#CCP4I VERSION CCP4Interface 7.0.024 #CCP4I SCRIPT LOG arp_warp_classic #CCP4I DATE 02 Dec 2016 15:13:48 #CCP4I USER marek #CCP4I PROJECT lyso #CCP4I JOB_ID 3 #CCP4I SCRATCH /tmp/marek #CCP4I HOSTNAME Lenovo #CCP4I PID 2910 ############### You are running ARP/wARP 7.6, patch 1 ############### ================================================================================== | Please cite at least one of the publications below for | | the ARP/wARP application you are using: | | | | Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. | | Acta Cryst. D49, 129-147 | | | | Perrakis A, Sixma TK, Wilson KS, Lamzin VS. (1997) wARP: improvement and | | extension of crystallographic phases by weighted averaging of multiple refined | | dummy atomic models. Acta Cryst. D53, 448-455 | | | | Use of Refmac is an essential part of model building with ARP/wARP. | | Please acknowledge the use of Refmac by citing the following publications: | | | | Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, | | Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular | | crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 | ================================================================================== Fri Dec 2 15:13:50 CET 2016 You are running ARP/wARP version 7.6 Entering warp_tracing.sh from CCP4GUI The working directory: /home/marek/Desktop/LYSOZYM-seminar/ccp4 ARP/wARP software version: 7.6 The parameter file: /home/marek/Desktop/LYSOZYM-seminar/ccp4/3_arp_warp_classic.par ARP/wARP will run in subdirectory: 3_arp_warp_classic Checking the estimated solvent content Target number of residues in the AU: 130 Target solvent content: 0.3876 Input MTZ file: lyso-2016-HD_sg96_refmac1.mtz.cad Column labels for model refinement: F_XDSdataset SIGF_XDSdataset FreeR_flag Rfree value for free reflections: 0 Space group number: 96 Cell parameters: 78.715 78.715 37.084 90.000 90.000 90.000 Input PDB file: 1JUG_molrep1_refmac1.pdb_lf Setting PDB header to reflect the MTZ header content Number of atoms in the PDB file: 980 ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 10 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with bulk solvent correction Resolution range: 20.0 1.550 Wilson plot Bfac: 9.61 Checking whether input PDB contains ligands unknown to the Refmac library 16360 reflections ( 98.72 % complete ) and 1004 restraints for refining 979 atoms. Observations/parameters ratio is 4.18 ------------------------------------------------------ Starting model: R = 0.3981 (Rfree = 0.415). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3648 (Rfree = 0.395) for 979 atoms. Found 69 (69 requested) and removed 34 (34 requested) atoms. 16360 reflections ( 98.72 % complete ) and 936 restraints for refining 966 atoms. 4 conditional restraints added. Observations/parameters ratio is 4.23 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3310 (Rfree = 0.367) for 966 atoms. Found 71 (71 requested) and removed 35 (35 requested) atoms. Cycle 2: After refmac, R = 0.2718 (Rfree = 0.317) for 1002 atoms. Found 70 (70 requested) and removed 35 (35 requested) atoms. Cycle 3: After refmac, R = 0.2361 (Rfree = 0.278) for 1036 atoms. Found 73 (73 requested) and removed 30 (36 requested) atoms. Cycle 4: After refmac, R = 0.2096 (Rfree = 0.256) for 1079 atoms. Found 76 (76 requested) and removed 10 (38 requested) atoms. Cycle 5: After refmac, R = 0.1972 (Rfree = 0.246) for 1144 atoms. Found 80 (80 requested) and removed 10 (40 requested) atoms. Cycle 6: After refmac, R = 0.1859 (Rfree = 0.254) for 1214 atoms. Found 72 (85 requested) and removed 10 (42 requested) atoms. Cycle 7: After refmac, R = 0.1820 (Rfree = 0.267) for 1275 atoms. Found 49 (90 requested) and removed 22 (45 requested) atoms. Cycle 8: After refmac, R = 0.1779 (Rfree = 0.260) for 1302 atoms. Found 41 (91 requested) and removed 19 (45 requested) atoms. #CCP4I TERMINATION STATUS 1 #CCP4I TERMINATION TIME 02 Dec 2016 15:20:51 #CCP4I TERMINATION OUTPUT_FILES /home/marek/Desktop/LYSOZYM-seminar/ccp4/3_arp_warp_classic.par lyso /home/marek/Desktop/LYSOZYM-seminar/ccp4/1_wilson.loggraph lyso #CCP4I MESSAGE Task completed successfully Cycle 9: After refmac, R = 0.1758 (Rfree = 0.265) for 1322 atoms.