null Tue 25 Dec 19:27:57 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 1vkm-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkm-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkm-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkm-3.6-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/1vkm-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkm-3.6-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 ============================================================ Tue 25 Dec 19:28:06 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/1vkm-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkm-3.6-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 1181 and 0 Target number of residues in the AU: 1181 Target solvent content: 0.6199 Checking the provided sequence file Detected sequence length: 297 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1782 Adjusted target solvent content: 0.43 Input MTZ file: 1vkm-3.6-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: 19 Cell parameters: 91.732 131.100 139.844 90.000 90.000 90.000 Input sequence file: 1vkm-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 14256 target number of atoms Had to go as low as 0.60 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: 75.160 3.600 Wilson plot Bfac: 61.41 20157 reflections ( 99.97 % complete ) and 0 restraints for refining 15858 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3028 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2900 (Rfree = 0.000) for 15858 atoms. Found 83 (101 requested) and removed 115 (50 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.32 3.65 Search for helices and strands: 0 residues in 0 chains, 16154 seeds are put forward NCS extension: 0 residues added, 16154 seeds are put forward Round 1: 721 peptides, 142 chains. Longest chain 15 peptides. Score 0.331 Round 2: 873 peptides, 146 chains. Longest chain 19 peptides. Score 0.458 Round 3: 958 peptides, 142 chains. Longest chain 22 peptides. Score 0.542 Round 4: 1023 peptides, 147 chains. Longest chain 20 peptides. Score 0.574 Round 5: 1030 peptides, 143 chains. Longest chain 21 peptides. Score 0.592 Taking the results from Round 5 Chains 146, Residues 887, Estimated correctness of the model 11.5 % 8 chains (67 residues) have been docked in sequence ------------------------------------------------------ 20157 reflections ( 99.97 % complete ) and 29166 restraints for refining 12912 atoms. 25571 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2536 (Rfree = 0.000) for 12912 atoms. Found 34 (82 requested) and removed 102 (41 requested) atoms. Cycle 2: After refmac, R = 0.2266 (Rfree = 0.000) for 12620 atoms. Found 27 (82 requested) and removed 76 (41 requested) atoms. Cycle 3: After refmac, R = 0.2109 (Rfree = 0.000) for 12479 atoms. Found 17 (80 requested) and removed 61 (40 requested) atoms. Cycle 4: After refmac, R = 0.2054 (Rfree = 0.000) for 12390 atoms. Found 18 (79 requested) and removed 59 (39 requested) atoms. Cycle 5: After refmac, R = 0.2012 (Rfree = 0.000) for 12332 atoms. Found 12 (79 requested) and removed 54 (39 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.24 3.56 Search for helices and strands: 0 residues in 0 chains, 12780 seeds are put forward NCS extension: 13 residues added (7 deleted due to clashes), 12793 seeds are put forward Round 1: 848 peptides, 148 chains. Longest chain 18 peptides. Score 0.428 Round 2: 997 peptides, 151 chains. Longest chain 19 peptides. Score 0.542 Round 3: 1017 peptides, 138 chains. Longest chain 25 peptides. Score 0.598 Round 4: 1035 peptides, 138 chains. Longest chain 26 peptides. Score 0.611 Round 5: 1030 peptides, 137 chains. Longest chain 21 peptides. Score 0.610 Taking the results from Round 4 Chains 141, Residues 897, Estimated correctness of the model 18.9 % 9 chains (87 residues) have been docked in sequence ------------------------------------------------------ 20157 reflections ( 99.97 % complete ) and 28394 restraints for refining 12711 atoms. 24693 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2290 (Rfree = 0.000) for 12711 atoms. Found 42 (81 requested) and removed 128 (40 requested) atoms. Cycle 7: After refmac, R = 0.2131 (Rfree = 0.000) for 12537 atoms. Found 25 (80 requested) and removed 95 (40 requested) atoms. Cycle 8: After refmac, R = 0.2107 (Rfree = 0.000) for 12430 atoms. Found 20 (79 requested) and removed 69 (39 requested) atoms. Cycle 9: After refmac, R = 0.2027 (Rfree = 0.000) for 12368 atoms. Found 13 (79 requested) and removed 63 (39 requested) atoms. Cycle 10: After refmac, R = 0.2053 (Rfree = 0.000) for 12300 atoms. Found 29 (79 requested) and removed 60 (39 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.26 3.58 Search for helices and strands: 0 residues in 0 chains, 12703 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 12717 seeds are put forward Round 1: 894 peptides, 150 chains. Longest chain 16 peptides. Score 0.461 Round 2: 1021 peptides, 146 chains. Longest chain 20 peptides. Score 0.576 Round 3: 1006 peptides, 138 chains. Longest chain 24 peptides. Score 0.591 Round 4: 977 peptides, 135 chains. Longest chain 26 peptides. Score 0.579 Round 5: 992 peptides, 132 chains. Longest chain 22 peptides. Score 0.600 Taking the results from Round 5 Chains 135, Residues 860, Estimated correctness of the model 14.7 % 8 chains (68 residues) have been docked in sequence ------------------------------------------------------ 20157 reflections ( 99.97 % complete ) and 29227 restraints for refining 12924 atoms. 25749 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2266 (Rfree = 0.000) for 12924 atoms. Found 42 (82 requested) and removed 115 (41 requested) atoms. Cycle 12: After refmac, R = 0.2156 (Rfree = 0.000) for 12787 atoms. Found 37 (82 requested) and removed 81 (41 requested) atoms. Cycle 13: After refmac, R = 0.2200 (Rfree = 0.000) for 12720 atoms. Found 29 (81 requested) and removed 80 (40 requested) atoms. Cycle 14: After refmac, R = 0.1921 (Rfree = 0.000) for 12646 atoms. Found 9 (81 requested) and removed 55 (40 requested) atoms. Cycle 15: After refmac, R = 0.1901 (Rfree = 0.000) for 12588 atoms. Found 9 (80 requested) and removed 56 (40 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.27 3.59 Search for helices and strands: 0 residues in 0 chains, 12997 seeds are put forward NCS extension: 8 residues added (11 deleted due to clashes), 13005 seeds are put forward Round 1: 815 peptides, 144 chains. Longest chain 16 peptides. Score 0.413 Round 2: 888 peptides, 127 chains. Longest chain 22 peptides. Score 0.539 Round 3: 906 peptides, 131 chains. Longest chain 18 peptides. Score 0.539 Round 4: 926 peptides, 126 chains. Longest chain 21 peptides. Score 0.571 Round 5: 913 peptides, 121 chains. Longest chain 22 peptides. Score 0.578 Taking the results from Round 5 Chains 122, Residues 792, Estimated correctness of the model 5.9 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 20157 reflections ( 99.97 % complete ) and 29876 restraints for refining 12922 atoms. 26720 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2154 (Rfree = 0.000) for 12922 atoms. Found 35 (82 requested) and removed 87 (41 requested) atoms. Cycle 17: After refmac, R = 0.2061 (Rfree = 0.000) for 12833 atoms. Found 16 (82 requested) and removed 77 (41 requested) atoms. Cycle 18: After refmac, R = 0.2086 (Rfree = 0.000) for 12758 atoms. Found 46 (81 requested) and removed 68 (40 requested) atoms. Cycle 19: After refmac, R = 0.2065 (Rfree = 0.000) for 12720 atoms. Found 32 (81 requested) and removed 71 (40 requested) atoms. Cycle 20: After refmac, R = 0.2001 (Rfree = 0.000) for 12665 atoms. Found 29 (81 requested) and removed 51 (40 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.26 3.58 Search for helices and strands: 0 residues in 0 chains, 13047 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 13070 seeds are put forward Round 1: 789 peptides, 149 chains. Longest chain 18 peptides. Score 0.369 Round 2: 873 peptides, 134 chains. Longest chain 23 peptides. Score 0.502 Round 3: 889 peptides, 136 chains. Longest chain 31 peptides. Score 0.508 Round 4: 882 peptides, 135 chains. Longest chain 17 peptides. Score 0.506 Round 5: 902 peptides, 133 chains. Longest chain 19 peptides. Score 0.529 Taking the results from Round 5 Chains 133, Residues 769, Estimated correctness of the model 0.0 % 6 chains (35 residues) have been docked in sequence ------------------------------------------------------ 20157 reflections ( 99.97 % complete ) and 29350 restraints for refining 12924 atoms. 26316 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2077 (Rfree = 0.000) for 12924 atoms. Found 45 (82 requested) and removed 80 (41 requested) atoms. Cycle 22: After refmac, R = 0.1913 (Rfree = 0.000) for 12838 atoms. Found 41 (82 requested) and removed 64 (41 requested) atoms. Cycle 23: After refmac, R = 0.1867 (Rfree = 0.000) for 12794 atoms. Found 35 (82 requested) and removed 53 (41 requested) atoms. Cycle 24: After refmac, R = 0.1860 (Rfree = 0.000) for 12756 atoms. Found 43 (81 requested) and removed 55 (40 requested) atoms. Cycle 25: After refmac, R = 0.1584 (Rfree = 0.000) for 12726 atoms. Found 11 (81 requested) and removed 46 (40 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.28 3.60 Search for helices and strands: 0 residues in 0 chains, 13156 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 13176 seeds are put forward Round 1: 689 peptides, 138 chains. Longest chain 15 peptides. Score 0.315 Round 2: 815 peptides, 132 chains. Longest chain 18 peptides. Score 0.460 Round 3: 776 peptides, 122 chains. Longest chain 25 peptides. Score 0.464 Round 4: 815 peptides, 124 chains. Longest chain 26 peptides. Score 0.490 Round 5: 790 peptides, 118 chains. Longest chain 16 peptides. Score 0.491 Taking the results from Round 5 Chains 119, Residues 672, Estimated correctness of the model 0.0 % 5 chains (38 residues) have been docked in sequence ------------------------------------------------------ 20157 reflections ( 99.97 % complete ) and 30336 restraints for refining 12924 atoms. 27658 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1955 (Rfree = 0.000) for 12924 atoms. Found 42 (82 requested) and removed 64 (41 requested) atoms. Cycle 27: After refmac, R = 0.1848 (Rfree = 0.000) for 12858 atoms. Found 39 (82 requested) and removed 64 (41 requested) atoms. Cycle 28: After refmac, R = 0.1811 (Rfree = 0.000) for 12815 atoms. Found 33 (82 requested) and removed 65 (41 requested) atoms. Cycle 29: After refmac, R = 0.1776 (Rfree = 0.000) for 12771 atoms. Found 46 (82 requested) and removed 56 (41 requested) atoms. Cycle 30: After refmac, R = 0.1660 (Rfree = 0.000) for 12749 atoms. Found 30 (81 requested) and removed 52 (40 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.25 3.57 Search for helices and strands: 0 residues in 0 chains, 13089 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 13101 seeds are put forward Round 1: 689 peptides, 136 chains. Longest chain 12 peptides. Score 0.324 Round 2: 744 peptides, 121 chains. Longest chain 17 peptides. Score 0.439 Round 3: 738 peptides, 117 chains. Longest chain 20 peptides. Score 0.449 Round 4: 752 peptides, 122 chains. Longest chain 23 peptides. Score 0.442 Round 5: 768 peptides, 117 chains. Longest chain 18 peptides. Score 0.476 Taking the results from Round 5 Chains 119, Residues 651, Estimated correctness of the model 0.0 % 7 chains (54 residues) have been docked in sequence ------------------------------------------------------ 20157 reflections ( 99.97 % complete ) and 29998 restraints for refining 12924 atoms. 27380 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1863 (Rfree = 0.000) for 12924 atoms. Found 54 (82 requested) and removed 68 (41 requested) atoms. Cycle 32: After refmac, R = 0.1781 (Rfree = 0.000) for 12875 atoms. Found 48 (82 requested) and removed 53 (41 requested) atoms. Cycle 33: After refmac, R = 0.1769 (Rfree = 0.000) for 12846 atoms. Found 41 (82 requested) and removed 49 (41 requested) atoms. Cycle 34: After refmac, R = 0.1730 (Rfree = 0.000) for 12825 atoms. Found 46 (82 requested) and removed 55 (41 requested) atoms. Cycle 35: After refmac, R = 0.1711 (Rfree = 0.000) for 12803 atoms. Found 33 (82 requested) and removed 47 (41 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 3.61 Search for helices and strands: 0 residues in 0 chains, 13134 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 13152 seeds are put forward Round 1: 646 peptides, 126 chains. Longest chain 11 peptides. Score 0.323 Round 2: 725 peptides, 119 chains. Longest chain 15 peptides. Score 0.429 Round 3: 741 peptides, 119 chains. Longest chain 16 peptides. Score 0.444 Round 4: 738 peptides, 114 chains. Longest chain 17 peptides. Score 0.461 Round 5: 730 peptides, 113 chains. Longest chain 17 peptides. Score 0.458 Taking the results from Round 4 Chains 116, Residues 624, Estimated correctness of the model 0.0 % 9 chains (50 residues) have been docked in sequence ------------------------------------------------------ 20157 reflections ( 99.97 % complete ) and 29810 restraints for refining 12923 atoms. 27317 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1794 (Rfree = 0.000) for 12923 atoms. Found 39 (82 requested) and removed 66 (41 requested) atoms. Cycle 37: After refmac, R = 0.1790 (Rfree = 0.000) for 12878 atoms. Found 43 (82 requested) and removed 55 (41 requested) atoms. Cycle 38: After refmac, R = 0.1869 (Rfree = 0.000) for 12851 atoms. Found 58 (82 requested) and removed 57 (41 requested) atoms. Cycle 39: After refmac, R = 0.1767 (Rfree = 0.000) for 12838 atoms. Found 38 (82 requested) and removed 55 (41 requested) atoms. Cycle 40: After refmac, R = 0.1783 (Rfree = 0.000) for 12805 atoms. Found 45 (82 requested) and removed 48 (41 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.26 3.58 Search for helices and strands: 0 residues in 0 chains, 13163 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 13176 seeds are put forward Round 1: 607 peptides, 116 chains. Longest chain 13 peptides. Score 0.327 Round 2: 686 peptides, 117 chains. Longest chain 17 peptides. Score 0.401 Round 3: 690 peptides, 115 chains. Longest chain 15 peptides. Score 0.413 Round 4: 705 peptides, 109 chains. Longest chain 16 peptides. Score 0.451 Round 5: 680 peptides, 113 chains. Longest chain 18 peptides. Score 0.412 Taking the results from Round 4 Chains 111, Residues 596, Estimated correctness of the model 0.0 % 6 chains (45 residues) have been docked in sequence ------------------------------------------------------ 20157 reflections ( 99.97 % complete ) and 30026 restraints for refining 12923 atoms. 27637 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1863 (Rfree = 0.000) for 12923 atoms. Found 50 (82 requested) and removed 59 (41 requested) atoms. Cycle 42: After refmac, R = 0.1813 (Rfree = 0.000) for 12886 atoms. Found 53 (82 requested) and removed 52 (41 requested) atoms. Cycle 43: After refmac, R = 0.1784 (Rfree = 0.000) for 12862 atoms. Found 34 (82 requested) and removed 55 (41 requested) atoms. Cycle 44: After refmac, R = 0.1803 (Rfree = 0.000) for 12837 atoms. Found 41 (82 requested) and removed 48 (41 requested) atoms. Cycle 45: After refmac, R = 0.1768 (Rfree = 0.000) for 12826 atoms. Found 36 (82 requested) and removed 47 (41 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.28 3.60 Search for helices and strands: 0 residues in 0 chains, 13166 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 13185 seeds are put forward Round 1: 563 peptides, 111 chains. Longest chain 14 peptides. Score 0.303 Round 2: 610 peptides, 106 chains. Longest chain 15 peptides. Score 0.373 Round 3: 632 peptides, 106 chains. Longest chain 15 peptides. Score 0.395 Round 4: 623 peptides, 103 chains. Longest chain 15 peptides. Score 0.399 Round 5: 627 peptides, 102 chains. Longest chain 15 peptides. Score 0.407 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 104, Residues 525, Estimated correctness of the model 0.0 % 4 chains (33 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 1vkm-3_warpNtrace.pdb as input Building loops using Loopy2018 104 chains (525 residues) following loop building 4 chains (33 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 20157 reflections ( 99.97 % complete ) and 30624 restraints for refining 12922 atoms. 28526 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1870 (Rfree = 0.000) for 12922 atoms. Found 0 (82 requested) and removed 41 (41 requested) atoms. Cycle 47: After refmac, R = 0.1789 (Rfree = 0.000) for 12862 atoms. Found 0 (82 requested) and removed 41 (41 requested) atoms. Cycle 48: After refmac, R = 0.1852 (Rfree = 0.000) for 12813 atoms. Found 0 (82 requested) and removed 41 (41 requested) atoms. Cycle 49: After refmac, R = 0.1788 (Rfree = 0.000) for 12763 atoms. Found 0 (81 requested) and removed 40 (40 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 22:12:03 GMT 2018 Job finished. TimeTaking 164.1 Used memory is bytes: 27410200