Mon 24 Dec 07:55:46 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vkd-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkd-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkd-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkd-3.6-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vkd-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkd-3.6-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:55:51 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/noncs/ArpWArp/wArpResults/WorkingDir/1vkd-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkd-3.6-parrot-noncs/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 1656 and 0 Target number of residues in the AU: 1656 Target solvent content: 0.6015 Checking the provided sequence file Detected sequence length: 338 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 2028 Adjusted target solvent content: 0.51 Input MTZ file: 1vkd-3.6-parrot-noncs.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: 86.922 101.512 254.880 90.000 90.000 90.000 Input sequence file: 1vkd-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 16224 target number of atoms Had to go as low as 0.65 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: 127.440 3.600 Wilson plot Bfac: 53.16 26847 reflections ( 99.71 % complete ) and 0 restraints for refining 17864 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3167 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2748 (Rfree = 0.000) for 17864 atoms. Found 114 (114 requested) and removed 122 (57 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.16 3.12 Search for helices and strands: 0 residues in 0 chains, 18016 seeds are put forward NCS extension: 0 residues added, 18016 seeds are put forward Round 1: 823 peptides, 169 chains. Longest chain 11 peptides. Score 0.290 Round 2: 1069 peptides, 179 chains. Longest chain 16 peptides. Score 0.439 Round 3: 1140 peptides, 179 chains. Longest chain 23 peptides. Score 0.485 Round 4: 1190 peptides, 177 chains. Longest chain 22 peptides. Score 0.521 Round 5: 1196 peptides, 174 chains. Longest chain 23 peptides. Score 0.533 Taking the results from Round 5 Chains 179, Residues 1022, Estimated correctness of the model 0.0 % 15 chains (137 residues) have been docked in sequence ------------------------------------------------------ 26847 reflections ( 99.71 % complete ) and 31700 restraints for refining 14705 atoms. 27277 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2387 (Rfree = 0.000) for 14705 atoms. Found 62 (94 requested) and removed 106 (47 requested) atoms. Cycle 2: After refmac, R = 0.2247 (Rfree = 0.000) for 14449 atoms. Found 29 (94 requested) and removed 86 (47 requested) atoms. Cycle 3: After refmac, R = 0.2115 (Rfree = 0.000) for 14304 atoms. Found 26 (92 requested) and removed 67 (46 requested) atoms. Cycle 4: After refmac, R = 0.2048 (Rfree = 0.000) for 14231 atoms. Found 18 (91 requested) and removed 63 (45 requested) atoms. Cycle 5: After refmac, R = 0.2011 (Rfree = 0.000) for 14155 atoms. Found 21 (91 requested) and removed 60 (45 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.18 3.14 Search for helices and strands: 0 residues in 0 chains, 14378 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 14406 seeds are put forward Round 1: 1066 peptides, 189 chains. Longest chain 14 peptides. Score 0.407 Round 2: 1142 peptides, 168 chains. Longest chain 22 peptides. Score 0.516 Round 3: 1165 peptides, 175 chains. Longest chain 19 peptides. Score 0.511 Round 4: 1192 peptides, 156 chains. Longest chain 26 peptides. Score 0.576 Round 5: 1192 peptides, 168 chains. Longest chain 19 peptides. Score 0.546 Taking the results from Round 4 Chains 159, Residues 1036, Estimated correctness of the model 5.1 % 13 chains (97 residues) have been docked in sequence ------------------------------------------------------ 26847 reflections ( 99.71 % complete ) and 32202 restraints for refining 14704 atoms. 27875 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2384 (Rfree = 0.000) for 14704 atoms. Found 89 (94 requested) and removed 101 (47 requested) atoms. Cycle 7: After refmac, R = 0.2124 (Rfree = 0.000) for 14630 atoms. Found 36 (94 requested) and removed 71 (47 requested) atoms. Cycle 8: After refmac, R = 0.2033 (Rfree = 0.000) for 14529 atoms. Found 34 (93 requested) and removed 64 (46 requested) atoms. Cycle 9: After refmac, R = 0.1995 (Rfree = 0.000) for 14466 atoms. Found 27 (93 requested) and removed 65 (46 requested) atoms. Cycle 10: After refmac, R = 0.1918 (Rfree = 0.000) for 14399 atoms. Found 16 (92 requested) and removed 55 (46 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 3.16 Search for helices and strands: 0 residues in 0 chains, 14560 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 14573 seeds are put forward Round 1: 1088 peptides, 192 chains. Longest chain 16 peptides. Score 0.413 Round 2: 1188 peptides, 178 chains. Longest chain 22 peptides. Score 0.517 Round 3: 1190 peptides, 165 chains. Longest chain 23 peptides. Score 0.552 Round 4: 1199 peptides, 157 chains. Longest chain 21 peptides. Score 0.578 Round 5: 1233 peptides, 169 chains. Longest chain 23 peptides. Score 0.567 Taking the results from Round 4 Chains 166, Residues 1042, Estimated correctness of the model 5.9 % 10 chains (91 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 26847 reflections ( 99.71 % complete ) and 32130 restraints for refining 14706 atoms. 27776 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2309 (Rfree = 0.000) for 14706 atoms. Found 60 (94 requested) and removed 79 (47 requested) atoms. Cycle 12: After refmac, R = 0.2139 (Rfree = 0.000) for 14621 atoms. Found 23 (94 requested) and removed 69 (47 requested) atoms. Cycle 13: After refmac, R = 0.2049 (Rfree = 0.000) for 14536 atoms. Found 23 (93 requested) and removed 58 (46 requested) atoms. Cycle 14: After refmac, R = 0.2009 (Rfree = 0.000) for 14474 atoms. Found 20 (93 requested) and removed 59 (46 requested) atoms. Cycle 15: After refmac, R = 0.1948 (Rfree = 0.000) for 14421 atoms. Found 15 (92 requested) and removed 53 (46 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.20 3.16 Search for helices and strands: 0 residues in 0 chains, 14654 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 14666 seeds are put forward Round 1: 1004 peptides, 182 chains. Longest chain 18 peptides. Score 0.384 Round 2: 1108 peptides, 160 chains. Longest chain 25 peptides. Score 0.517 Round 3: 1158 peptides, 167 chains. Longest chain 24 peptides. Score 0.528 Round 4: 1183 peptides, 158 chains. Longest chain 22 peptides. Score 0.566 Round 5: 1132 peptides, 159 chains. Longest chain 18 peptides. Score 0.534 Taking the results from Round 4 Chains 165, Residues 1025, Estimated correctness of the model 0.9 % 12 chains (113 residues) have been docked in sequence ------------------------------------------------------ 26847 reflections ( 99.71 % complete ) and 31913 restraints for refining 14703 atoms. 27528 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2232 (Rfree = 0.000) for 14703 atoms. Found 61 (94 requested) and removed 82 (47 requested) atoms. Cycle 17: After refmac, R = 0.2106 (Rfree = 0.000) for 14603 atoms. Found 30 (94 requested) and removed 65 (47 requested) atoms. Cycle 18: After refmac, R = 0.2056 (Rfree = 0.000) for 14528 atoms. Found 33 (93 requested) and removed 65 (46 requested) atoms. Cycle 19: After refmac, R = 0.1998 (Rfree = 0.000) for 14455 atoms. Found 36 (93 requested) and removed 62 (46 requested) atoms. Cycle 20: After refmac, R = 0.1950 (Rfree = 0.000) for 14400 atoms. Found 28 (92 requested) and removed 59 (46 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.18 3.14 Search for helices and strands: 0 residues in 0 chains, 14606 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 14621 seeds are put forward Round 1: 983 peptides, 171 chains. Longest chain 15 peptides. Score 0.403 Round 2: 1107 peptides, 163 chains. Longest chain 20 peptides. Score 0.508 Round 3: 1152 peptides, 162 chains. Longest chain 19 peptides. Score 0.538 Round 4: 1143 peptides, 163 chains. Longest chain 24 peptides. Score 0.530 Round 5: 1154 peptides, 163 chains. Longest chain 25 peptides. Score 0.537 Taking the results from Round 3 Chains 165, Residues 990, Estimated correctness of the model 0.0 % 11 chains (81 residues) have been docked in sequence ------------------------------------------------------ 26847 reflections ( 99.71 % complete ) and 32262 restraints for refining 14705 atoms. 28134 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2159 (Rfree = 0.000) for 14705 atoms. Found 65 (94 requested) and removed 78 (47 requested) atoms. Cycle 22: After refmac, R = 0.2009 (Rfree = 0.000) for 14630 atoms. Found 32 (94 requested) and removed 69 (47 requested) atoms. Cycle 23: After refmac, R = 0.1937 (Rfree = 0.000) for 14570 atoms. Found 18 (93 requested) and removed 62 (46 requested) atoms. Cycle 24: After refmac, R = 0.1894 (Rfree = 0.000) for 14508 atoms. Found 19 (93 requested) and removed 64 (46 requested) atoms. Cycle 25: After refmac, R = 0.1869 (Rfree = 0.000) for 14449 atoms. Found 21 (92 requested) and removed 62 (46 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.20 3.16 Search for helices and strands: 0 residues in 0 chains, 14603 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 14624 seeds are put forward Round 1: 1008 peptides, 178 chains. Longest chain 17 peptides. Score 0.399 Round 2: 1115 peptides, 170 chains. Longest chain 22 peptides. Score 0.494 Round 3: 1129 peptides, 163 chains. Longest chain 20 peptides. Score 0.522 Round 4: 1105 peptides, 152 chains. Longest chain 20 peptides. Score 0.537 Round 5: 1107 peptides, 155 chains. Longest chain 19 peptides. Score 0.530 Taking the results from Round 4 Chains 157, Residues 953, Estimated correctness of the model 0.0 % 9 chains (64 residues) have been docked in sequence ------------------------------------------------------ 26847 reflections ( 99.71 % complete ) and 32910 restraints for refining 14704 atoms. 29055 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2126 (Rfree = 0.000) for 14704 atoms. Found 64 (94 requested) and removed 72 (47 requested) atoms. Cycle 27: After refmac, R = 0.1982 (Rfree = 0.000) for 14638 atoms. Found 34 (94 requested) and removed 65 (47 requested) atoms. Cycle 28: After refmac, R = 0.1905 (Rfree = 0.000) for 14579 atoms. Found 38 (93 requested) and removed 60 (46 requested) atoms. Cycle 29: After refmac, R = 0.1812 (Rfree = 0.000) for 14533 atoms. Found 20 (93 requested) and removed 60 (46 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1790 (Rfree = 0.000) for 14478 atoms. Found 29 (92 requested) and removed 51 (46 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.22 3.18 Search for helices and strands: 0 residues in 0 chains, 14650 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 14664 seeds are put forward Round 1: 936 peptides, 172 chains. Longest chain 18 peptides. Score 0.366 Round 2: 1022 peptides, 159 chains. Longest chain 17 peptides. Score 0.465 Round 3: 1062 peptides, 157 chains. Longest chain 33 peptides. Score 0.496 Round 4: 1062 peptides, 146 chains. Longest chain 23 peptides. Score 0.527 Round 5: 1070 peptides, 144 chains. Longest chain 32 peptides. Score 0.537 Taking the results from Round 5 Chains 145, Residues 926, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 26847 reflections ( 99.71 % complete ) and 33317 restraints for refining 14704 atoms. 29665 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2137 (Rfree = 0.000) for 14704 atoms. Found 59 (94 requested) and removed 71 (47 requested) atoms. Cycle 32: After refmac, R = 0.1997 (Rfree = 0.000) for 14639 atoms. Found 26 (94 requested) and removed 58 (47 requested) atoms. Cycle 33: After refmac, R = 0.1958 (Rfree = 0.000) for 14580 atoms. Found 19 (93 requested) and removed 52 (46 requested) atoms. Cycle 34: After refmac, R = 0.1921 (Rfree = 0.000) for 14520 atoms. Found 13 (93 requested) and removed 49 (46 requested) atoms. Cycle 35: After refmac, R = 0.1888 (Rfree = 0.000) for 14472 atoms. Found 10 (92 requested) and removed 52 (46 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.18 3.14 Search for helices and strands: 0 residues in 0 chains, 14636 seeds are put forward NCS extension: 35 residues added (1 deleted due to clashes), 14671 seeds are put forward Round 1: 886 peptides, 164 chains. Longest chain 14 peptides. Score 0.354 Round 2: 992 peptides, 151 chains. Longest chain 20 peptides. Score 0.468 Round 3: 1060 peptides, 157 chains. Longest chain 23 peptides. Score 0.495 Round 4: 1044 peptides, 152 chains. Longest chain 27 peptides. Score 0.499 Round 5: 1030 peptides, 144 chains. Longest chain 31 peptides. Score 0.513 Taking the results from Round 5 Chains 144, Residues 886, Estimated correctness of the model 0.0 % 12 chains (45 residues) have been docked in sequence ------------------------------------------------------ 26847 reflections ( 99.71 % complete ) and 33488 restraints for refining 14707 atoms. 29983 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2215 (Rfree = 0.000) for 14707 atoms. Found 73 (94 requested) and removed 64 (47 requested) atoms. Cycle 37: After refmac, R = 0.2004 (Rfree = 0.000) for 14673 atoms. Found 32 (94 requested) and removed 55 (47 requested) atoms. Cycle 38: After refmac, R = 0.1929 (Rfree = 0.000) for 14621 atoms. Found 21 (93 requested) and removed 55 (46 requested) atoms. Cycle 39: After refmac, R = 0.1895 (Rfree = 0.000) for 14579 atoms. Found 14 (93 requested) and removed 51 (46 requested) atoms. Cycle 40: After refmac, R = 0.1881 (Rfree = 0.000) for 14533 atoms. Found 12 (93 requested) and removed 54 (46 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.22 3.18 Search for helices and strands: 0 residues in 0 chains, 14694 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 14709 seeds are put forward Round 1: 858 peptides, 163 chains. Longest chain 21 peptides. Score 0.336 Round 2: 935 peptides, 148 chains. Longest chain 29 peptides. Score 0.439 Round 3: 966 peptides, 148 chains. Longest chain 22 peptides. Score 0.460 Round 4: 967 peptides, 155 chains. Longest chain 17 peptides. Score 0.440 Round 5: 1007 peptides, 155 chains. Longest chain 19 peptides. Score 0.467 Taking the results from Round 5 Chains 158, Residues 852, Estimated correctness of the model 0.0 % 7 chains (51 residues) have been docked in sequence ------------------------------------------------------ 26847 reflections ( 99.71 % complete ) and 33646 restraints for refining 14707 atoms. 30220 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2194 (Rfree = 0.000) for 14707 atoms. Found 67 (94 requested) and removed 60 (47 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2082 (Rfree = 0.000) for 14674 atoms. Found 24 (94 requested) and removed 54 (47 requested) atoms. Cycle 43: After refmac, R = 0.2046 (Rfree = 0.000) for 14633 atoms. Found 18 (93 requested) and removed 52 (46 requested) atoms. Cycle 44: After refmac, R = 0.2049 (Rfree = 0.000) for 14580 atoms. Found 22 (93 requested) and removed 50 (46 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1987 (Rfree = 0.000) for 14536 atoms. Found 16 (93 requested) and removed 50 (46 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.23 3.19 Search for helices and strands: 0 residues in 0 chains, 14691 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 14703 seeds are put forward Round 1: 817 peptides, 159 chains. Longest chain 12 peptides. Score 0.318 Round 2: 908 peptides, 157 chains. Longest chain 15 peptides. Score 0.392 Round 3: 892 peptides, 145 chains. Longest chain 16 peptides. Score 0.418 Round 4: 916 peptides, 148 chains. Longest chain 20 peptides. Score 0.426 Round 5: 924 peptides, 136 chains. Longest chain 23 peptides. Score 0.467 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 138, Residues 788, Estimated correctness of the model 0.0 % 5 chains (31 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vkd-3_warpNtrace.pdb as input Building loops using Loopy2018 138 chains (788 residues) following loop building 5 chains (31 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 26847 reflections ( 99.71 % complete ) and 34227 restraints for refining 14707 atoms. 31116 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2205 (Rfree = 0.000) for 14707 atoms. Found 0 (94 requested) and removed 47 (47 requested) atoms. Cycle 47: After refmac, R = 0.2080 (Rfree = 0.000) for 14619 atoms. Found 0 (94 requested) and removed 47 (47 requested) atoms. Cycle 48: After refmac, R = 0.2041 (Rfree = 0.000) for 14552 atoms. Found 0 (93 requested) and removed 46 (46 requested) atoms. Cycle 49: After refmac, R = 0.2025 (Rfree = 0.000) for 14495 atoms. TimeTaking 138.73