#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
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### CCP4 7.1: MRBUMP version 2.2.6 : 20 Sep 2021 ##
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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
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Keyword input summary:
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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
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Web connectivity test enabled. Checking PDB servers for file availability....
(Note: Disable this in the MrBUMP interface if running without a web connection)
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Checking to see if the https_proxy has been set...
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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
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Mode of operation: FULLMR -
Search models will be created and used in Molecular Replacement.
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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.
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### Target Information ###
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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
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### Input column data ###
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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:
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### Ctruncate Results ###
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TRANSLATIONAL NCS:
No translational NCS detected
ANISOTROPY CORRECTION:
Eigenvalue ratios: 1.0000 1.0000 0.9332
TWINNING ANALYSIS:
No twinning detected.
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### PHMMER search ###
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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
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-------------------------------
Processing PDB files (PDBclip):
-------------------------------
-------------
Process PDBs
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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
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