1_PHR_MO_s0.53_r1-123.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfr_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_HKLOUT_1gfr_A1_PHR_MO_s0.53_r1-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfr_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1gfr_A1_PHR_MO_s0.53_r1-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfr_A1_PHR\molrep\mr\phaser\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfr_A1_PHR\molrep\mr\phaser\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1gfr_A1_PHR_MO_s0.53_r1-123' ######################################################################### ###################################################################### ##### Results from Phaser for 1gfr_A1_PHR_MO_s0.53_r1-123: ##### ###################################################################### Template Model: 1gfr_A1_PHR_MO_s0.53_r1-123 has produced a marginal solution, final Rfree = 0.399 Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfr_A1_PHR\molrep\mr\phaser\phaser_1gfr_A1_PHR_MO_s0.53_r1-123.log Phaser PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfr_A1_PHR\molrep\mr\phaser\phaser_1gfr_A1_PHR_MO_s0.53_r1-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfr_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1gfr_A1_PHR_MO_s0.53_r1-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfr_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1gfr_A1_PHR_MO_s0.53_r1-123.pdb #################################################################################################### ##### Refinement results from Refmac for 1gfr_A1_PHR_MO_s0.53_r1-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1gfr_A1_PHR_MO_s0.53_r1-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4712 0.4793 0.459 92824. 4913.4 0.0283 2.299 2.561 1.569 0.344 1 0.4586 0.4705 0.462 92429. 4896.8 0.0081 0.635 1.893 1.164 0.279 2 0.4501 0.4618 0.474 92040. 4879.5 0.0060 0.479 1.688 1.037 0.228 3 0.4445 0.4561 0.484 91778. 4866.8 0.0054 0.431 1.564 0.961 0.184 4 0.4387 0.4494 0.496 91536. 4856.3 0.0051 0.408 1.481 0.908 0.155 5 0.4330 0.4429 0.505 91317. 4846.0 0.0050 0.393 1.425 0.869 0.136 6 0.4270 0.4354 0.517 91182. 4840.4 0.0049 0.388 1.390 0.843 0.122 7 0.4207 0.4276 0.532 91038. 4834.2 0.0050 0.385 1.373 0.826 0.114 8 0.4183 0.4244 0.538 90988. 4832.5 0.0045 0.354 1.334 0.798 0.106 9 0.4156 0.4218 0.544 90921. 4829.0 0.0043 0.340 1.309 0.779 0.102 10 0.4131 0.4195 0.550 90871. 4827.1 0.0042 0.330 1.290 0.763 0.099 11 0.4105 0.4167 0.557 90819. 4824.9 0.0041 0.322 1.276 0.749 0.097 12 0.4080 0.4140 0.561 90801. 4824.4 0.0040 0.316 1.263 0.738 0.096 13 0.4055 0.4117 0.565 90775. 4823.1 0.0039 0.311 1.254 0.728 0.095 14 0.4031 0.4091 0.570 90719. 4819.6 0.0039 0.306 1.248 0.722 0.094 15 0.4019 0.4081 0.576 90739. 4821.7 0.0037 0.293 1.229 0.709 0.093 16 0.4006 0.4070 0.579 90749. 4821.7 0.0035 0.284 1.214 0.699 0.092 17 0.3994 0.4055 0.584 90710. 4818.6 0.0034 0.277 1.203 0.692 0.091 18 0.3983 0.4044 0.589 90675. 4816.6 0.0034 0.272 1.194 0.685 0.091 19 0.3971 0.4036 0.592 90662. 4815.7 0.0033 0.266 1.186 0.678 0.090 20 0.3959 0.4030 0.594 90620. 4813.3 0.0032 0.262 1.181 0.674 0.090 21 0.3949 0.4020 0.596 90587. 4811.2 0.0032 0.258 1.176 0.669 0.090 22 0.3938 0.4011 0.601 90553. 4808.9 0.0031 0.254 1.172 0.665 0.089 23 0.3928 0.4008 0.604 90499. 4806.5 0.0030 0.249 1.167 0.661 0.089 24 0.3919 0.4006 0.605 90454. 4804.3 0.0030 0.246 1.161 0.656 0.088 25 0.3911 0.4004 0.607 90440. 4803.3 0.0029 0.241 1.156 0.652 0.088 26 0.3903 0.4000 0.610 90406. 4802.1 0.0028 0.238 1.150 0.647 0.087 27 0.3897 0.3996 0.611 90394. 4801.9 0.0028 0.235 1.143 0.643 0.086 28 0.3891 0.3992 0.612 90393. 4802.1 0.0027 0.232 1.137 0.639 0.086 29 0.3885 0.3991 0.613 90384. 4801.6 0.0027 0.229 1.131 0.635 0.086 30 0.3879 0.3988 0.615 90364. 4801.0 0.0027 0.226 1.126 0.631 0.085 $$ Output MTZ file from Refmac for model 1gfr_A1_PHR_MO_s0.53_r1-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfr_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1gfr_A1_PHR_MO_s0.53_r1-123.mtz Output PDB file from Refmac for model 1gfr_A1_PHR_MO_s0.53_r1-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfr_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1gfr_A1_PHR_MO_s0.53_r1-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 46 MR programs being used: MOLREP PHASER Best search model so far: 1lze_A1_PHR_MO_s0.55_r2-121 using MOLREP Initial Rfree: 0.401 Final Rfree: 0.366 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1lze_A1_PHR_MO_s0.55_r2-121.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1lze_A1_PHR_MO_s0.55_r2-121.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1lze_A1_PHR_MO_s0.55_r2-121.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_1lze_A1_PHR_MO_s0.55_r2-121.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 1lze_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.37 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2663.00 56.60 0.35 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 PHASER MARGINAL 1571.00 42.20 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 PHASER MARGINAL 1567.00 41.40 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 PHASER MARGINAL 1083.00 38.10 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 MOLREP MARGINAL -- -- 0.40 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 PHASER MARGINAL 558.00 27.80 0.40 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 680.00 29.10 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 662.00 28.50 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 46: 1gfk_A1_PHR_MO_s0.53_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfk_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1gfk_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.53 Search model type: MOLREP Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfk_A1_PHR\molrep\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfk_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1gfk_A1_PHR_MO_s0.53_r1-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfk_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1gfk_A1_PHR_MO_s0.53_r1-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfk_A1_PHR\molrep\mr\molrep\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfk_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1gfk_A1_PHR_MO_s0.53_r1-123' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 1gfk_A1_PHR_MO_s0.53_r1-123: ##### ################################################################################################# Template Model: 1gfk_A1_PHR_MO_s0.53_r1-123 has produced a marginal solution, final Rfree = 0.403 Molrep log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfk_A1_PHR\molrep\mr\molrep\molrep.log Molrep PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfk_A1_PHR\molrep\mr\molrep\molrep_1gfk_A1_PHR_MO_s0.53_r1-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfk_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1gfk_A1_PHR_MO_s0.53_r1-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfk_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1gfk_A1_PHR_MO_s0.53_r1-123.pdb #################################################################################################### ##### Refinement results from Refmac for 1gfk_A1_PHR_MO_s0.53_r1-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1gfk_A1_PHR_MO_s0.53_r1-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4804 0.4850 0.434 93353. 4936.2 0.0293 2.297 2.531 1.549 0.344 1 0.4498 0.4589 0.469 92474. 4904.0 0.0083 0.650 1.894 1.161 0.276 2 0.4356 0.4446 0.500 91947. 4880.0 0.0067 0.518 1.730 1.060 0.229 3 0.4256 0.4346 0.522 91531. 4859.5 0.0061 0.470 1.624 0.994 0.188 4 0.4193 0.4277 0.538 91348. 4851.3 0.0056 0.438 1.543 0.941 0.156 5 0.4142 0.4238 0.553 91216. 4845.2 0.0053 0.413 1.485 0.897 0.131 6 0.4105 0.4219 0.562 91089. 4838.9 0.0050 0.390 1.440 0.861 0.117 7 0.4072 0.4201 0.568 91005. 4835.1 0.0047 0.373 1.401 0.832 0.108 8 0.4047 0.4188 0.573 90948. 4832.9 0.0044 0.355 1.368 0.808 0.103 9 0.4023 0.4175 0.575 90926. 4832.6 0.0043 0.342 1.337 0.785 0.100 10 0.4005 0.4164 0.579 90873. 4830.7 0.0041 0.329 1.310 0.765 0.098 11 0.3991 0.4153 0.582 90866. 4831.2 0.0039 0.316 1.286 0.749 0.097 12 0.3976 0.4143 0.584 90834. 4830.2 0.0037 0.304 1.266 0.734 0.096 13 0.3962 0.4132 0.588 90784. 4827.2 0.0036 0.294 1.248 0.722 0.095 14 0.3951 0.4121 0.592 90697. 4823.0 0.0035 0.286 1.232 0.711 0.094 15 0.3939 0.4113 0.595 90629. 4819.9 0.0034 0.278 1.217 0.700 0.094 16 0.3930 0.4112 0.597 90547. 4816.0 0.0033 0.271 1.204 0.691 0.093 17 0.3920 0.4105 0.597 90525. 4815.2 0.0032 0.265 1.192 0.682 0.092 18 0.3911 0.4098 0.599 90504. 4814.2 0.0031 0.260 1.180 0.674 0.091 19 0.3903 0.4086 0.600 90488. 4813.5 0.0030 0.255 1.170 0.667 0.091 20 0.3896 0.4080 0.602 90425. 4810.4 0.0030 0.250 1.159 0.660 0.090 21 0.3889 0.4073 0.604 90406. 4809.8 0.0029 0.246 1.150 0.655 0.089 22 0.3883 0.4070 0.605 90378. 4808.9 0.0029 0.242 1.142 0.649 0.089 23 0.3876 0.4063 0.607 90332. 4806.7 0.0028 0.238 1.135 0.644 0.088 24 0.3870 0.4058 0.607 90305. 4805.5 0.0028 0.235 1.128 0.639 0.088 25 0.3865 0.4054 0.608 90275. 4804.2 0.0027 0.232 1.122 0.635 0.087 26 0.3859 0.4048 0.608 90255. 4803.2 0.0027 0.229 1.116 0.631 0.087 27 0.3855 0.4043 0.609 90236. 4802.4 0.0027 0.227 1.111 0.627 0.086 28 0.3850 0.4038 0.611 90203. 4800.6 0.0026 0.224 1.106 0.624 0.086 29 0.3845 0.4034 0.612 90169. 4799.2 0.0026 0.222 1.100 0.621 0.085 30 0.3841 0.4028 0.613 90143. 4798.1 0.0026 0.220 1.096 0.618 0.085 $$ Output MTZ file from Refmac for model 1gfk_A1_PHR_MO_s0.53_r1-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfk_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1gfk_A1_PHR_MO_s0.53_r1-123.mtz Output PDB file from Refmac for model 1gfk_A1_PHR_MO_s0.53_r1-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfk_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1gfk_A1_PHR_MO_s0.53_r1-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 47 MR programs being used: MOLREP PHASER Best search model so far: 1lze_A1_PHR_MO_s0.55_r2-121 using MOLREP Initial Rfree: 0.401 Final Rfree: 0.366 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1lze_A1_PHR_MO_s0.55_r2-121.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1lze_A1_PHR_MO_s0.55_r2-121.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1lze_A1_PHR_MO_s0.55_r2-121.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_1lze_A1_PHR_MO_s0.55_r2-121.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 1lze_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.37 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2663.00 56.60 0.35 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 PHASER MARGINAL 1571.00 42.20 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 PHASER MARGINAL 1567.00 41.40 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 PHASER MARGINAL 1083.00 38.10 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 MOLREP MARGINAL -- -- 0.40 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 PHASER MARGINAL 558.00 27.80 0.40 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 680.00 29.10 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.38 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 662.00 28.50 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 47: 1gfk_A1_PHR_MO_s0.53_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfk_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1gfk_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.53 Search model type: MOLREP Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfk_A1_PHR\molrep\mr\phaser\phaser_1gfk_A1_PHR_MO_s0.53_r1-123.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfk_A1_PHR\molrep\mr\phaser\phaser_1gfk_A1_PHR_MO_s0.53_r1-123.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfk_A1_PHR\molrep\mr\phaser\phaser_1gfk_A1_PHR_MO_s0.53_r1-123.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfk_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_HKLOUT_1gfk_A1_PHR_MO_s0.53_r1-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfk_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1gfk_A1_PHR_MO_s0.53_r1-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfk_A1_PHR\molrep\mr\phaser\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfk_A1_PHR\molrep\mr\phaser\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1gfk_A1_PHR_MO_s0.53_r1-123' ######################################################################### ###################################################################### ##### Results from Phaser for 1gfk_A1_PHR_MO_s0.53_r1-123: ##### ###################################################################### Template Model: 1gfk_A1_PHR_MO_s0.53_r1-123 has produced a marginal solution, final Rfree = 0.404 Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfk_A1_PHR\molrep\mr\phaser\phaser_1gfk_A1_PHR_MO_s0.53_r1-123.log Phaser PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfk_A1_PHR\molrep\mr\phaser\phaser_1gfk_A1_PHR_MO_s0.53_r1-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfk_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1gfk_A1_PHR_MO_s0.53_r1-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfk_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1gfk_A1_PHR_MO_s0.53_r1-123.pdb #################################################################################################### ##### Refinement results from Refmac for 1gfk_A1_PHR_MO_s0.53_r1-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1gfk_A1_PHR_MO_s0.53_r1-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4683 0.4756 0.473 92667. 4904.6 0.0292 2.296 2.531 1.548 0.344 1 0.4482 0.4553 0.488 92123. 4884.1 0.0091 0.673 1.867 1.148 0.282 2 0.4340 0.4397 0.511 91719. 4867.7 0.0067 0.520 1.705 1.047 0.234 3 0.4253 0.4312 0.529 91443. 4854.3 0.0060 0.466 1.606 0.983 0.190 4 0.4189 0.4257 0.544 91299. 4848.0 0.0056 0.434 1.534 0.933 0.157 5 0.4172 0.4242 0.549 91216. 4844.4 0.0048 0.384 1.458 0.881 0.131 6 0.4153 0.4228 0.552 91128. 4840.0 0.0045 0.360 1.402 0.843 0.118 7 0.4131 0.4214 0.557 91059. 4836.6 0.0043 0.345 1.360 0.812 0.110 8 0.4108 0.4204 0.563 90983. 4833.1 0.0041 0.335 1.326 0.788 0.104 9 0.4083 0.4186 0.566 90906. 4829.7 0.0041 0.328 1.302 0.769 0.101 10 0.4058 0.4171 0.572 90863. 4827.7 0.0040 0.321 1.286 0.755 0.099 11 0.4032 0.4156 0.577 90786. 4824.0 0.0039 0.317 1.276 0.744 0.098 12 0.4009 0.4144 0.579 90731. 4821.3 0.0039 0.312 1.268 0.734 0.097 13 0.3988 0.4131 0.584 90678. 4818.5 0.0038 0.304 1.259 0.725 0.096 14 0.3972 0.4122 0.588 90667. 4819.0 0.0036 0.295 1.248 0.716 0.095 15 0.3958 0.4109 0.590 90640. 4817.7 0.0035 0.287 1.234 0.706 0.094 16 0.3945 0.4104 0.592 90593. 4815.5 0.0034 0.280 1.221 0.698 0.093 17 0.3935 0.4095 0.596 90562. 4813.7 0.0033 0.274 1.209 0.690 0.093 18 0.3924 0.4089 0.600 90524. 4812.3 0.0032 0.268 1.200 0.683 0.092 19 0.3915 0.4092 0.602 90510. 4812.0 0.0031 0.262 1.190 0.676 0.091 20 0.3906 0.4085 0.603 90493. 4811.6 0.0031 0.257 1.181 0.670 0.091 21 0.3899 0.4082 0.604 90461. 4810.5 0.0030 0.252 1.172 0.664 0.090 22 0.3893 0.4079 0.605 90428. 4808.9 0.0029 0.248 1.163 0.658 0.089 23 0.3886 0.4075 0.605 90377. 4806.6 0.0029 0.244 1.155 0.653 0.089 24 0.3879 0.4069 0.606 90347. 4805.3 0.0028 0.240 1.147 0.648 0.088 25 0.3873 0.4063 0.607 90320. 4804.1 0.0028 0.237 1.140 0.643 0.087 26 0.3867 0.4056 0.608 90284. 4802.6 0.0028 0.234 1.134 0.639 0.087 27 0.3862 0.4053 0.608 90260. 4801.5 0.0027 0.230 1.128 0.635 0.086 28 0.3856 0.4048 0.610 90241. 4800.8 0.0027 0.228 1.123 0.632 0.086 29 0.3852 0.4044 0.612 90221. 4799.7 0.0026 0.225 1.117 0.628 0.086 30 0.3847 0.4041 0.614 90198. 4799.1 0.0026 0.223 1.111 0.624 0.085 $$ Output MTZ file from Refmac for model 1gfk_A1_PHR_MO_s0.53_r1-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfk_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1gfk_A1_PHR_MO_s0.53_r1-123.mtz Output PDB file from Refmac for model 1gfk_A1_PHR_MO_s0.53_r1-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gfk_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1gfk_A1_PHR_MO_s0.53_r1-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 48 MR programs being used: MOLREP PHASER Best search model so far: 1lze_A1_PHR_MO_s0.55_r2-121 using MOLREP Initial Rfree: 0.401 Final Rfree: 0.366 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1lze_A1_PHR_MO_s0.55_r2-121.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1lze_A1_PHR_MO_s0.55_r2-121.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1lze_A1_PHR_MO_s0.55_r2-121.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1lze_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_1lze_A1_PHR_MO_s0.55_r2-121.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 1lze_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.37 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2663.00 56.60 0.35 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 PHASER MARGINAL 1571.00 42.20 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 PHASER MARGINAL 1567.00 41.40 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 PHASER MARGINAL 1083.00 38.10 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 MOLREP MARGINAL -- -- 0.40 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 PHASER MARGINAL 558.00 27.80 0.40 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 680.00 29.10 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.38 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 724.00 29.70 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 662.00 28.50 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 48: 1iot_A1_PHR_MO_s0.55_r2-121 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1iot_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.55 Search model type: MOLREP Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1iot_A1_PHR_MO_s0.55_r2-121.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1iot_A1_PHR_MO_s0.55_r2-121' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 1iot_A1_PHR_MO_s0.55_r2-121: ##### ################################################################################################# Template Model: 1iot_A1_PHR_MO_s0.55_r2-121 has produced a marginal solution, final Rfree = 0.353 Molrep log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\molrep.log Molrep PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\molrep_1iot_A1_PHR_MO_s0.55_r2-121.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb #################################################################################################### ##### Refinement results from Refmac for 1iot_A1_PHR_MO_s0.55_r2-121: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1iot_A1_PHR_MO_s0.55_r2-121: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4057 0.3982 0.610 90815. 4794.7 0.0338 2.559 2.490 1.526 0.269 1 0.3815 0.3828 0.641 89605. 4740.8 0.0084 0.619 1.805 1.105 0.208 2 0.3735 0.3718 0.656 89123. 4716.2 0.0058 0.446 1.616 0.985 0.173 3 0.3690 0.3681 0.663 88885. 4706.1 0.0049 0.390 1.488 0.904 0.140 4 0.3661 0.3659 0.667 88711. 4698.3 0.0044 0.354 1.394 0.845 0.121 5 0.3641 0.3638 0.668 88628. 4695.3 0.0040 0.327 1.322 0.800 0.109 6 0.3627 0.3622 0.670 88530. 4690.8 0.0038 0.305 1.265 0.765 0.102 7 0.3616 0.3610 0.673 88448. 4687.4 0.0035 0.288 1.216 0.734 0.094 8 0.3608 0.3600 0.674 88383. 4684.5 0.0033 0.275 1.179 0.710 0.092 9 0.3601 0.3591 0.675 88330. 4682.4 0.0032 0.264 1.149 0.691 0.090 10 0.3595 0.3586 0.676 88299. 4681.3 0.0031 0.254 1.124 0.674 0.089 11 0.3589 0.3580 0.676 88273. 4680.6 0.0030 0.246 1.102 0.660 0.088 12 0.3584 0.3574 0.677 88253. 4679.6 0.0029 0.240 1.083 0.647 0.087 13 0.3580 0.3571 0.678 88230. 4679.5 0.0028 0.234 1.066 0.636 0.086 14 0.3576 0.3570 0.679 88219. 4679.6 0.0027 0.230 1.052 0.626 0.086 15 0.3573 0.3567 0.679 88213. 4679.8 0.0027 0.226 1.039 0.618 0.085 16 0.3570 0.3562 0.679 88196. 4679.4 0.0026 0.222 1.027 0.610 0.085 17 0.3567 0.3561 0.680 88188. 4679.2 0.0026 0.219 1.017 0.603 0.085 18 0.3564 0.3558 0.681 88180. 4678.6 0.0025 0.216 1.008 0.597 0.084 19 0.3561 0.3556 0.683 88177. 4678.9 0.0025 0.213 0.999 0.591 0.084 20 0.3558 0.3554 0.683 88164. 4678.6 0.0025 0.211 0.991 0.586 0.083 21 0.3556 0.3551 0.683 88156. 4678.4 0.0024 0.209 0.983 0.581 0.083 22 0.3554 0.3550 0.684 88146. 4678.1 0.0024 0.208 0.976 0.576 0.083 23 0.3552 0.3546 0.684 88123. 4676.9 0.0024 0.206 0.970 0.572 0.082 24 0.3550 0.3543 0.684 88100. 4675.9 0.0024 0.205 0.964 0.568 0.082 25 0.3548 0.3540 0.685 88087. 4675.5 0.0023 0.203 0.959 0.565 0.082 26 0.3546 0.3538 0.685 88078. 4675.4 0.0023 0.202 0.954 0.562 0.081 27 0.3545 0.3535 0.685 88079. 4675.8 0.0023 0.201 0.949 0.559 0.081 28 0.3543 0.3534 0.686 88078. 4676.0 0.0023 0.200 0.945 0.556 0.081 29 0.3542 0.3533 0.686 88067. 4675.6 0.0023 0.199 0.941 0.554 0.080 30 0.3541 0.3531 0.687 88061. 4675.2 0.0023 0.198 0.937 0.551 0.080 $$ Output MTZ file from Refmac for model 1iot_A1_PHR_MO_s0.55_r2-121 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1iot_A1_PHR_MO_s0.55_r2-121.mtz Output PDB file from Refmac for model 1iot_A1_PHR_MO_s0.55_r2-121: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 49 MR programs being used: MOLREP PHASER Best search model so far: 1iot_A1_PHR_MO_s0.55_r2-121 using MOLREP Initial Rfree: 0.406 Final Rfree: 0.353 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1iot_A1_PHR_MO_s0.55_r2-121.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 1iot_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.35 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.37 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2663.00 56.60 0.35 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 PHASER MARGINAL 1571.00 42.20 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 PHASER MARGINAL 1567.00 41.40 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 PHASER MARGINAL 1083.00 38.10 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 MOLREP MARGINAL -- -- 0.40 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 PHASER MARGINAL 558.00 27.80 0.40 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 680.00 29.10 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.38 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 724.00 29.70 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 662.00 28.50 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 49: 1iot_A1_PHR_MO_s0.55_r2-121 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1iot_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.55 Search model type: MOLREP Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\phaser\phaser_1iot_A1_PHR_MO_s0.55_r2-121.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\phaser\phaser_1iot_A1_PHR_MO_s0.55_r2-121.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\phaser\phaser_1iot_A1_PHR_MO_s0.55_r2-121.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_HKLOUT_1iot_A1_PHR_MO_s0.55_r2-121.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1iot_A1_PHR_MO_s0.55_r2-121.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\phaser\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\phaser\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1iot_A1_PHR_MO_s0.55_r2-121' ######################################################################### ###################################################################### ##### Results from Phaser for 1iot_A1_PHR_MO_s0.55_r2-121: ##### ###################################################################### Template Model: 1iot_A1_PHR_MO_s0.55_r2-121 has produced a marginal solution, final Rfree = 0.354 Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\phaser\phaser_1iot_A1_PHR_MO_s0.55_r2-121.log Phaser PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\phaser\phaser_1iot_A1_PHR_MO_s0.55_r2-121.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1iot_A1_PHR_MO_s0.55_r2-121.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1iot_A1_PHR_MO_s0.55_r2-121.pdb #################################################################################################### ##### Refinement results from Refmac for 1iot_A1_PHR_MO_s0.55_r2-121: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1iot_A1_PHR_MO_s0.55_r2-121: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.3845 0.3753 0.659 89124. 4700.2 0.0338 2.560 2.488 1.525 0.269 1 0.3794 0.3737 0.661 89119. 4707.8 0.0086 0.649 1.797 1.100 0.211 2 0.3712 0.3675 0.670 88821. 4695.6 0.0057 0.446 1.606 0.979 0.178 3 0.3673 0.3654 0.675 88732. 4694.6 0.0049 0.386 1.480 0.901 0.153 4 0.3650 0.3640 0.676 88610. 4690.6 0.0044 0.350 1.388 0.843 0.129 5 0.3635 0.3625 0.677 88542. 4688.6 0.0040 0.322 1.317 0.799 0.115 6 0.3624 0.3612 0.679 88475. 4686.1 0.0037 0.301 1.262 0.764 0.106 7 0.3614 0.3606 0.680 88388. 4682.9 0.0035 0.284 1.217 0.736 0.100 8 0.3606 0.3598 0.681 88322. 4680.2 0.0033 0.271 1.178 0.710 0.094 9 0.3600 0.3592 0.681 88315. 4680.5 0.0031 0.260 1.147 0.690 0.092 10 0.3595 0.3587 0.682 88296. 4680.3 0.0030 0.251 1.121 0.673 0.090 11 0.3590 0.3585 0.682 88269. 4679.7 0.0029 0.244 1.099 0.659 0.089 12 0.3586 0.3581 0.683 88262. 4679.7 0.0028 0.237 1.080 0.646 0.088 13 0.3582 0.3578 0.684 88248. 4679.8 0.0027 0.232 1.063 0.635 0.087 14 0.3578 0.3574 0.684 88253. 4680.7 0.0027 0.227 1.049 0.625 0.087 15 0.3575 0.3574 0.684 88261. 4681.7 0.0026 0.223 1.035 0.617 0.086 16 0.3572 0.3572 0.685 88242. 4681.2 0.0026 0.219 1.024 0.609 0.086 17 0.3569 0.3569 0.685 88233. 4681.2 0.0025 0.216 1.013 0.602 0.085 18 0.3567 0.3567 0.685 88214. 4680.3 0.0025 0.215 1.007 0.598 0.085 19 0.3566 0.3566 0.685 88197. 4679.7 0.0025 0.213 1.002 0.594 0.084 20 0.3563 0.3564 0.686 88189. 4679.6 0.0024 0.211 0.994 0.589 0.084 21 0.3561 0.3561 0.686 88170. 4679.1 0.0024 0.209 0.986 0.584 0.084 22 0.3559 0.3560 0.687 88157. 4678.8 0.0024 0.207 0.979 0.579 0.083 23 0.3556 0.3558 0.687 88150. 4678.7 0.0024 0.206 0.972 0.575 0.083 24 0.3554 0.3555 0.687 88132. 4677.9 0.0024 0.204 0.966 0.571 0.082 25 0.3552 0.3553 0.687 88122. 4677.6 0.0023 0.203 0.961 0.567 0.082 26 0.3550 0.3550 0.688 88114. 4677.5 0.0023 0.202 0.956 0.564 0.082 27 0.3548 0.3548 0.688 88109. 4677.5 0.0023 0.201 0.952 0.561 0.082 28 0.3547 0.3546 0.688 88093. 4676.9 0.0023 0.200 0.947 0.558 0.081 29 0.3545 0.3543 0.688 88074. 4676.0 0.0023 0.199 0.943 0.555 0.081 30 0.3544 0.3542 0.688 88066. 4675.9 0.0023 0.198 0.939 0.553 0.081 $$ Output MTZ file from Refmac for model 1iot_A1_PHR_MO_s0.55_r2-121 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1iot_A1_PHR_MO_s0.55_r2-121.mtz Output PDB file from Refmac for model 1iot_A1_PHR_MO_s0.55_r2-121: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 50 MR programs being used: MOLREP PHASER Best search model so far: 1iot_A1_PHR_MO_s0.55_r2-121 using MOLREP Initial Rfree: 0.406 Final Rfree: 0.353 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1iot_A1_PHR_MO_s0.55_r2-121.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 1iot_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.35 1.00 1.00 -- -- -- -- 1iot_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2816.00 57.30 0.35 0.35 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.37 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2663.00 56.60 0.35 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 PHASER MARGINAL 1571.00 42.20 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 PHASER MARGINAL 1567.00 41.40 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 PHASER MARGINAL 1083.00 38.10 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 MOLREP MARGINAL -- -- 0.40 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 PHASER MARGINAL 558.00 27.80 0.40 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 680.00 29.10 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.38 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 724.00 29.70 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 662.00 28.50 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 50: 1fly_A1_PHR_MO_s0.55_r2-121 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1fly_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1fly_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.55 Search model type: MOLREP Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1fly_A1_PHR\molrep\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1fly_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1fly_A1_PHR_MO_s0.55_r2-121.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1fly_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1fly_A1_PHR_MO_s0.55_r2-121.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1fly_A1_PHR\molrep\mr\molrep\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1fly_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1fly_A1_PHR_MO_s0.55_r2-121' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 1fly_A1_PHR_MO_s0.55_r2-121: ##### ################################################################################################# Template Model: 1fly_A1_PHR_MO_s0.55_r2-121 has produced a marginal solution, final Rfree = 0.357 Molrep log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1fly_A1_PHR\molrep\mr\molrep\molrep.log Molrep PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1fly_A1_PHR\molrep\mr\molrep\molrep_1fly_A1_PHR_MO_s0.55_r2-121.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1fly_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1fly_A1_PHR_MO_s0.55_r2-121.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1fly_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1fly_A1_PHR_MO_s0.55_r2-121.pdb #################################################################################################### ##### Refinement results from Refmac for 1fly_A1_PHR_MO_s0.55_r2-121: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1fly_A1_PHR_MO_s0.55_r2-121: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4117 0.4019 0.601 90799. 4782.0 0.0347 2.632 2.513 1.542 0.268 1 0.3864 0.3846 0.630 89749. 4741.5 0.0086 0.651 1.875 1.151 0.206 2 0.3768 0.3776 0.646 89226. 4716.8 0.0062 0.481 1.664 1.015 0.168 3 0.3714 0.3746 0.654 88936. 4705.0 0.0053 0.414 1.535 0.933 0.142 4 0.3680 0.3715 0.661 88715. 4697.0 0.0047 0.373 1.440 0.874 0.123 5 0.3659 0.3694 0.664 88614. 4693.7 0.0043 0.341 1.366 0.828 0.112 6 0.3644 0.3680 0.668 88542. 4690.8 0.0039 0.318 1.308 0.792 0.105 7 0.3631 0.3668 0.670 88490. 4689.3 0.0037 0.299 1.262 0.763 0.098 8 0.3621 0.3657 0.672 88447. 4687.6 0.0035 0.284 1.225 0.739 0.094 9 0.3613 0.3650 0.672 88406. 4686.1 0.0033 0.272 1.193 0.719 0.091 10 0.3606 0.3645 0.674 88376. 4685.5 0.0032 0.262 1.166 0.702 0.089 11 0.3600 0.3638 0.674 88345. 4684.4 0.0031 0.254 1.143 0.687 0.088 12 0.3594 0.3631 0.675 88322. 4683.8 0.0030 0.247 1.124 0.676 0.086 13 0.3589 0.3622 0.676 88295. 4683.1 0.0029 0.241 1.105 0.664 0.085 14 0.3585 0.3617 0.676 88260. 4681.7 0.0028 0.235 1.089 0.654 0.084 15 0.3580 0.3612 0.677 88236. 4680.7 0.0027 0.230 1.075 0.645 0.084 16 0.3576 0.3607 0.679 88210. 4679.8 0.0027 0.226 1.062 0.636 0.083 17 0.3572 0.3601 0.680 88201. 4679.5 0.0026 0.222 1.051 0.629 0.082 18 0.3569 0.3599 0.680 88191. 4679.1 0.0026 0.218 1.041 0.622 0.082 19 0.3567 0.3594 0.680 88184. 4678.9 0.0025 0.215 1.032 0.616 0.081 20 0.3564 0.3590 0.681 88174. 4678.5 0.0025 0.213 1.023 0.611 0.081 21 0.3562 0.3589 0.681 88166. 4678.4 0.0025 0.211 1.014 0.605 0.080 22 0.3560 0.3587 0.681 88162. 4678.4 0.0024 0.208 1.007 0.601 0.080 23 0.3558 0.3584 0.682 88150. 4678.0 0.0024 0.206 1.000 0.596 0.080 24 0.3556 0.3581 0.683 88140. 4677.5 0.0024 0.204 0.994 0.592 0.079 25 0.3554 0.3579 0.683 88131. 4677.2 0.0023 0.203 0.988 0.589 0.079 26 0.3552 0.3579 0.684 88126. 4677.1 0.0023 0.202 0.983 0.585 0.079 27 0.3550 0.3577 0.684 88127. 4677.3 0.0023 0.201 0.976 0.582 0.079 28 0.3548 0.3575 0.684 88123. 4677.2 0.0023 0.200 0.972 0.579 0.078 29 0.3546 0.3575 0.684 88124. 4677.4 0.0023 0.199 0.968 0.576 0.078 30 0.3545 0.3573 0.684 88122. 4677.4 0.0023 0.198 0.964 0.574 0.078 $$ Output MTZ file from Refmac for model 1fly_A1_PHR_MO_s0.55_r2-121 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1fly_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1fly_A1_PHR_MO_s0.55_r2-121.mtz Output PDB file from Refmac for model 1fly_A1_PHR_MO_s0.55_r2-121: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1fly_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1fly_A1_PHR_MO_s0.55_r2-121.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 51 MR programs being used: MOLREP PHASER Best search model so far: 1iot_A1_PHR_MO_s0.55_r2-121 using MOLREP Initial Rfree: 0.406 Final Rfree: 0.353 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1iot_A1_PHR_MO_s0.55_r2-121.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 1iot_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.35 1.00 1.00 -- -- -- -- 1iot_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2816.00 57.30 0.35 0.35 1.00 1.00 -- -- -- -- 1fly_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.36 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.37 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2663.00 56.60 0.35 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 PHASER MARGINAL 1571.00 42.20 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 PHASER MARGINAL 1567.00 41.40 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 PHASER MARGINAL 1083.00 38.10 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 MOLREP MARGINAL -- -- 0.40 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 PHASER MARGINAL 558.00 27.80 0.40 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 680.00 29.10 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.38 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 724.00 29.70 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 662.00 28.50 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 51: 1fly_A1_PHR_MO_s0.55_r2-121 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1fly_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1fly_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.55 Search model type: MOLREP Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1fly_A1_PHR\molrep\mr\phaser\phaser_1fly_A1_PHR_MO_s0.55_r2-121.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1fly_A1_PHR\molrep\mr\phaser\phaser_1fly_A1_PHR_MO_s0.55_r2-121.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1fly_A1_PHR\molrep\mr\phaser\phaser_1fly_A1_PHR_MO_s0.55_r2-121.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1fly_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_HKLOUT_1fly_A1_PHR_MO_s0.55_r2-121.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1fly_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1fly_A1_PHR_MO_s0.55_r2-121.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1fly_A1_PHR\molrep\mr\phaser\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1fly_A1_PHR\molrep\mr\phaser\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1fly_A1_PHR_MO_s0.55_r2-121' ######################################################################### ###################################################################### ##### Results from Phaser for 1fly_A1_PHR_MO_s0.55_r2-121: ##### ###################################################################### Template Model: 1fly_A1_PHR_MO_s0.55_r2-121 has produced a marginal solution, final Rfree = 0.358 Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1fly_A1_PHR\molrep\mr\phaser\phaser_1fly_A1_PHR_MO_s0.55_r2-121.log Phaser PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1fly_A1_PHR\molrep\mr\phaser\phaser_1fly_A1_PHR_MO_s0.55_r2-121.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1fly_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1fly_A1_PHR_MO_s0.55_r2-121.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1fly_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1fly_A1_PHR_MO_s0.55_r2-121.pdb #################################################################################################### ##### Refinement results from Refmac for 1fly_A1_PHR_MO_s0.55_r2-121: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1fly_A1_PHR_MO_s0.55_r2-121: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.3898 0.3786 0.650 89443. 4714.3 0.0347 2.631 2.512 1.542 0.268 1 0.3886 0.3805 0.646 89608. 4728.7 0.0094 0.694 1.890 1.167 0.218 2 0.3833 0.3782 0.651 89441. 4723.8 0.0064 0.488 1.682 1.034 0.184 3 0.3800 0.3768 0.654 89297. 4718.5 0.0054 0.418 1.546 0.949 0.158 4 0.3774 0.3744 0.658 89142. 4711.5 0.0048 0.375 1.450 0.887 0.138 5 0.3747 0.3729 0.661 88982. 4704.7 0.0043 0.343 1.374 0.839 0.123 6 0.3718 0.3709 0.664 88885. 4701.7 0.0040 0.320 1.317 0.802 0.113 7 0.3687 0.3685 0.668 88724. 4696.1 0.0038 0.304 1.272 0.773 0.105 8 0.3661 0.3659 0.672 88608. 4691.9 0.0036 0.291 1.236 0.749 0.100 9 0.3644 0.3645 0.674 88538. 4690.0 0.0034 0.278 1.203 0.728 0.094 10 0.3631 0.3639 0.676 88491. 4688.9 0.0032 0.267 1.175 0.710 0.091 11 0.3621 0.3633 0.677 88448. 4687.6 0.0031 0.258 1.151 0.694 0.089 12 0.3609 0.3640 0.677 88377. 4685.2 0.0030 0.250 1.131 0.681 0.088 13 0.3602 0.3635 0.678 88336. 4683.7 0.0029 0.244 1.113 0.670 0.087 14 0.3595 0.3630 0.678 88294. 4682.2 0.0029 0.239 1.099 0.660 0.086 15 0.3590 0.3623 0.679 88256. 4680.9 0.0028 0.234 1.085 0.651 0.085 16 0.3585 0.3617 0.680 88246. 4680.8 0.0027 0.229 1.070 0.642 0.084 17 0.3581 0.3612 0.680 88232. 4680.6 0.0027 0.225 1.057 0.634 0.083 18 0.3576 0.3608 0.681 88217. 4680.1 0.0026 0.221 1.047 0.627 0.083 19 0.3573 0.3603 0.681 88199. 4679.6 0.0026 0.217 1.037 0.620 0.082 20 0.3569 0.3600 0.682 88178. 4678.8 0.0025 0.214 1.029 0.615 0.082 21 0.3566 0.3597 0.682 88171. 4678.8 0.0025 0.212 1.020 0.609 0.081 22 0.3563 0.3595 0.682 88163. 4678.6 0.0024 0.210 1.012 0.604 0.081 23 0.3561 0.3592 0.683 88155. 4678.2 0.0024 0.207 1.005 0.599 0.081 24 0.3559 0.3590 0.683 88148. 4678.2 0.0024 0.206 0.998 0.595 0.080 25 0.3556 0.3587 0.683 88138. 4677.9 0.0024 0.204 0.992 0.591 0.080 26 0.3554 0.3584 0.684 88133. 4677.6 0.0024 0.203 0.985 0.587 0.080 27 0.3552 0.3583 0.684 88134. 4677.9 0.0023 0.201 0.979 0.583 0.079 28 0.3550 0.3580 0.684 88133. 4677.8 0.0023 0.200 0.975 0.580 0.079 29 0.3548 0.3579 0.685 88145. 4678.6 0.0023 0.199 0.970 0.578 0.079 30 0.3546 0.3577 0.685 88144. 4678.7 0.0023 0.198 0.966 0.575 0.079 $$ Output MTZ file from Refmac for model 1fly_A1_PHR_MO_s0.55_r2-121 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1fly_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1fly_A1_PHR_MO_s0.55_r2-121.mtz Output PDB file from Refmac for model 1fly_A1_PHR_MO_s0.55_r2-121: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1fly_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1fly_A1_PHR_MO_s0.55_r2-121.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 52 MR programs being used: MOLREP PHASER Best search model so far: 1iot_A1_PHR_MO_s0.55_r2-121 using MOLREP Initial Rfree: 0.406 Final Rfree: 0.353 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1iot_A1_PHR_MO_s0.55_r2-121.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 1iot_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.35 1.00 1.00 -- -- -- -- 1iot_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2816.00 57.30 0.35 0.35 1.00 1.00 -- -- -- -- 1fly_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.36 1.00 1.00 -- -- -- -- 1fly_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2601.00 56.60 0.35 0.36 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.37 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2663.00 56.60 0.35 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 PHASER MARGINAL 1571.00 42.20 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 PHASER MARGINAL 1567.00 41.40 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 PHASER MARGINAL 1083.00 38.10 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 MOLREP MARGINAL -- -- 0.40 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 PHASER MARGINAL 558.00 27.80 0.40 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 680.00 29.10 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.38 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 724.00 29.70 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 662.00 28.50 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 52: 6p4d_A1_PHR_MO_s0.55_r2-121 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6p4d_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_6p4d_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.55 Search model type: MOLREP Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6p4d_A1_PHR\molrep\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6p4d_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_6p4d_A1_PHR_MO_s0.55_r2-121.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6p4d_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_6p4d_A1_PHR_MO_s0.55_r2-121.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6p4d_A1_PHR\molrep\mr\molrep\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6p4d_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '6p4d_A1_PHR_MO_s0.55_r2-121' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 6p4d_A1_PHR_MO_s0.55_r2-121: ##### ################################################################################################# Template Model: 6p4d_A1_PHR_MO_s0.55_r2-121 has produced a marginal solution, final Rfree = 0.353 Molrep log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6p4d_A1_PHR\molrep\mr\molrep\molrep.log Molrep PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6p4d_A1_PHR\molrep\mr\molrep\molrep_6p4d_A1_PHR_MO_s0.55_r2-121.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6p4d_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_6p4d_A1_PHR_MO_s0.55_r2-121.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6p4d_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_6p4d_A1_PHR_MO_s0.55_r2-121.pdb #################################################################################################### ##### Refinement results from Refmac for 6p4d_A1_PHR_MO_s0.55_r2-121: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 6p4d_A1_PHR_MO_s0.55_r2-121: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.3983 0.3898 0.636 90345. 4769.5 0.0343 2.562 2.282 1.376 0.239 1 0.3764 0.3709 0.662 89305. 4724.2 0.0081 0.642 1.733 1.040 0.175 2 0.3696 0.3652 0.670 88857. 4703.8 0.0058 0.458 1.573 0.942 0.149 3 0.3653 0.3616 0.675 88626. 4694.8 0.0049 0.393 1.472 0.879 0.131 4 0.3624 0.3599 0.678 88521. 4691.3 0.0044 0.353 1.398 0.834 0.119 5 0.3605 0.3585 0.681 88412. 4686.8 0.0040 0.325 1.338 0.798 0.108 6 0.3591 0.3573 0.682 88316. 4682.7 0.0037 0.305 1.288 0.768 0.100 7 0.3580 0.3568 0.682 88207. 4677.8 0.0035 0.289 1.252 0.746 0.097 8 0.3572 0.3562 0.684 88173. 4675.9 0.0033 0.276 1.222 0.727 0.095 9 0.3566 0.3558 0.685 88138. 4674.5 0.0031 0.265 1.198 0.712 0.094 10 0.3560 0.3553 0.686 88113. 4673.6 0.0030 0.256 1.178 0.699 0.092 11 0.3556 0.3550 0.688 88102. 4672.9 0.0029 0.249 1.158 0.686 0.091 12 0.3552 0.3549 0.689 88114. 4674.1 0.0028 0.242 1.141 0.675 0.090 13 0.3549 0.3546 0.689 88111. 4674.3 0.0027 0.237 1.126 0.666 0.089 14 0.3547 0.3543 0.689 88125. 4675.2 0.0027 0.232 1.112 0.657 0.088 15 0.3545 0.3541 0.689 88130. 4675.7 0.0026 0.228 1.100 0.650 0.088 16 0.3543 0.3540 0.690 88123. 4675.5 0.0026 0.224 1.089 0.643 0.087 17 0.3541 0.3539 0.689 88115. 4675.2 0.0025 0.221 1.080 0.637 0.087 18 0.3539 0.3537 0.690 88104. 4674.8 0.0025 0.218 1.071 0.631 0.086 19 0.3537 0.3535 0.690 88099. 4674.5 0.0025 0.216 1.062 0.626 0.086 20 0.3536 0.3532 0.690 88091. 4674.2 0.0024 0.213 1.055 0.621 0.085 21 0.3534 0.3532 0.690 88083. 4674.0 0.0024 0.211 1.048 0.616 0.085 22 0.3533 0.3532 0.691 88076. 4673.8 0.0024 0.209 1.041 0.612 0.084 23 0.3532 0.3533 0.691 88062. 4673.2 0.0024 0.207 1.036 0.608 0.084 24 0.3531 0.3535 0.691 88041. 4672.4 0.0023 0.206 1.030 0.604 0.084 25 0.3529 0.3535 0.691 88032. 4672.2 0.0023 0.204 1.025 0.601 0.083 26 0.3528 0.3535 0.691 88026. 4672.1 0.0023 0.203 1.020 0.598 0.083 27 0.3527 0.3534 0.691 88022. 4671.9 0.0023 0.202 1.015 0.594 0.083 28 0.3526 0.3534 0.692 88016. 4671.7 0.0023 0.201 1.011 0.592 0.082 29 0.3525 0.3534 0.692 88021. 4672.2 0.0023 0.200 1.007 0.589 0.082 30 0.3525 0.3535 0.692 88016. 4672.1 0.0023 0.199 1.004 0.587 0.082 $$ Output MTZ file from Refmac for model 6p4d_A1_PHR_MO_s0.55_r2-121 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6p4d_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_6p4d_A1_PHR_MO_s0.55_r2-121.mtz Output PDB file from Refmac for model 6p4d_A1_PHR_MO_s0.55_r2-121: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6p4d_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_6p4d_A1_PHR_MO_s0.55_r2-121.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 53 MR programs being used: MOLREP PHASER Best search model so far: 1iot_A1_PHR_MO_s0.55_r2-121 using MOLREP Initial Rfree: 0.406 Final Rfree: 0.353 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1iot_A1_PHR_MO_s0.55_r2-121.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 1iot_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.35 1.00 1.00 -- -- -- -- 6p4d_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.35 1.00 1.00 -- -- -- -- 1iot_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2816.00 57.30 0.35 0.35 1.00 1.00 -- -- -- -- 1fly_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.36 1.00 1.00 -- -- -- -- 1fly_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2601.00 56.60 0.35 0.36 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.37 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2663.00 56.60 0.35 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 PHASER MARGINAL 1571.00 42.20 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 PHASER MARGINAL 1567.00 41.40 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 PHASER MARGINAL 1083.00 38.10 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 MOLREP MARGINAL -- -- 0.40 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 PHASER MARGINAL 558.00 27.80 0.40 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 680.00 29.10 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.38 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 724.00 29.70 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 662.00 28.50 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 53: 6p4d_A1_PHR_MO_s0.55_r2-121 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6p4d_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_6p4d_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.55 Search model type: MOLREP Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6p4d_A1_PHR\molrep\mr\phaser\phaser_6p4d_A1_PHR_MO_s0.55_r2-121.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6p4d_A1_PHR\molrep\mr\phaser\phaser_6p4d_A1_PHR_MO_s0.55_r2-121.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6p4d_A1_PHR\molrep\mr\phaser\phaser_6p4d_A1_PHR_MO_s0.55_r2-121.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6p4d_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_HKLOUT_6p4d_A1_PHR_MO_s0.55_r2-121.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6p4d_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_6p4d_A1_PHR_MO_s0.55_r2-121.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6p4d_A1_PHR\molrep\mr\phaser\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6p4d_A1_PHR\molrep\mr\phaser\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '6p4d_A1_PHR_MO_s0.55_r2-121' ######################################################################### ###################################################################### ##### Results from Phaser for 6p4d_A1_PHR_MO_s0.55_r2-121: ##### ###################################################################### Template Model: 6p4d_A1_PHR_MO_s0.55_r2-121 has produced a marginal solution, final Rfree = 0.355 Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6p4d_A1_PHR\molrep\mr\phaser\phaser_6p4d_A1_PHR_MO_s0.55_r2-121.log Phaser PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6p4d_A1_PHR\molrep\mr\phaser\phaser_6p4d_A1_PHR_MO_s0.55_r2-121.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6p4d_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_6p4d_A1_PHR_MO_s0.55_r2-121.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6p4d_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_6p4d_A1_PHR_MO_s0.55_r2-121.pdb #################################################################################################### ##### Refinement results from Refmac for 6p4d_A1_PHR_MO_s0.55_r2-121: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 6p4d_A1_PHR_MO_s0.55_r2-121: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.3797 0.3752 0.669 89321. 4715.3 0.0343 2.564 2.282 1.376 0.239 1 0.3728 0.3679 0.671 88922. 4704.0 0.0081 0.642 1.729 1.037 0.186 2 0.3670 0.3634 0.676 88628. 4692.7 0.0057 0.457 1.574 0.942 0.159 3 0.3637 0.3610 0.680 88493. 4688.3 0.0049 0.394 1.473 0.880 0.139 4 0.3614 0.3592 0.683 88385. 4684.1 0.0044 0.354 1.399 0.836 0.125 5 0.3597 0.3582 0.684 88336. 4682.8 0.0040 0.326 1.339 0.800 0.115 6 0.3586 0.3577 0.685 88252. 4679.4 0.0037 0.305 1.287 0.768 0.101 7 0.3576 0.3571 0.686 88212. 4678.0 0.0035 0.289 1.251 0.745 0.098 8 0.3569 0.3567 0.686 88183. 4676.9 0.0033 0.275 1.222 0.727 0.096 9 0.3563 0.3567 0.687 88155. 4675.8 0.0031 0.265 1.198 0.712 0.095 10 0.3558 0.3562 0.687 88137. 4675.1 0.0030 0.256 1.177 0.699 0.094 11 0.3554 0.3559 0.688 88117. 4674.1 0.0029 0.249 1.159 0.687 0.093 12 0.3550 0.3556 0.689 88111. 4674.1 0.0028 0.243 1.141 0.676 0.091 13 0.3547 0.3552 0.690 88094. 4673.5 0.0027 0.237 1.126 0.666 0.090 14 0.3545 0.3549 0.690 88086. 4673.2 0.0027 0.232 1.113 0.658 0.090 15 0.3544 0.3544 0.690 88089. 4673.4 0.0026 0.228 1.101 0.650 0.089 16 0.3540 0.3543 0.690 88090. 4673.9 0.0026 0.224 1.090 0.643 0.088 17 0.3538 0.3545 0.691 88091. 4674.3 0.0025 0.221 1.080 0.637 0.088 18 0.3537 0.3543 0.691 88096. 4674.9 0.0025 0.218 1.071 0.631 0.087 19 0.3537 0.3539 0.691 88078. 4673.7 0.0025 0.215 1.063 0.626 0.087 20 0.3536 0.3539 0.691 88075. 4673.8 0.0024 0.213 1.056 0.621 0.086 21 0.3534 0.3538 0.692 88074. 4674.1 0.0024 0.211 1.049 0.616 0.086 22 0.3533 0.3540 0.692 88072. 4674.2 0.0024 0.209 1.043 0.612 0.085 23 0.3532 0.3541 0.692 88059. 4673.8 0.0024 0.208 1.037 0.608 0.085 24 0.3531 0.3539 0.691 88051. 4673.6 0.0024 0.206 1.032 0.605 0.085 25 0.3530 0.3540 0.692 88042. 4673.3 0.0023 0.205 1.029 0.603 0.085 26 0.3530 0.3542 0.692 88040. 4673.3 0.0023 0.204 1.026 0.601 0.084 27 0.3529 0.3543 0.692 88029. 4672.9 0.0023 0.203 1.023 0.599 0.084 28 0.3527 0.3546 0.692 88015. 4672.6 0.0023 0.202 1.018 0.596 0.084 29 0.3526 0.3545 0.692 88014. 4672.7 0.0023 0.201 1.016 0.594 0.084 30 0.3526 0.3546 0.692 88023. 4673.6 0.0023 0.201 1.013 0.592 0.084 $$ Output MTZ file from Refmac for model 6p4d_A1_PHR_MO_s0.55_r2-121 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6p4d_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_6p4d_A1_PHR_MO_s0.55_r2-121.mtz Output PDB file from Refmac for model 6p4d_A1_PHR_MO_s0.55_r2-121: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\6p4d_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_6p4d_A1_PHR_MO_s0.55_r2-121.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 54 MR programs being used: MOLREP PHASER Best search model so far: 1iot_A1_PHR_MO_s0.55_r2-121 using MOLREP Initial Rfree: 0.406 Final Rfree: 0.353 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1iot_A1_PHR_MO_s0.55_r2-121.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 1iot_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.35 1.00 1.00 -- -- -- -- 6p4d_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.35 1.00 1.00 -- -- -- -- 1iot_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2816.00 57.30 0.35 0.35 1.00 1.00 -- -- -- -- 6p4d_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2999.00 56.40 0.35 0.35 1.00 1.00 -- -- -- -- 1fly_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.36 1.00 1.00 -- -- -- -- 1fly_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2601.00 56.60 0.35 0.36 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.37 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2663.00 56.60 0.35 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 PHASER MARGINAL 1571.00 42.20 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 PHASER MARGINAL 1567.00 41.40 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 PHASER MARGINAL 1083.00 38.10 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 MOLREP MARGINAL -- -- 0.40 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 PHASER MARGINAL 558.00 27.80 0.40 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 680.00 29.10 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.38 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 724.00 29.70 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 662.00 28.50 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 54: 1gf3_A1_PHR_MO_s0.53_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gf3_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1gf3_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.53 Search model type: MOLREP Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gf3_A1_PHR\molrep\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gf3_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1gf3_A1_PHR_MO_s0.53_r1-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gf3_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1gf3_A1_PHR_MO_s0.53_r1-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gf3_A1_PHR\molrep\mr\molrep\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gf3_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1gf3_A1_PHR_MO_s0.53_r1-123' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 1gf3_A1_PHR_MO_s0.53_r1-123: ##### ################################################################################################# Template Model: 1gf3_A1_PHR_MO_s0.53_r1-123 has produced a marginal solution, final Rfree = 0.401 Molrep log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gf3_A1_PHR\molrep\mr\molrep\molrep.log Molrep PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gf3_A1_PHR\molrep\mr\molrep\molrep_1gf3_A1_PHR_MO_s0.53_r1-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gf3_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1gf3_A1_PHR_MO_s0.53_r1-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gf3_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1gf3_A1_PHR_MO_s0.53_r1-123.pdb #################################################################################################### ##### Refinement results from Refmac for 1gf3_A1_PHR_MO_s0.53_r1-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1gf3_A1_PHR_MO_s0.53_r1-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4785 0.4917 0.444 93288. 4935.4 0.0281 2.298 2.529 1.554 0.346 1 0.4512 0.4671 0.471 92498. 4904.9 0.0083 0.650 1.908 1.163 0.275 2 0.4373 0.4518 0.497 91933. 4878.1 0.0067 0.525 1.738 1.054 0.222 3 0.4280 0.4394 0.519 91632. 4863.7 0.0061 0.475 1.638 0.987 0.174 4 0.4210 0.4309 0.534 91395. 4852.3 0.0057 0.443 1.574 0.938 0.147 5 0.4156 0.4257 0.544 91228. 4845.3 0.0054 0.419 1.525 0.901 0.132 6 0.4115 0.4231 0.553 91132. 4840.8 0.0051 0.399 1.481 0.870 0.123 7 0.4083 0.4212 0.560 91059. 4838.1 0.0049 0.380 1.445 0.844 0.117 8 0.4056 0.4200 0.566 90986. 4835.5 0.0047 0.366 1.416 0.822 0.113 9 0.4035 0.4188 0.570 90946. 4834.4 0.0044 0.350 1.385 0.800 0.107 10 0.4016 0.4176 0.575 90912. 4832.5 0.0042 0.336 1.365 0.784 0.105 11 0.4000 0.4167 0.579 90885. 4832.2 0.0040 0.323 1.340 0.768 0.105 12 0.3985 0.4157 0.582 90740. 4824.8 0.0038 0.312 1.318 0.755 0.104 13 0.3972 0.4146 0.584 90717. 4823.9 0.0037 0.302 1.299 0.743 0.104 14 0.3960 0.4131 0.587 90677. 4822.4 0.0035 0.292 1.282 0.732 0.103 15 0.3948 0.4121 0.589 90645. 4821.4 0.0034 0.284 1.267 0.723 0.103 16 0.3938 0.4107 0.591 90626. 4820.2 0.0033 0.278 1.253 0.714 0.102 17 0.3928 0.4094 0.593 90578. 4818.2 0.0033 0.272 1.240 0.706 0.102 18 0.3920 0.4088 0.594 90544. 4816.7 0.0032 0.267 1.228 0.699 0.101 19 0.3912 0.4077 0.594 90519. 4815.8 0.0031 0.263 1.217 0.693 0.101 20 0.3904 0.4069 0.595 90494. 4814.9 0.0031 0.258 1.208 0.688 0.101 21 0.3896 0.4061 0.597 90466. 4813.6 0.0030 0.255 1.200 0.682 0.100 22 0.3889 0.4055 0.598 90443. 4812.9 0.0030 0.251 1.192 0.677 0.100 23 0.3882 0.4048 0.599 90422. 4812.2 0.0029 0.248 1.184 0.672 0.100 24 0.3875 0.4043 0.602 90404. 4811.7 0.0029 0.245 1.177 0.668 0.100 25 0.3870 0.4037 0.604 90379. 4811.0 0.0029 0.242 1.168 0.663 0.100 26 0.3864 0.4031 0.604 90358. 4810.2 0.0028 0.239 1.162 0.659 0.100 27 0.3858 0.4026 0.605 90332. 4809.2 0.0028 0.237 1.156 0.655 0.099 28 0.3853 0.4021 0.605 90312. 4808.5 0.0028 0.235 1.150 0.651 0.099 29 0.3848 0.4016 0.606 90283. 4807.2 0.0027 0.233 1.145 0.648 0.099 30 0.3844 0.4010 0.606 90266. 4806.6 0.0027 0.231 1.141 0.645 0.099 $$ Output MTZ file from Refmac for model 1gf3_A1_PHR_MO_s0.53_r1-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gf3_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1gf3_A1_PHR_MO_s0.53_r1-123.mtz Output PDB file from Refmac for model 1gf3_A1_PHR_MO_s0.53_r1-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gf3_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1gf3_A1_PHR_MO_s0.53_r1-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 55 MR programs being used: MOLREP PHASER Best search model so far: 1iot_A1_PHR_MO_s0.55_r2-121 using MOLREP Initial Rfree: 0.406 Final Rfree: 0.353 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1iot_A1_PHR_MO_s0.55_r2-121.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 1iot_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.35 1.00 1.00 -- -- -- -- 6p4d_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.35 1.00 1.00 -- -- -- -- 1iot_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2816.00 57.30 0.35 0.35 1.00 1.00 -- -- -- -- 6p4d_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2999.00 56.40 0.35 0.35 1.00 1.00 -- -- -- -- 1fly_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.36 1.00 1.00 -- -- -- -- 1fly_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2601.00 56.60 0.35 0.36 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.37 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2663.00 56.60 0.35 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 PHASER MARGINAL 1571.00 42.20 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 PHASER MARGINAL 1567.00 41.40 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 PHASER MARGINAL 1083.00 38.10 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 MOLREP MARGINAL -- -- 0.40 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 PHASER MARGINAL 558.00 27.80 0.40 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 680.00 29.10 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1gf3_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.38 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.38 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 724.00 29.70 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 662.00 28.50 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 55: 1gf3_A1_PHR_MO_s0.53_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gf3_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1gf3_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.53 Search model type: MOLREP Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gf3_A1_PHR\molrep\mr\phaser\phaser_1gf3_A1_PHR_MO_s0.53_r1-123.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gf3_A1_PHR\molrep\mr\phaser\phaser_1gf3_A1_PHR_MO_s0.53_r1-123.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gf3_A1_PHR\molrep\mr\phaser\phaser_1gf3_A1_PHR_MO_s0.53_r1-123.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gf3_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_HKLOUT_1gf3_A1_PHR_MO_s0.53_r1-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gf3_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1gf3_A1_PHR_MO_s0.53_r1-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gf3_A1_PHR\molrep\mr\phaser\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gf3_A1_PHR\molrep\mr\phaser\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1gf3_A1_PHR_MO_s0.53_r1-123' ######################################################################### ###################################################################### ##### Results from Phaser for 1gf3_A1_PHR_MO_s0.53_r1-123: ##### ###################################################################### Template Model: 1gf3_A1_PHR_MO_s0.53_r1-123 has produced a marginal solution, final Rfree = 0.402 Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gf3_A1_PHR\molrep\mr\phaser\phaser_1gf3_A1_PHR_MO_s0.53_r1-123.log Phaser PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gf3_A1_PHR\molrep\mr\phaser\phaser_1gf3_A1_PHR_MO_s0.53_r1-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gf3_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1gf3_A1_PHR_MO_s0.53_r1-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gf3_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1gf3_A1_PHR_MO_s0.53_r1-123.pdb #################################################################################################### ##### Refinement results from Refmac for 1gf3_A1_PHR_MO_s0.53_r1-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1gf3_A1_PHR_MO_s0.53_r1-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4697 0.4750 0.469 92773. 4909.3 0.0281 2.302 2.530 1.555 0.346 1 0.4483 0.4551 0.486 92244. 4889.2 0.0091 0.698 1.894 1.154 0.278 2 0.4341 0.4407 0.510 91715. 4865.8 0.0068 0.533 1.731 1.050 0.225 3 0.4312 0.4362 0.520 91561. 4857.9 0.0055 0.440 1.615 0.974 0.186 4 0.4278 0.4326 0.523 91450. 4852.3 0.0050 0.402 1.537 0.922 0.156 5 0.4248 0.4299 0.533 91348. 4847.6 0.0047 0.381 1.479 0.883 0.137 6 0.4214 0.4270 0.541 91278. 4845.2 0.0045 0.365 1.432 0.851 0.125 7 0.4175 0.4244 0.548 91206. 4842.4 0.0044 0.355 1.400 0.828 0.118 8 0.4138 0.4225 0.555 91148. 4841.1 0.0043 0.349 1.377 0.810 0.113 9 0.4098 0.4210 0.561 91026. 4835.9 0.0043 0.347 1.363 0.797 0.109 10 0.4066 0.4194 0.566 90958. 4833.8 0.0043 0.342 1.352 0.785 0.105 11 0.4039 0.4187 0.570 90910. 4832.0 0.0042 0.333 1.338 0.773 0.104 12 0.4017 0.4177 0.574 90877. 4831.4 0.0040 0.324 1.322 0.762 0.103 13 0.3998 0.4160 0.579 90843. 4829.6 0.0039 0.315 1.304 0.750 0.103 14 0.3982 0.4153 0.583 90791. 4827.4 0.0038 0.305 1.286 0.739 0.102 15 0.3967 0.4140 0.585 90748. 4826.0 0.0036 0.295 1.272 0.729 0.102 16 0.3957 0.4133 0.588 90680. 4822.7 0.0035 0.287 1.258 0.720 0.102 17 0.3945 0.4122 0.591 90608. 4819.0 0.0034 0.280 1.245 0.712 0.101 18 0.3936 0.4110 0.593 90603. 4819.2 0.0033 0.274 1.232 0.704 0.101 19 0.3926 0.4097 0.594 90599. 4818.8 0.0032 0.269 1.220 0.697 0.100 20 0.3918 0.4085 0.596 90552. 4816.9 0.0031 0.264 1.209 0.690 0.100 21 0.3910 0.4075 0.598 90501. 4814.3 0.0031 0.259 1.199 0.684 0.100 22 0.3901 0.4065 0.600 90449. 4812.4 0.0030 0.255 1.191 0.679 0.099 23 0.3894 0.4057 0.601 90417. 4811.0 0.0030 0.251 1.182 0.674 0.099 24 0.3887 0.4051 0.602 90412. 4811.2 0.0029 0.248 1.175 0.669 0.099 25 0.3880 0.4045 0.603 90398. 4811.0 0.0029 0.245 1.168 0.664 0.098 26 0.3873 0.4041 0.604 90361. 4809.6 0.0029 0.243 1.161 0.660 0.098 27 0.3868 0.4036 0.605 90350. 4809.2 0.0028 0.240 1.155 0.657 0.098 28 0.3862 0.4029 0.608 90332. 4808.3 0.0028 0.237 1.150 0.653 0.098 29 0.3857 0.4024 0.610 90299. 4807.1 0.0028 0.234 1.144 0.649 0.097 30 0.3852 0.4019 0.609 90285. 4806.5 0.0027 0.232 1.139 0.646 0.097 $$ Output MTZ file from Refmac for model 1gf3_A1_PHR_MO_s0.53_r1-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gf3_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1gf3_A1_PHR_MO_s0.53_r1-123.mtz Output PDB file from Refmac for model 1gf3_A1_PHR_MO_s0.53_r1-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1gf3_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1gf3_A1_PHR_MO_s0.53_r1-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 56 MR programs being used: MOLREP PHASER Best search model so far: 1iot_A1_PHR_MO_s0.55_r2-121 using MOLREP Initial Rfree: 0.406 Final Rfree: 0.353 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1iot_A1_PHR_MO_s0.55_r2-121.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 1iot_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.35 1.00 1.00 -- -- -- -- 6p4d_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.35 1.00 1.00 -- -- -- -- 1iot_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2816.00 57.30 0.35 0.35 1.00 1.00 -- -- -- -- 6p4d_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2999.00 56.40 0.35 0.35 1.00 1.00 -- -- -- -- 1fly_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.36 1.00 1.00 -- -- -- -- 1fly_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2601.00 56.60 0.35 0.36 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.37 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2663.00 56.60 0.35 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 PHASER MARGINAL 1571.00 42.20 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 PHASER MARGINAL 1567.00 41.40 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 PHASER MARGINAL 1083.00 38.10 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 MOLREP MARGINAL -- -- 0.40 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 PHASER MARGINAL 558.00 27.80 0.40 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 680.00 29.10 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1gf3_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.38 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1gf3_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 697.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.38 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 724.00 29.70 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 662.00 28.50 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 56: 1b7s_A1_PHR_MO_s0.53_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1b7s_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1b7s_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.53 Search model type: MOLREP Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1b7s_A1_PHR\molrep\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1b7s_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1b7s_A1_PHR_MO_s0.53_r1-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1b7s_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1b7s_A1_PHR_MO_s0.53_r1-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1b7s_A1_PHR\molrep\mr\molrep\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1b7s_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1b7s_A1_PHR_MO_s0.53_r1-123' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 1b7s_A1_PHR_MO_s0.53_r1-123: ##### ################################################################################################# Template Model: 1b7s_A1_PHR_MO_s0.53_r1-123 has produced a marginal solution, final Rfree = 0.415 Molrep log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1b7s_A1_PHR\molrep\mr\molrep\molrep.log Molrep PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1b7s_A1_PHR\molrep\mr\molrep\molrep_1b7s_A1_PHR_MO_s0.53_r1-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1b7s_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1b7s_A1_PHR_MO_s0.53_r1-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1b7s_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1b7s_A1_PHR_MO_s0.53_r1-123.pdb #################################################################################################### ##### Refinement results from Refmac for 1b7s_A1_PHR_MO_s0.53_r1-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1b7s_A1_PHR_MO_s0.53_r1-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4871 0.4937 0.418 93818. 4957.1 0.0282 2.312 2.560 1.583 0.337 1 0.4624 0.4731 0.442 93011. 4924.9 0.0089 0.690 1.920 1.195 0.245 2 0.4483 0.4586 0.464 92450. 4897.2 0.0071 0.545 1.758 1.087 0.192 3 0.4373 0.4493 0.488 92041. 4877.6 0.0064 0.495 1.669 1.026 0.165 4 0.4298 0.4438 0.506 91746. 4863.9 0.0059 0.461 1.600 0.977 0.143 5 0.4251 0.4394 0.518 91673. 4861.8 0.0055 0.434 1.542 0.935 0.124 6 0.4234 0.4377 0.523 91588. 4858.4 0.0049 0.389 1.482 0.895 0.117 7 0.4216 0.4361 0.525 91529. 4856.0 0.0046 0.365 1.440 0.866 0.114 8 0.4197 0.4344 0.529 91463. 4853.3 0.0044 0.349 1.408 0.843 0.112 9 0.4177 0.4334 0.534 91387. 4851.5 0.0042 0.337 1.384 0.826 0.111 10 0.4156 0.4321 0.539 91299. 4847.6 0.0041 0.328 1.366 0.812 0.110 11 0.4134 0.4307 0.542 91192. 4843.0 0.0040 0.321 1.353 0.801 0.109 12 0.4108 0.4290 0.546 91128. 4840.3 0.0040 0.319 1.347 0.794 0.109 13 0.4084 0.4273 0.553 91085. 4837.7 0.0039 0.314 1.343 0.787 0.108 14 0.4064 0.4259 0.558 91001. 4833.8 0.0038 0.307 1.338 0.780 0.108 15 0.4047 0.4241 0.561 90958. 4831.9 0.0037 0.300 1.331 0.772 0.107 16 0.4031 0.4230 0.563 90898. 4828.6 0.0037 0.294 1.323 0.764 0.107 17 0.4016 0.4219 0.567 90826. 4824.8 0.0036 0.289 1.316 0.757 0.107 18 0.4004 0.4211 0.570 90790. 4823.3 0.0035 0.282 1.307 0.750 0.107 19 0.3992 0.4208 0.572 90792. 4823.4 0.0034 0.276 1.300 0.743 0.107 20 0.3981 0.4202 0.573 90766. 4822.7 0.0033 0.271 1.293 0.736 0.107 21 0.3972 0.4196 0.575 90759. 4822.5 0.0032 0.267 1.287 0.730 0.106 22 0.3963 0.4190 0.576 90730. 4820.8 0.0032 0.262 1.281 0.725 0.106 23 0.3955 0.4184 0.578 90709. 4819.1 0.0031 0.258 1.275 0.720 0.106 24 0.3947 0.4181 0.580 90676. 4818.0 0.0031 0.255 1.270 0.715 0.106 25 0.3940 0.4176 0.581 90654. 4817.0 0.0030 0.252 1.265 0.711 0.106 26 0.3933 0.4170 0.584 90628. 4815.4 0.0030 0.249 1.261 0.707 0.106 27 0.3927 0.4165 0.586 90608. 4814.7 0.0030 0.246 1.256 0.703 0.106 28 0.3921 0.4158 0.588 90605. 4814.6 0.0029 0.243 1.251 0.699 0.106 29 0.3915 0.4152 0.589 90586. 4813.8 0.0029 0.241 1.247 0.696 0.106 30 0.3909 0.4146 0.590 90568. 4812.9 0.0029 0.239 1.242 0.692 0.106 $$ Output MTZ file from Refmac for model 1b7s_A1_PHR_MO_s0.53_r1-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1b7s_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1b7s_A1_PHR_MO_s0.53_r1-123.mtz Output PDB file from Refmac for model 1b7s_A1_PHR_MO_s0.53_r1-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1b7s_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1b7s_A1_PHR_MO_s0.53_r1-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 57 MR programs being used: MOLREP PHASER Best search model so far: 1iot_A1_PHR_MO_s0.55_r2-121 using MOLREP Initial Rfree: 0.406 Final Rfree: 0.353 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1iot_A1_PHR_MO_s0.55_r2-121.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 1iot_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.35 1.00 1.00 -- -- -- -- 6p4d_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.35 1.00 1.00 -- -- -- -- 1iot_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2816.00 57.30 0.35 0.35 1.00 1.00 -- -- -- -- 6p4d_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2999.00 56.40 0.35 0.35 1.00 1.00 -- -- -- -- 1fly_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.36 1.00 1.00 -- -- -- -- 1fly_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2601.00 56.60 0.35 0.36 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.37 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2663.00 56.60 0.35 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 PHASER MARGINAL 1571.00 42.20 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 PHASER MARGINAL 1567.00 41.40 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 PHASER MARGINAL 1083.00 38.10 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 MOLREP MARGINAL -- -- 0.40 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 PHASER MARGINAL 558.00 27.80 0.40 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 680.00 29.10 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1gf3_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.38 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1gf3_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 697.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.38 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 724.00 29.70 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 662.00 28.50 0.39 0.41 1.00 1.00 -- -- -- -- 1b7s_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 57: 1b7s_A1_PHR_MO_s0.53_r1-123 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1b7s_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1b7s_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.53 Search model type: MOLREP Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1b7s_A1_PHR\molrep\mr\phaser\phaser_1b7s_A1_PHR_MO_s0.53_r1-123.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1b7s_A1_PHR\molrep\mr\phaser\phaser_1b7s_A1_PHR_MO_s0.53_r1-123.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1b7s_A1_PHR\molrep\mr\phaser\phaser_1b7s_A1_PHR_MO_s0.53_r1-123.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1b7s_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_HKLOUT_1b7s_A1_PHR_MO_s0.53_r1-123.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1b7s_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1b7s_A1_PHR_MO_s0.53_r1-123.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1b7s_A1_PHR\molrep\mr\phaser\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1b7s_A1_PHR\molrep\mr\phaser\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1b7s_A1_PHR_MO_s0.53_r1-123' ######################################################################### ###################################################################### ##### Results from Phaser for 1b7s_A1_PHR_MO_s0.53_r1-123: ##### ###################################################################### Template Model: 1b7s_A1_PHR_MO_s0.53_r1-123 has produced a marginal solution, final Rfree = 0.414 Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1b7s_A1_PHR\molrep\mr\phaser\phaser_1b7s_A1_PHR_MO_s0.53_r1-123.log Phaser PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1b7s_A1_PHR\molrep\mr\phaser\phaser_1b7s_A1_PHR_MO_s0.53_r1-123.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1b7s_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1b7s_A1_PHR_MO_s0.53_r1-123.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1b7s_A1_PHR\molrep\mr\phaser\refine\refmac_phaser_1b7s_A1_PHR_MO_s0.53_r1-123.pdb #################################################################################################### ##### Refinement results from Refmac for 1b7s_A1_PHR_MO_s0.53_r1-123: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1b7s_A1_PHR_MO_s0.53_r1-123: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4790 0.4875 0.432 92550. 4892.0 0.0282 2.314 2.561 1.583 0.337 1 0.4626 0.4673 0.448 92466. 4891.1 0.0085 0.675 1.936 1.205 0.260 2 0.4540 0.4591 0.459 92305. 4884.5 0.0061 0.490 1.748 1.080 0.204 3 0.4483 0.4535 0.476 92086. 4874.0 0.0054 0.441 1.637 1.007 0.173 4 0.4432 0.4478 0.489 91900. 4864.9 0.0052 0.415 1.564 0.959 0.157 5 0.4378 0.4434 0.499 91817. 4861.6 0.0050 0.399 1.507 0.919 0.133 6 0.4326 0.4397 0.510 91708. 4857.4 0.0049 0.390 1.468 0.892 0.122 7 0.4272 0.4356 0.522 91526. 4850.2 0.0049 0.388 1.447 0.874 0.118 8 0.4250 0.4340 0.527 91476. 4849.0 0.0045 0.358 1.412 0.849 0.116 9 0.4227 0.4320 0.532 91379. 4844.7 0.0043 0.345 1.388 0.831 0.114 10 0.4205 0.4304 0.535 91317. 4842.8 0.0042 0.335 1.368 0.816 0.113 11 0.4181 0.4294 0.541 91228. 4839.4 0.0041 0.328 1.354 0.804 0.112 12 0.4158 0.4277 0.545 91163. 4837.3 0.0041 0.322 1.344 0.795 0.112 13 0.4132 0.4266 0.552 91060. 4832.2 0.0040 0.317 1.337 0.788 0.111 14 0.4109 0.4248 0.555 91058. 4833.5 0.0039 0.313 1.332 0.781 0.111 15 0.4083 0.4228 0.560 90985. 4830.4 0.0039 0.309 1.328 0.775 0.110 16 0.4063 0.4218 0.564 90980. 4830.6 0.0038 0.303 1.321 0.767 0.110 17 0.4045 0.4214 0.567 90927. 4828.3 0.0037 0.296 1.312 0.759 0.109 18 0.4030 0.4203 0.570 90864. 4825.1 0.0036 0.291 1.305 0.752 0.109 19 0.4016 0.4197 0.572 90819. 4822.8 0.0035 0.284 1.297 0.745 0.108 20 0.4002 0.4189 0.575 90769. 4820.2 0.0035 0.280 1.290 0.739 0.108 21 0.3989 0.4183 0.578 90718. 4817.8 0.0034 0.275 1.283 0.732 0.108 22 0.3978 0.4177 0.581 90692. 4816.9 0.0033 0.270 1.275 0.726 0.107 23 0.3968 0.4174 0.582 90680. 4816.6 0.0032 0.265 1.269 0.720 0.107 24 0.3959 0.4169 0.583 90687. 4817.2 0.0032 0.261 1.263 0.715 0.107 25 0.3951 0.4163 0.584 90677. 4816.8 0.0031 0.257 1.257 0.710 0.107 26 0.3943 0.4161 0.585 90655. 4815.9 0.0031 0.253 1.252 0.706 0.106 27 0.3937 0.4155 0.587 90644. 4815.5 0.0030 0.250 1.246 0.702 0.106 28 0.3929 0.4147 0.588 90603. 4813.5 0.0030 0.247 1.240 0.697 0.106 29 0.3923 0.4143 0.590 90579. 4812.3 0.0029 0.244 1.234 0.693 0.105 30 0.3917 0.4141 0.591 90561. 4811.7 0.0029 0.241 1.228 0.689 0.105 $$ Output MTZ file from Refmac for model 1b7s_A1_PHR_MO_s0.53_r1-123 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1b7s_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1b7s_A1_PHR_MO_s0.53_r1-123.mtz Output PDB file from Refmac for model 1b7s_A1_PHR_MO_s0.53_r1-123: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1b7s_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1b7s_A1_PHR_MO_s0.53_r1-123.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 58 MR programs being used: MOLREP PHASER Best search model so far: 1iot_A1_PHR_MO_s0.55_r2-121 using MOLREP Initial Rfree: 0.406 Final Rfree: 0.353 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1iot_A1_PHR_MO_s0.55_r2-121.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 1iot_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.35 1.00 1.00 -- -- -- -- 6p4d_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.35 1.00 1.00 -- -- -- -- 1iot_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2816.00 57.30 0.35 0.35 1.00 1.00 -- -- -- -- 6p4d_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2999.00 56.40 0.35 0.35 1.00 1.00 -- -- -- -- 1fly_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.36 1.00 1.00 -- -- -- -- 1fly_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2601.00 56.60 0.35 0.36 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.37 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2663.00 56.60 0.35 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 PHASER MARGINAL 1571.00 42.20 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 PHASER MARGINAL 1567.00 41.40 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 PHASER MARGINAL 1083.00 38.10 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 MOLREP MARGINAL -- -- 0.40 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 PHASER MARGINAL 558.00 27.80 0.40 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 680.00 29.10 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1gf3_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.38 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1gf3_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 697.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.38 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 724.00 29.70 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 662.00 28.50 0.39 0.41 1.00 1.00 -- -- -- -- 1b7s_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 573.00 26.40 0.39 0.41 1.00 1.00 -- -- -- -- 1b7s_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 58: 2iff_Y1_PHR_MO_s0.55_r2-121 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2iff_Y1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_2iff_Y1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.55 Search model type: MOLREP Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2iff_Y1_PHR\molrep\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2iff_Y1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_2iff_Y1_PHR_MO_s0.55_r2-121.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2iff_Y1_PHR\molrep\mr\molrep\refine\refmac_molrep_2iff_Y1_PHR_MO_s0.55_r2-121.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2iff_Y1_PHR\molrep\mr\molrep\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2iff_Y1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '2iff_Y1_PHR_MO_s0.55_r2-121' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 2iff_Y1_PHR_MO_s0.55_r2-121: ##### ################################################################################################# Template Model: 2iff_Y1_PHR_MO_s0.55_r2-121 has produced a marginal solution, final Rfree = 0.388 Molrep log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2iff_Y1_PHR\molrep\mr\molrep\molrep.log Molrep PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2iff_Y1_PHR\molrep\mr\molrep\molrep_2iff_Y1_PHR_MO_s0.55_r2-121.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2iff_Y1_PHR\molrep\mr\molrep\refine\refmac_molrep_2iff_Y1_PHR_MO_s0.55_r2-121.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2iff_Y1_PHR\molrep\mr\molrep\refine\refmac_molrep_2iff_Y1_PHR_MO_s0.55_r2-121.pdb #################################################################################################### ##### Refinement results from Refmac for 2iff_Y1_PHR_MO_s0.55_r2-121: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 2iff_Y1_PHR_MO_s0.55_r2-121: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4634 0.4670 0.479 92484. 4888.2 0.0354 2.704 3.232 2.007 0.263 1 0.4376 0.4403 0.503 91488. 4843.9 0.0102 0.828 2.362 1.451 0.221 2 0.4266 0.4244 0.529 91032. 4818.3 0.0078 0.639 2.141 1.302 0.189 3 0.4193 0.4127 0.546 90754. 4802.5 0.0068 0.561 2.013 1.212 0.165 4 0.4141 0.4055 0.560 90470. 4787.2 0.0062 0.511 1.920 1.145 0.150 5 0.4128 0.4043 0.564 90394. 4783.4 0.0055 0.455 1.840 1.089 0.142 6 0.4110 0.4029 0.567 90355. 4781.6 0.0051 0.419 1.771 1.042 0.137 7 0.4093 0.4019 0.570 90320. 4780.8 0.0048 0.395 1.703 1.000 0.133 8 0.4075 0.4009 0.572 90288. 4779.8 0.0046 0.378 1.638 0.963 0.127 9 0.4056 0.4002 0.574 90237. 4778.4 0.0044 0.365 1.583 0.931 0.123 10 0.4035 0.3997 0.577 90161. 4775.1 0.0043 0.355 1.534 0.904 0.120 11 0.4013 0.3989 0.583 90077. 4772.4 0.0042 0.346 1.492 0.881 0.117 12 0.4003 0.3987 0.585 90032. 4770.9 0.0040 0.330 1.454 0.858 0.116 13 0.3990 0.3979 0.587 90002. 4770.3 0.0039 0.319 1.422 0.840 0.114 14 0.3979 0.3974 0.590 89948. 4768.0 0.0038 0.311 1.395 0.823 0.113 15 0.3968 0.3968 0.592 89916. 4767.3 0.0037 0.304 1.372 0.808 0.111 16 0.3957 0.3959 0.596 89879. 4766.0 0.0036 0.298 1.352 0.795 0.110 17 0.3945 0.3955 0.598 89845. 4764.9 0.0036 0.294 1.334 0.783 0.109 18 0.3934 0.3949 0.599 89803. 4763.5 0.0035 0.291 1.320 0.774 0.108 19 0.3924 0.3942 0.602 89769. 4762.4 0.0035 0.288 1.306 0.764 0.108 20 0.3915 0.3937 0.604 89731. 4761.4 0.0034 0.283 1.292 0.755 0.107 21 0.3905 0.3932 0.605 89707. 4760.5 0.0034 0.279 1.278 0.747 0.106 22 0.3897 0.3926 0.605 89690. 4760.0 0.0033 0.275 1.266 0.739 0.105 23 0.3890 0.3922 0.606 89674. 4759.7 0.0033 0.271 1.254 0.731 0.105 24 0.3883 0.3919 0.606 89668. 4760.0 0.0032 0.267 1.243 0.724 0.104 25 0.3876 0.3915 0.607 89655. 4759.7 0.0032 0.264 1.233 0.718 0.103 26 0.3870 0.3912 0.608 89640. 4759.3 0.0031 0.261 1.223 0.712 0.103 27 0.3865 0.3905 0.609 89647. 4759.9 0.0031 0.258 1.214 0.706 0.102 28 0.3859 0.3900 0.611 89624. 4758.6 0.0031 0.256 1.206 0.701 0.101 29 0.3854 0.3896 0.612 89603. 4757.5 0.0036 0.303 1.195 0.697 0.101 30 0.3848 0.3884 0.616 89585. 4757.2 0.0030 0.252 1.185 0.690 0.100 $$ Output MTZ file from Refmac for model 2iff_Y1_PHR_MO_s0.55_r2-121 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2iff_Y1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_2iff_Y1_PHR_MO_s0.55_r2-121.mtz Output PDB file from Refmac for model 2iff_Y1_PHR_MO_s0.55_r2-121: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2iff_Y1_PHR\molrep\mr\molrep\refine\refmac_molrep_2iff_Y1_PHR_MO_s0.55_r2-121.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 59 MR programs being used: MOLREP PHASER Best search model so far: 1iot_A1_PHR_MO_s0.55_r2-121 using MOLREP Initial Rfree: 0.406 Final Rfree: 0.353 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1iot_A1_PHR_MO_s0.55_r2-121.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 1iot_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.35 1.00 1.00 -- -- -- -- 6p4d_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.35 1.00 1.00 -- -- -- -- 1iot_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2816.00 57.30 0.35 0.35 1.00 1.00 -- -- -- -- 6p4d_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2999.00 56.40 0.35 0.35 1.00 1.00 -- -- -- -- 1fly_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.36 1.00 1.00 -- -- -- -- 1fly_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2601.00 56.60 0.35 0.36 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.37 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2663.00 56.60 0.35 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 PHASER MARGINAL 1571.00 42.20 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 PHASER MARGINAL 1567.00 41.40 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 PHASER MARGINAL 1083.00 38.10 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 2iff_Y1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 MOLREP MARGINAL -- -- 0.40 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 PHASER MARGINAL 558.00 27.80 0.40 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 680.00 29.10 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1gf3_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.38 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1gf3_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 697.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.38 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 724.00 29.70 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 662.00 28.50 0.39 0.41 1.00 1.00 -- -- -- -- 1b7s_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 573.00 26.40 0.39 0.41 1.00 1.00 -- -- -- -- 1b7s_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 59: 2iff_Y1_PHR_MO_s0.55_r2-121 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2iff_Y1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_2iff_Y1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.55 Search model type: MOLREP Molecular Replacement Program: PHASER Refinement Program: Refmac5 ####################################### Running Phaser...... ####################################### Phaser completed successfully Output Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2iff_Y1_PHR\molrep\mr\phaser\phaser_2iff_Y1_PHR_MO_s0.55_r2-121.log Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2iff_Y1_PHR\molrep\mr\phaser\phaser_2iff_Y1_PHR_MO_s0.55_r2-121.1.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2iff_Y1_PHR\molrep\mr\phaser\phaser_2iff_Y1_PHR_MO_s0.55_r2-121.1.pdb MR log: Spacegroup of solution from Phaser is: P 43 21 2 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Phaser) found 1 molecule(s) out of 1 requested. ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2iff_Y1_PHR\molrep\mr\phaser\refine\refmac_phaser_HKLOUT_2iff_Y1_PHR_MO_s0.55_r2-121.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2iff_Y1_PHR\molrep\mr\phaser\refine\refmac_phaser_2iff_Y1_PHR_MO_s0.55_r2-121.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2iff_Y1_PHR\molrep\mr\phaser\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2iff_Y1_PHR\molrep\mr\phaser\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '2iff_Y1_PHR_MO_s0.55_r2-121' ######################################################################### ###################################################################### ##### Results from Phaser for 2iff_Y1_PHR_MO_s0.55_r2-121: ##### ###################################################################### Template Model: 2iff_Y1_PHR_MO_s0.55_r2-121 has produced a marginal solution, final Rfree = 0.387 Phaser log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2iff_Y1_PHR\molrep\mr\phaser\phaser_2iff_Y1_PHR_MO_s0.55_r2-121.log Phaser PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2iff_Y1_PHR\molrep\mr\phaser\phaser_2iff_Y1_PHR_MO_s0.55_r2-121.1.pdb Refmac log file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2iff_Y1_PHR\molrep\mr\phaser\refine\refmac_phaser_2iff_Y1_PHR_MO_s0.55_r2-121.log Refmac PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2iff_Y1_PHR\molrep\mr\phaser\refine\refmac_phaser_2iff_Y1_PHR_MO_s0.55_r2-121.pdb #################################################################################################### ##### Refinement results from Refmac for 2iff_Y1_PHR_MO_s0.55_r2-121: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 2iff_Y1_PHR_MO_s0.55_r2-121: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4645 0.4589 0.467 90851. 4797.1 0.0354 2.701 3.233 2.007 0.263 1 0.4443 0.4398 0.488 90944. 4810.2 0.0105 0.835 2.438 1.501 0.227 2 0.4369 0.4320 0.509 90837. 4805.7 0.0077 0.636 2.193 1.335 0.199 3 0.4322 0.4268 0.523 90782. 4802.0 0.0067 0.552 2.048 1.235 0.174 4 0.4280 0.4225 0.533 90723. 4798.4 0.0061 0.500 1.947 1.162 0.157 5 0.4241 0.4179 0.544 90634. 4794.3 0.0056 0.464 1.878 1.108 0.145 6 0.4197 0.4122 0.554 90544. 4789.1 0.0053 0.438 1.813 1.062 0.136 7 0.4150 0.4057 0.561 90351. 4779.7 0.0051 0.419 1.734 1.017 0.127 8 0.4129 0.4035 0.564 90284. 4776.8 0.0047 0.390 1.663 0.977 0.124 9 0.4109 0.4020 0.567 90230. 4774.7 0.0045 0.375 1.602 0.944 0.122 10 0.4085 0.4001 0.572 90188. 4772.9 0.0044 0.363 1.550 0.916 0.119 11 0.4062 0.3989 0.577 90172. 4773.1 0.0043 0.353 1.506 0.891 0.116 12 0.4039 0.3970 0.581 90114. 4771.1 0.0042 0.344 1.469 0.870 0.114 13 0.4018 0.3958 0.585 90029. 4768.0 0.0041 0.338 1.441 0.853 0.112 14 0.3997 0.3952 0.588 89949. 4765.0 0.0040 0.331 1.415 0.837 0.111 15 0.3984 0.3947 0.590 89903. 4763.5 0.0039 0.318 1.388 0.820 0.110 16 0.3972 0.3942 0.592 89858. 4761.9 0.0038 0.310 1.366 0.806 0.109 17 0.3960 0.3936 0.594 89806. 4759.5 0.0037 0.303 1.348 0.794 0.108 18 0.3950 0.3932 0.596 89750. 4757.4 0.0036 0.298 1.331 0.783 0.107 19 0.3938 0.3924 0.599 89706. 4756.0 0.0036 0.293 1.316 0.773 0.106 20 0.3928 0.3914 0.602 89670. 4754.8 0.0035 0.288 1.301 0.763 0.105 21 0.3918 0.3905 0.605 89664. 4754.9 0.0035 0.285 1.286 0.754 0.105 22 0.3908 0.3899 0.607 89666. 4755.6 0.0034 0.281 1.272 0.745 0.104 23 0.3900 0.3896 0.608 89657. 4755.8 0.0034 0.277 1.260 0.737 0.103 24 0.3892 0.3891 0.609 89658. 4756.1 0.0033 0.274 1.249 0.730 0.102 25 0.3884 0.3887 0.610 89658. 4756.6 0.0033 0.270 1.238 0.723 0.102 26 0.3877 0.3884 0.612 89642. 4755.9 0.0032 0.267 1.228 0.717 0.101 27 0.3870 0.3879 0.614 89619. 4755.0 0.0032 0.263 1.219 0.711 0.100 28 0.3864 0.3876 0.615 89609. 4754.7 0.0031 0.260 1.209 0.704 0.100 29 0.3858 0.3871 0.617 89600. 4754.4 0.0031 0.257 1.201 0.699 0.099 30 0.3852 0.3870 0.617 89580. 4753.4 0.0036 0.306 1.189 0.694 0.098 $$ Output MTZ file from Refmac for model 2iff_Y1_PHR_MO_s0.55_r2-121 (marginal solution search model): C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2iff_Y1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_2iff_Y1_PHR_MO_s0.55_r2-121.mtz Output PDB file from Refmac for model 2iff_Y1_PHR_MO_s0.55_r2-121: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\2iff_Y1_PHR\molrep\mr\molrep\refine\refmac_molrep_2iff_Y1_PHR_MO_s0.55_r2-121.pdb ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 60 MR programs being used: MOLREP PHASER Best search model so far: 1iot_A1_PHR_MO_s0.55_r2-121 using MOLREP Initial Rfree: 0.406 Final Rfree: 0.353 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1iot_A1_PHR_MO_s0.55_r2-121.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 1iot_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.35 1.00 1.00 -- -- -- -- 6p4d_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.35 1.00 1.00 -- -- -- -- 1iot_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2816.00 57.30 0.35 0.35 1.00 1.00 -- -- -- -- 6p4d_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2999.00 56.40 0.35 0.35 1.00 1.00 -- -- -- -- 1fly_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.36 1.00 1.00 -- -- -- -- 1fly_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2601.00 56.60 0.35 0.36 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.37 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2663.00 56.60 0.35 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 PHASER MARGINAL 1571.00 42.20 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 PHASER MARGINAL 1567.00 41.40 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 PHASER MARGINAL 1083.00 38.10 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 2iff_Y1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 832.00 33.80 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 2iff_Y1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 MOLREP MARGINAL -- -- 0.40 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 PHASER MARGINAL 558.00 27.80 0.40 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 680.00 29.10 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1gf3_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.38 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1gf3_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 697.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.38 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 724.00 29.70 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 662.00 28.50 0.39 0.41 1.00 1.00 -- -- -- -- 1b7s_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 573.00 26.40 0.39 0.41 1.00 1.00 -- -- -- -- 1b7s_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ********************************************************************************* ********************************************************************************* ********************************************************************************* ##################################################### Template Model 60: 1kxy_A1_PHR_MO_s0.55_r2-121 ##################################################### Working directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1kxy_A1_PHR\molrep Input search model: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\models\range_1\MODEL_MOLREP_1kxy_A1_PHR.pdb Resolution range for this model: Not Known Estimated sequence identity: 0.55 Search model type: MOLREP Molecular Replacement Program: MOLREP Refinement Program: Refmac5 ################################################# Running Molrep...... ################################################# MR log: Molrep has produced a solution Output PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1kxy_A1_PHR\molrep\mr\molrep\molrep_hklinSG_out.pdb MR log: Spacegroup of solution from Molrep is: P43212 - this is the spacegroup of the input target MTZ file MR log: Molecular replacement (using Molrep) found 1 copies out of 1 requested ############################################################ Running Refmac: Restrained Refinement with Jelly Body...... ############################################################ Refinement log: Refmac completed successfully Output MTZ file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1kxy_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1kxy_A1_PHR_MO_s0.55_r2-121.mtz Output PDB file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1kxy_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1kxy_A1_PHR_MO_s0.55_r2-121.pdb ############################################################ Running Buccaneer to attempt model build... ############################################################ Running directory is: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1kxy_A1_PHR\molrep\mr\molrep\build\buccaneer Warning: no file output from cbuccaneer for this job Error: No output pdb file from cbuccaneer Log file written to: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1kxy_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_run.log No PDB output file from Buccaneer Finished job, checking results.... ######################################################################### Job has completed for model '1kxy_A1_PHR_MO_s0.55_r2-121' ######################################################################### ################################################################################################# ##### Summary of solutions from Molrep for 1kxy_A1_PHR_MO_s0.55_r2-121: ##### ################################################################################################# Template Model: 1kxy_A1_PHR_MO_s0.55_r2-121 has produced a solution, final Rfree = 0.343 #################################################################################################### ##### Refinement results from Refmac for 1kxy_A1_PHR_MO_s0.55_r2-121: ##### #################################################################################################### $TABLE: Rfactor analysis, stats vs cycle for model 1kxy_A1_PHR_MO_s0.55_r2-121: $GRAPHS :<Rfactor> vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.4036 0.3895 0.626 90708. 4772.3 0.0342 2.586 2.491 1.524 0.266 1 0.3797 0.3700 0.651 89466. 4720.3 0.0084 0.625 1.830 1.123 0.190 2 0.3712 0.3631 0.665 89019. 4698.3 0.0059 0.459 1.626 0.994 0.157 3 0.3661 0.3592 0.675 88798. 4688.0 0.0050 0.399 1.495 0.911 0.127 4 0.3630 0.3563 0.681 88634. 4681.6 0.0044 0.361 1.399 0.852 0.112 5 0.3611 0.3547 0.682 88572. 4680.2 0.0041 0.332 1.326 0.806 0.104 6 0.3596 0.3530 0.684 88489. 4677.0 0.0037 0.309 1.265 0.767 0.096 7 0.3585 0.3517 0.686 88427. 4675.3 0.0035 0.291 1.219 0.738 0.093 8 0.3575 0.3503 0.687 88358. 4672.6 0.0033 0.277 1.182 0.714 0.091 9 0.3567 0.3493 0.687 88303. 4670.4 0.0032 0.265 1.152 0.695 0.090 10 0.3561 0.3483 0.687 88279. 4670.2 0.0031 0.256 1.127 0.679 0.089 11 0.3555 0.3477 0.688 88250. 4669.4 0.0029 0.248 1.105 0.664 0.089 12 0.3549 0.3469 0.689 88219. 4668.1 0.0028 0.241 1.087 0.652 0.088 13 0.3545 0.3464 0.690 88194. 4667.8 0.0028 0.234 1.071 0.641 0.088 14 0.3541 0.3462 0.690 88164. 4666.8 0.0027 0.229 1.055 0.631 0.087 15 0.3537 0.3458 0.691 88147. 4666.4 0.0026 0.225 1.039 0.621 0.087 16 0.3533 0.3454 0.691 88131. 4666.1 0.0026 0.221 1.027 0.613 0.086 17 0.3530 0.3450 0.691 88125. 4666.2 0.0025 0.217 1.017 0.606 0.086 18 0.3526 0.3448 0.691 88112. 4666.0 0.0025 0.215 1.008 0.600 0.086 19 0.3525 0.3446 0.692 88098. 4665.5 0.0025 0.213 1.003 0.597 0.086 20 0.3523 0.3445 0.692 88077. 4664.6 0.0024 0.212 0.998 0.594 0.085 21 0.3520 0.3442 0.692 88063. 4664.2 0.0024 0.209 0.990 0.589 0.085 22 0.3518 0.3440 0.692 88051. 4663.9 0.0024 0.207 0.983 0.584 0.085 23 0.3516 0.3439 0.693 88053. 4664.5 0.0024 0.206 0.977 0.580 0.084 24 0.3514 0.3436 0.693 88046. 4664.4 0.0023 0.204 0.972 0.576 0.084 25 0.3512 0.3435 0.693 88037. 4664.0 0.0023 0.203 0.966 0.573 0.084 26 0.3511 0.3433 0.693 88030. 4664.0 0.0023 0.202 0.961 0.570 0.084 27 0.3509 0.3433 0.694 88021. 4663.8 0.0023 0.201 0.957 0.567 0.084 28 0.3508 0.3432 0.694 88013. 4663.6 0.0023 0.200 0.953 0.564 0.083 29 0.3506 0.3432 0.694 88003. 4663.5 0.0023 0.199 0.949 0.562 0.083 30 0.3505 0.3432 0.694 87996. 4663.4 0.0023 0.198 0.946 0.560 0.083 $$ $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 60 MR programs being used: MOLREP PHASER Best search model so far: 1iot_A1_PHR_MO_s0.55_r2-121 using MOLREP Initial Rfree: 0.406 Final Rfree: 0.353 Solution Type: MARGINAL Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1iot_A1_PHR_MO_s0.55_r2-121.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1iot_A1_PHR_MO_s0.55_r2-121.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1iot_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_1iot_A1_PHR_MO_s0.55_r2-121.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 1iot_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.35 1.00 1.00 -- -- -- -- 6p4d_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.35 1.00 1.00 -- -- -- -- 1iot_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2816.00 57.30 0.35 0.35 1.00 1.00 -- -- -- -- 6p4d_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2999.00 56.40 0.35 0.35 1.00 1.00 -- -- -- -- 1fly_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.36 1.00 1.00 -- -- -- -- 1fly_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2601.00 56.60 0.35 0.36 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.37 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2663.00 56.60 0.35 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 PHASER MARGINAL 1571.00 42.20 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 PHASER MARGINAL 1567.00 41.40 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 PHASER MARGINAL 1083.00 38.10 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 2iff_Y1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 832.00 33.80 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 2iff_Y1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 MOLREP MARGINAL -- -- 0.40 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 PHASER MARGINAL 558.00 27.80 0.40 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 680.00 29.10 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1gf3_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.38 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1gf3_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 697.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.38 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 724.00 29.70 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 662.00 28.50 0.39 0.41 1.00 1.00 -- -- -- -- 1b7s_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 573.00 26.40 0.39 0.41 1.00 1.00 -- -- -- -- 1b7s_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ############################################################## ####### Solution for Target/Job: 1 ######## ############################################################## Solution template structure: 1kxy Chain: 1kxy_A1_PHR Model Preparation Method: MOLREP Molecular Replacement Method: MOLREP Refinement Method: Refmac Initial Rfree: 0.404 and Rfree after 30 cycles: 0.343 Refined PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1kxy_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1kxy_A1_PHR_MO_s0.55_r2-121.pdbUdpdated MTZ file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1kxy_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1kxy_A1_PHR_MO_s0.55_r2-121.mtz Solution files can be found in the following directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\results\solution ############################################################## ******************************************************************************************* $$ $TEXT:Summary: $$ Summary $$ ################################################################# ### MrBUMP Summary: Sorted results so far... ### ################################################################# Total number of MR jobs: 180 Number of MR jobs run so far: 60 MR programs being used: MOLREP PHASER Best search model so far: 1kxy_A1_PHR_MO_s0.55_r2-121 using MOLREP Initial Rfree: 0.404 Final Rfree: 0.343 Solution Type: GOOD Solution Spacegroup: Files for best search model: Refmac PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1kxy_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1kxy_A1_PHR_MO_s0.55_r2-121.pdb Refmac MTZOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1kxy_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1kxy_A1_PHR_MO_s0.55_r2-121.mtz Refmac LOG: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1kxy_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1kxy_A1_PHR_MO_s0.55_r2-121.log Buccaneer PDBOUT: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1kxy_A1_PHR\molrep\mr\molrep\build\buccaneer\buccaneer_molrep_1kxy_A1_PHR_MO_s0.55_r2-121.pdb Complete list of solutions so far: LEGEND: Model_Name = chain from PDB model and what program was used to prepare it for MR MR_Program = molecular replacement program used Solution_Type = rough assesement of correctness of MR solution Phaser_LLG = Final Log Likelihood Gain score from Phaser Phaser_TFZ = Final Translation function Z-score from Phaser final_Rfact = final Rfactor for MR solution after 30 cycles of restrained refinement in Refmac final_Rfree = final Rfree for MR solution after 30 cycles of restrained refinement in Refmac Bucc_final_Rfact = final Rfactor from Buccaneer model building step post MR and refinement Bucc_final_Rfree = final Rfree from Buccaneer model building step post MR and refinement ARP_final_Rfact = final Rfactor from ARP/wARP model building step post MR and refinement ARP_final_Rfree = final Rfree from ARP/wARP model building step post MR and refinement SHELXE_CC = correlation coefficient between model and experimental data from SHELXE after density modification and c-alpha tracing (greater than 25% for possible solution) SHELXE_ACL = average chain fragment length in SHELXE c-alpha trace (greater than 10 for possible solution) Model_Name MR_Program Solution_Type Phaser_LLG Phaser_TFZ final_Rfact final_Rfree Bucc_final_Rfact Bucc_final_Rfree ARP_final_Rfact ARP_final_Rfree SHELXE_CC SHELXE_ACL 1kxy_A1_PHR_MO_s0.55_r2-121 MOLREP GOOD -- -- 0.35 0.34 1.00 1.00 -- -- -- -- 1iot_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.35 1.00 1.00 -- -- -- -- 6p4d_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.35 1.00 1.00 -- -- -- -- 1iot_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2816.00 57.30 0.35 0.35 1.00 1.00 -- -- -- -- 6p4d_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2999.00 56.40 0.35 0.35 1.00 1.00 -- -- -- -- 1fly_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.36 1.00 1.00 -- -- -- -- 1fly_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2601.00 56.60 0.35 0.36 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.35 0.37 1.00 1.00 -- -- -- -- 1lze_A1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 2663.00 56.60 0.35 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.37 1.00 1.00 -- -- -- -- 5v92_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1094.00 35.70 0.38 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_CH_s0.57_r2-123 PHASER MARGINAL 1571.00 42.20 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 PHASER MARGINAL 1567.00 41.40 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_SC_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 MOLREP MARGINAL -- -- 0.37 0.37 1.00 1.00 -- -- -- -- 5v8g_A1_PHR_MO_s0.57_r2-123 PHASER MARGINAL 1615.00 42.30 0.37 0.37 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.38 1.00 1.00 -- -- -- -- 2ihl_A1_PHR_MO_s0.56_r4-121 PHASER MARGINAL 1083.00 38.10 0.38 0.38 1.00 1.00 -- -- -- -- 6d9i_B1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1124.00 36.40 0.38 0.38 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 PHASER MARGINAL 1072.00 36.80 0.38 0.39 1.00 1.00 -- -- -- -- 1lmq_A1_PHR_MO_s0.56_r2-123 MOLREP MARGINAL -- -- 0.38 0.39 1.00 1.00 -- -- -- -- 2iff_Y1_PHR_MO_s0.55_r2-121 PHASER MARGINAL 832.00 33.80 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 593.00 27.90 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 2iff_Y1_PHR_MO_s0.55_r2-121 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1d6q_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 760.00 29.50 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i1z_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 650.00 29.10 0.39 0.39 1.00 1.00 -- -- -- -- 1oub_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 MOLREP MARGINAL -- -- 0.39 0.39 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_MO_s0.56_r1-123 PHASER MARGINAL 593.00 27.80 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 MOLREP MARGINAL -- -- 0.40 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 602.00 28.50 0.39 0.40 1.00 1.00 -- -- -- -- 1i22_D1_PHR_CH_s0.56_r1-123 PHASER MARGINAL 558.00 27.80 0.40 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1gfr_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 680.00 29.10 0.39 0.40 1.00 1.00 -- -- -- -- 1i20_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.40 1.00 1.00 -- -- -- -- 1gf3_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.38 0.40 1.00 1.00 -- -- -- -- 1wqm_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 643.00 28.80 0.39 0.40 1.00 1.00 -- -- -- -- 1gf3_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 697.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.38 0.40 1.00 1.00 -- -- -- -- 1ge3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 716.00 29.60 0.39 0.40 1.00 1.00 -- -- -- -- 1gfk_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 724.00 29.70 0.39 0.40 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 PHASER MARGINAL 547.00 27.20 0.39 0.41 1.00 1.00 -- -- -- -- 3lhm_A1_PHR_MO_s0.55_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1di3_A1_PHR_MO_s0.54_r1-123 PHASER MARGINAL 662.00 28.50 0.39 0.41 1.00 1.00 -- -- -- -- 1b7s_A1_PHR_MO_s0.53_r1-123 PHASER MARGINAL 573.00 26.40 0.39 0.41 1.00 1.00 -- -- -- -- 1b7s_A1_PHR_MO_s0.53_r1-123 MOLREP MARGINAL -- -- 0.39 0.41 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 PHASER MARGINAL 321.00 21.30 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_MO_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_CH_s1.00_r1-125 MOLREP MARGINAL -- -- 0.42 0.43 1.00 1.00 -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1jug_A1_PHR_SC_s1.00_r1-125 PHASER POOR 324.00 21.40 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 MOLREP POOR -- -- 1.00 1.00 N/A N/A -- -- -- -- 1i22_D1_PHR_SC_s0.56_r1-123 PHASER POOR 562.00 27.80 1.00 1.00 N/A N/A -- -- -- -- $$ ################################################################# ################################################################# ############################################################## ####### Solution for Target/Job: 1 ######## ############################################################## Solution template structure: 1kxy Chain: 1kxy_A1_PHR Model Preparation Method: MOLREP Molecular Replacement Method: MOLREP Refinement Method: Refmac Initial Rfree: 0.404 and Rfree after 30 cycles: 0.343 Refined PDB file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1kxy_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_1kxy_A1_PHR_MO_s0.55_r2-121.pdbUdpdated MTZ file: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\data\1kxy_A1_PHR\molrep\mr\molrep\refine\refmac_molrep_HKLOUT_1kxy_A1_PHR_MO_s0.55_r2-121.mtz Solution files can be found in the following directory: C:\DATA\Marek\2023\CB080\Lyso-teach\search_1\results\solution ############################################################## ############################################## ### MrBUMP Program References ### ############################################## $$ $TEXT:Program References: $$ References $$ Any publication arising from use of MrBUMP should include the following reference: R.M. Keegan, S.J. McNicholas, J.M.H. Thomas, A.J. Simpkin, F. Simkovic, V. Uski, C.C. Ballard, M.D. Winn, K.S. Wilson and D.J. Rigden (2018) Acta Cryst. D74, 167-182 In addition, authors of specific programs should be referenced where applicable: CCP4: M.D.Winn et al. (2011) Overview of the CCP4 suite and current developments Acta. Cryst. D67 , 235-242 CLUSTALW: Chenna, Ramu, Sugawara, Hideaki, Koike,Tadashi, Lopez, Rodrigo, Gibson, Toby J, Higgins, Desmond G, Thompson, Julie D. (2003) 'Multiple sequence alignment with the Clustal series of programs' Nucleic Acids Res 31, 3497-500 CHAINSAW: N.D.Stein (2008) 'CHAINSAW: a program for mutating pdb files used as templates in molecular replacement' J. Appl. Cryst. 41, 641-643 PHASER.SCULPTOR: Bunkoczi G. and Read R.J. (2011) 'Improvement of molecular-replacement models with Sculptor' Acta Cryst. D67, 303-312 MOLREP: Vagin A.A. & Teplyakov A. (1997) J. Appl. Cryst. 30, 1022-1025 PHASER: McCoy, A.J., Grosse-Kunstleve, R.W., Adams, P.D., Winn, M.D., Storoni, L.C. & Read, R.J. (2007) Phaser crystallographic software' J. Appl. Cryst. 40, 658-674 REFMAC: Murshudov G.N., Vagin A.A. and Dodson E.J., (1997) 'Refinement of Macromolecular Structures by the Maximum-Likelihood Method' Acta Cryst. D53, 240-255 BUCCANEER: Cowtan K. (2006) 'The Buccaneer software for automated model building' Acta Cryst. D62, 1002-1011. $$ *************************************************************************** * Information from CCP4Interface script *************************************************************************** The program run with command: C:/CCP4-8/8.0/bin/mrbump HKLIN C:/DATA/Marek/2023/CB080/molrep/lyso-2016-HD_sg96.mtz SEQIN C:/DATA/Marek/2023/CB080/molrep/1JUG.fasta.pir HKLOUT C:/DATA/Marek/2023/CB080/Lyso-teach/lyso-2016-HD_sg96_mrbump_soln1.mtz XYZOUT C:/DATA/Marek/2023/CB080/Lyso-teach/lyso-2016-HD_sg96_mrbump_soln1.pdb KEYIN C:/Users/Rigaku/AppData/Local/Temp/Lyso-T_1_1_com.tmp has failed with error message Error: Could not find output PDB from Refmac, can't run Buccaneer Error: Could not find output PDB from Refmac, can't run Buccaneer *************************************************************************** #CCP4I TERMINATION STATUS 0 "Error: Could not find output PDB from Refmac, can't run Buccaneer Error: Could not find output PDB from Refmac, can't run Buccaneer " #CCP4I TERMINATION TIME 20 Jan 2023 13:30:56 #CCP4I TERMINATION OUTPUT_FILES C:/DATA/Marek/2023/CB080/Lyso-teach/search_1 #CCP4I MESSAGE Task failed