Sun 23 Dec 22:22:52 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ouw-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ouw-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ouw-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ouw-3.4-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ouw-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ouw-3.4-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ 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 Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: 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 ============================================================ Sun 23 Dec 22:23:01 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ouw-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ouw-3.4-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 161 and 0 Target number of residues in the AU: 161 Target solvent content: 0.6455 Checking the provided sequence file Detected sequence length: 138 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 276 Adjusted target solvent content: 0.39 Input MTZ file: 2ouw-3.4-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 182 Cell parameters: 62.683 62.683 216.710 90.000 90.000 120.000 Input sequence file: 2ouw-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2208 target number of atoms Had to go as low as 0.70 sigma, to complete atoms search. 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 3 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 no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 108.355 3.400 Wilson plot Bfac: 74.07 3938 reflections ( 99.82 % complete ) and 0 restraints for refining 2471 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3519 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3196 (Rfree = 0.000) for 2471 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 3.93 Search for helices and strands: 0 residues in 0 chains, 2542 seeds are put forward NCS extension: 0 residues added, 2542 seeds are put forward Round 1: 87 peptides, 18 chains. Longest chain 8 peptides. Score 0.282 Round 2: 113 peptides, 22 chains. Longest chain 9 peptides. Score 0.347 Round 3: 127 peptides, 21 chains. Longest chain 11 peptides. Score 0.462 Round 4: 122 peptides, 19 chains. Longest chain 11 peptides. Score 0.484 Round 5: 122 peptides, 19 chains. Longest chain 14 peptides. Score 0.484 Taking the results from Round 5 Chains 19, Residues 103, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3938 reflections ( 99.82 % complete ) and 4708 restraints for refining 2006 atoms. 4295 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3122 (Rfree = 0.000) for 2006 atoms. Found 15 (15 requested) and removed 36 (7 requested) atoms. Cycle 2: After refmac, R = 0.3099 (Rfree = 0.000) for 1958 atoms. Found 10 (14 requested) and removed 47 (7 requested) atoms. Cycle 3: After refmac, R = 0.3114 (Rfree = 0.000) for 1906 atoms. Found 14 (14 requested) and removed 31 (7 requested) atoms. Cycle 4: After refmac, R = 0.3069 (Rfree = 0.000) for 1880 atoms. Found 14 (14 requested) and removed 21 (7 requested) atoms. Cycle 5: After refmac, R = 0.3109 (Rfree = 0.000) for 1868 atoms. Found 14 (14 requested) and removed 23 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.05 3.54 Search for helices and strands: 0 residues in 0 chains, 1911 seeds are put forward NCS extension: 0 residues added, 1911 seeds are put forward Round 1: 74 peptides, 16 chains. Longest chain 7 peptides. Score 0.247 Round 2: 94 peptides, 18 chains. Longest chain 9 peptides. Score 0.332 Round 3: 90 peptides, 16 chains. Longest chain 11 peptides. Score 0.364 Round 4: 96 peptides, 14 chains. Longest chain 14 peptides. Score 0.460 Round 5: 95 peptides, 14 chains. Longest chain 12 peptides. Score 0.454 Taking the results from Round 4 Chains 14, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3938 reflections ( 99.82 % complete ) and 4362 restraints for refining 1849 atoms. 4048 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3162 (Rfree = 0.000) for 1849 atoms. Found 13 (13 requested) and removed 24 (6 requested) atoms. Cycle 7: After refmac, R = 0.3002 (Rfree = 0.000) for 1830 atoms. Found 13 (13 requested) and removed 25 (6 requested) atoms. Cycle 8: After refmac, R = 0.2948 (Rfree = 0.000) for 1809 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 9: After refmac, R = 0.2775 (Rfree = 0.000) for 1802 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 10: After refmac, R = 0.2818 (Rfree = 0.000) for 1799 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.15 3.66 Search for helices and strands: 0 residues in 0 chains, 1883 seeds are put forward NCS extension: 0 residues added, 1883 seeds are put forward Round 1: 81 peptides, 16 chains. Longest chain 11 peptides. Score 0.300 Round 2: 101 peptides, 20 chains. Longest chain 10 peptides. Score 0.322 Round 3: 96 peptides, 17 chains. Longest chain 10 peptides. Score 0.375 Round 4: 91 peptides, 17 chains. Longest chain 9 peptides. Score 0.341 Round 5: 95 peptides, 17 chains. Longest chain 11 peptides. Score 0.368 Taking the results from Round 3 Chains 17, Residues 79, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3938 reflections ( 99.82 % complete ) and 3783 restraints for refining 1716 atoms. 3461 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2756 (Rfree = 0.000) for 1716 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 12: After refmac, R = 0.2921 (Rfree = 0.000) for 1713 atoms. Found 12 (12 requested) and removed 23 (6 requested) atoms. Cycle 13: After refmac, R = 0.2794 (Rfree = 0.000) for 1696 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 14: After refmac, R = 0.2784 (Rfree = 0.000) for 1690 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 15: After refmac, R = 0.2343 (Rfree = 0.000) for 1690 atoms. Found 8 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.07 3.56 Search for helices and strands: 0 residues in 0 chains, 1749 seeds are put forward NCS extension: 0 residues added, 1749 seeds are put forward Round 1: 94 peptides, 18 chains. Longest chain 11 peptides. Score 0.332 Round 2: 110 peptides, 18 chains. Longest chain 12 peptides. Score 0.438 Round 3: 101 peptides, 15 chains. Longest chain 14 peptides. Score 0.463 Round 4: 109 peptides, 17 chains. Longest chain 14 peptides. Score 0.458 Round 5: 110 peptides, 18 chains. Longest chain 9 peptides. Score 0.438 Taking the results from Round 3 Chains 15, Residues 86, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3938 reflections ( 99.82 % complete ) and 3582 restraints for refining 1732 atoms. 3221 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2509 (Rfree = 0.000) for 1732 atoms. Found 4 (13 requested) and removed 13 (6 requested) atoms. Cycle 17: After refmac, R = 0.2570 (Rfree = 0.000) for 1717 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 18: After refmac, R = 0.2562 (Rfree = 0.000) for 1714 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 19: After refmac, R = 0.2613 (Rfree = 0.000) for 1710 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 20: After refmac, R = 0.2577 (Rfree = 0.000) for 1705 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.13 3.63 Search for helices and strands: 0 residues in 0 chains, 1793 seeds are put forward NCS extension: 0 residues added, 1793 seeds are put forward Round 1: 93 peptides, 17 chains. Longest chain 14 peptides. Score 0.355 Round 2: 104 peptides, 17 chains. Longest chain 12 peptides. Score 0.427 Round 3: 110 peptides, 18 chains. Longest chain 14 peptides. Score 0.438 Round 4: 104 peptides, 16 chains. Longest chain 14 peptides. Score 0.455 Round 5: 105 peptides, 17 chains. Longest chain 10 peptides. Score 0.434 Taking the results from Round 4 Chains 16, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3938 reflections ( 99.82 % complete ) and 3693 restraints for refining 1740 atoms. 3357 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2577 (Rfree = 0.000) for 1740 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 22: After refmac, R = 0.2375 (Rfree = 0.000) for 1734 atoms. Found 7 (13 requested) and removed 18 (6 requested) atoms. Cycle 23: After refmac, R = 0.2760 (Rfree = 0.000) for 1723 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 24: After refmac, R = 0.2509 (Rfree = 0.000) for 1720 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 25: After refmac, R = 0.2570 (Rfree = 0.000) for 1724 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.17 3.68 Search for helices and strands: 0 residues in 0 chains, 1819 seeds are put forward NCS extension: 0 residues added, 1819 seeds are put forward Round 1: 96 peptides, 19 chains. Longest chain 11 peptides. Score 0.317 Round 2: 93 peptides, 17 chains. Longest chain 10 peptides. Score 0.355 Round 3: 102 peptides, 18 chains. Longest chain 11 peptides. Score 0.387 Round 4: 102 peptides, 18 chains. Longest chain 9 peptides. Score 0.387 Round 5: 105 peptides, 16 chains. Longest chain 14 peptides. Score 0.461 Taking the results from Round 5 Chains 16, Residues 89, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3938 reflections ( 99.82 % complete ) and 3949 restraints for refining 1836 atoms. 3591 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2746 (Rfree = 0.000) for 1836 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 27: After refmac, R = 0.2811 (Rfree = 0.000) for 1826 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 28: After refmac, R = 0.2814 (Rfree = 0.000) for 1828 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 29: After refmac, R = 0.2720 (Rfree = 0.000) for 1820 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 30: After refmac, R = 0.2824 (Rfree = 0.000) for 1822 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.20 3.71 Search for helices and strands: 0 residues in 0 chains, 1899 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 1912 seeds are put forward Round 1: 77 peptides, 17 chains. Longest chain 7 peptides. Score 0.238 Round 2: 87 peptides, 17 chains. Longest chain 8 peptides. Score 0.313 Round 3: 102 peptides, 18 chains. Longest chain 9 peptides. Score 0.387 Round 4: 114 peptides, 22 chains. Longest chain 8 peptides. Score 0.354 Round 5: 117 peptides, 21 chains. Longest chain 9 peptides. Score 0.401 Taking the results from Round 5 Chains 21, Residues 96, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3938 reflections ( 99.82 % complete ) and 4192 restraints for refining 1871 atoms. 3829 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2599 (Rfree = 0.000) for 1871 atoms. Found 13 (14 requested) and removed 18 (7 requested) atoms. Cycle 32: After refmac, R = 0.2688 (Rfree = 0.000) for 1859 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 33: After refmac, R = 0.2624 (Rfree = 0.000) for 1856 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 34: After refmac, R = 0.2683 (Rfree = 0.000) for 1855 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 35: After refmac, R = 0.2613 (Rfree = 0.000) for 1854 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.12 3.62 Search for helices and strands: 0 residues in 0 chains, 1928 seeds are put forward NCS extension: 0 residues added, 1928 seeds are put forward Round 1: 77 peptides, 18 chains. Longest chain 6 peptides. Score 0.207 Round 2: 84 peptides, 18 chains. Longest chain 6 peptides. Score 0.260 Round 3: 81 peptides, 16 chains. Longest chain 7 peptides. Score 0.300 Round 4: 96 peptides, 18 chains. Longest chain 9 peptides. Score 0.346 Round 5: 93 peptides, 18 chains. Longest chain 8 peptides. Score 0.325 Taking the results from Round 4 Chains 18, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3938 reflections ( 99.82 % complete ) and 4284 restraints for refining 1904 atoms. 3990 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2679 (Rfree = 0.000) for 1904 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Cycle 37: After refmac, R = 0.2680 (Rfree = 0.000) for 1892 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. Cycle 38: After refmac, R = 0.2662 (Rfree = 0.000) for 1885 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 39: After refmac, R = 0.2671 (Rfree = 0.000) for 1886 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 40: After refmac, R = 0.2747 (Rfree = 0.000) for 1884 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.16 3.67 Search for helices and strands: 0 residues in 0 chains, 1957 seeds are put forward NCS extension: 0 residues added, 1957 seeds are put forward Round 1: 80 peptides, 19 chains. Longest chain 5 peptides. Score 0.198 Round 2: 91 peptides, 17 chains. Longest chain 9 peptides. Score 0.341 Round 3: 91 peptides, 16 chains. Longest chain 11 peptides. Score 0.370 Round 4: 95 peptides, 19 chains. Longest chain 9 peptides. Score 0.310 Round 5: 87 peptides, 17 chains. Longest chain 9 peptides. Score 0.313 Taking the results from Round 3 Chains 16, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3938 reflections ( 99.82 % complete ) and 4263 restraints for refining 1885 atoms. 3979 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2693 (Rfree = 0.000) for 1885 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 42: After refmac, R = 0.2820 (Rfree = 0.000) for 1872 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 43: After refmac, R = 0.2795 (Rfree = 0.000) for 1870 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 44: After refmac, R = 0.2734 (Rfree = 0.000) for 1868 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 45: After refmac, R = 0.2689 (Rfree = 0.000) for 1870 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.20 3.71 Search for helices and strands: 0 residues in 0 chains, 1936 seeds are put forward NCS extension: 0 residues added, 1936 seeds are put forward Round 1: 65 peptides, 16 chains. Longest chain 5 peptides. Score 0.175 Round 2: 67 peptides, 13 chains. Longest chain 10 peptides. Score 0.291 Round 3: 71 peptides, 14 chains. Longest chain 9 peptides. Score 0.289 Round 4: 71 peptides, 14 chains. Longest chain 11 peptides. Score 0.289 Round 5: 68 peptides, 13 chains. Longest chain 13 peptides. Score 0.298 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 55, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 16 % Consider running further cycles of model building using 2ouw-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3938 reflections ( 99.82 % complete ) and 4174 restraints for refining 1852 atoms. 3942 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2642 (Rfree = 0.000) for 1852 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2759 (Rfree = 0.000) for 1844 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2711 (Rfree = 0.000) for 1836 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2696 (Rfree = 0.000) for 1825 atoms. TimeTaking 45.65