Mon 24 Dec 07:27:54 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-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkd-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkd-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkd-3.2-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-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkd-3.2-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 07:27:58 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-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkd-3.2-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 1743 and 0 Target number of residues in the AU: 1743 Target solvent content: 0.5806 Target number of residues exceeds 1700, conditional restraints are disabled 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-3.2-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-3.2-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. 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 3.200 Wilson plot Bfac: 45.23 37988 reflections ( 99.76 % complete ) and 0 restraints for refining 18019 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3153 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2687 (Rfree = 0.000) for 18019 atoms. Found 147 (161 requested) and removed 165 (80 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.91 2.87 Search for helices and strands: 0 residues in 0 chains, 18162 seeds are put forward NCS extension: 0 residues added, 18162 seeds are put forward Round 1: 960 peptides, 187 chains. Longest chain 19 peptides. Score 0.337 Round 2: 1197 peptides, 194 chains. Longest chain 18 peptides. Score 0.480 Round 3: 1211 peptides, 181 chains. Longest chain 24 peptides. Score 0.523 Round 4: 1277 peptides, 185 chains. Longest chain 25 peptides. Score 0.552 Round 5: 1303 peptides, 185 chains. Longest chain 23 peptides. Score 0.566 Taking the results from Round 5 Chains 192, Residues 1118, Estimated correctness of the model 31.6 % 9 chains (99 residues) have been docked in sequence ------------------------------------------------------ 37988 reflections ( 99.76 % complete ) and 4647 restraints for refining 14812 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2524 (Rfree = 0.000) for 14812 atoms. Found 103 (132 requested) and removed 98 (66 requested) atoms. Cycle 2: After refmac, R = 0.2396 (Rfree = 0.000) for 14817 atoms. Found 62 (132 requested) and removed 93 (66 requested) atoms. Cycle 3: After refmac, R = 0.2063 (Rfree = 0.000) for 14786 atoms. Found 46 (132 requested) and removed 83 (66 requested) atoms. Cycle 4: After refmac, R = 0.2007 (Rfree = 0.000) for 14749 atoms. Found 18 (132 requested) and removed 82 (66 requested) atoms. Cycle 5: After refmac, R = 0.1997 (Rfree = 0.000) for 14685 atoms. Found 22 (131 requested) and removed 72 (65 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.91 2.87 Search for helices and strands: 0 residues in 0 chains, 14862 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 14883 seeds are put forward Round 1: 1182 peptides, 188 chains. Longest chain 18 peptides. Score 0.487 Round 2: 1313 peptides, 177 chains. Longest chain 21 peptides. Score 0.591 Round 3: 1317 peptides, 180 chains. Longest chain 29 peptides. Score 0.586 Round 4: 1318 peptides, 171 chains. Longest chain 29 peptides. Score 0.608 Round 5: 1343 peptides, 177 chains. Longest chain 29 peptides. Score 0.607 Taking the results from Round 4 Chains 177, Residues 1147, Estimated correctness of the model 43.2 % 16 chains (154 residues) have been docked in sequence ------------------------------------------------------ 37988 reflections ( 99.76 % complete ) and 4956 restraints for refining 14812 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2404 (Rfree = 0.000) for 14812 atoms. Found 112 (132 requested) and removed 98 (66 requested) atoms. Cycle 7: After refmac, R = 0.2305 (Rfree = 0.000) for 14826 atoms. Found 85 (133 requested) and removed 94 (66 requested) atoms. Cycle 8: After refmac, R = 0.2053 (Rfree = 0.000) for 14817 atoms. Found 24 (132 requested) and removed 75 (66 requested) atoms. Cycle 9: After refmac, R = 0.2009 (Rfree = 0.000) for 14766 atoms. Found 23 (132 requested) and removed 78 (66 requested) atoms. Cycle 10: After refmac, R = 0.2005 (Rfree = 0.000) for 14711 atoms. Found 16 (132 requested) and removed 74 (66 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.93 2.89 Search for helices and strands: 0 residues in 0 chains, 14852 seeds are put forward NCS extension: 36 residues added (4 deleted due to clashes), 14888 seeds are put forward Round 1: 1175 peptides, 185 chains. Longest chain 27 peptides. Score 0.491 Round 2: 1316 peptides, 178 chains. Longest chain 34 peptides. Score 0.590 Round 3: 1321 peptides, 183 chains. Longest chain 29 peptides. Score 0.581 Round 4: 1317 peptides, 174 chains. Longest chain 31 peptides. Score 0.600 Round 5: 1315 peptides, 170 chains. Longest chain 32 peptides. Score 0.609 Taking the results from Round 5 Chains 175, Residues 1145, Estimated correctness of the model 43.5 % 13 chains (159 residues) have been docked in sequence ------------------------------------------------------ 37988 reflections ( 99.76 % complete ) and 5016 restraints for refining 14812 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2341 (Rfree = 0.000) for 14812 atoms. Found 108 (132 requested) and removed 96 (66 requested) atoms. Cycle 12: After refmac, R = 0.2232 (Rfree = 0.000) for 14824 atoms. Found 71 (133 requested) and removed 77 (66 requested) atoms. Cycle 13: After refmac, R = 0.2141 (Rfree = 0.000) for 14818 atoms. Found 39 (132 requested) and removed 75 (66 requested) atoms. Cycle 14: After refmac, R = 0.2071 (Rfree = 0.000) for 14782 atoms. Found 44 (132 requested) and removed 76 (66 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2031 (Rfree = 0.000) for 14750 atoms. Found 19 (132 requested) and removed 79 (66 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.93 2.89 Search for helices and strands: 0 residues in 0 chains, 14902 seeds are put forward NCS extension: 26 residues added (23 deleted due to clashes), 14928 seeds are put forward Round 1: 1147 peptides, 185 chains. Longest chain 26 peptides. Score 0.473 Round 2: 1292 peptides, 177 chains. Longest chain 27 peptides. Score 0.580 Round 3: 1290 peptides, 175 chains. Longest chain 28 peptides. Score 0.584 Round 4: 1276 peptides, 164 chains. Longest chain 32 peptides. Score 0.602 Round 5: 1284 peptides, 166 chains. Longest chain 23 peptides. Score 0.602 Taking the results from Round 5 Chains 173, Residues 1118, Estimated correctness of the model 41.6 % 17 chains (146 residues) have been docked in sequence ------------------------------------------------------ 37988 reflections ( 99.76 % complete ) and 4825 restraints for refining 14812 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2225 (Rfree = 0.000) for 14812 atoms. Found 107 (132 requested) and removed 95 (66 requested) atoms. Cycle 17: After refmac, R = 0.2095 (Rfree = 0.000) for 14824 atoms. Found 35 (133 requested) and removed 76 (66 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2064 (Rfree = 0.000) for 14783 atoms. Found 28 (132 requested) and removed 66 (66 requested) atoms. Cycle 19: After refmac, R = 0.2041 (Rfree = 0.000) for 14745 atoms. Found 17 (132 requested) and removed 67 (66 requested) atoms. Cycle 20: After refmac, R = 0.2049 (Rfree = 0.000) for 14695 atoms. Found 25 (131 requested) and removed 67 (65 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.93 2.89 Search for helices and strands: 0 residues in 0 chains, 14840 seeds are put forward NCS extension: 32 residues added (2 deleted due to clashes), 14872 seeds are put forward Round 1: 1155 peptides, 190 chains. Longest chain 23 peptides. Score 0.464 Round 2: 1275 peptides, 173 chains. Longest chain 23 peptides. Score 0.580 Round 3: 1306 peptides, 173 chains. Longest chain 23 peptides. Score 0.597 Round 4: 1318 peptides, 174 chains. Longest chain 29 peptides. Score 0.601 Round 5: 1281 peptides, 169 chains. Longest chain 28 peptides. Score 0.593 Taking the results from Round 4 Chains 181, Residues 1144, Estimated correctness of the model 41.3 % 10 chains (102 residues) have been docked in sequence ------------------------------------------------------ 37988 reflections ( 99.76 % complete ) and 4802 restraints for refining 14812 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2198 (Rfree = 0.000) for 14812 atoms. Found 87 (132 requested) and removed 82 (66 requested) atoms. Cycle 22: After refmac, R = 0.2060 (Rfree = 0.000) for 14817 atoms. Found 22 (132 requested) and removed 68 (66 requested) atoms. Cycle 23: After refmac, R = 0.2026 (Rfree = 0.000) for 14771 atoms. Found 15 (132 requested) and removed 66 (66 requested) atoms. Cycle 24: After refmac, R = 0.2001 (Rfree = 0.000) for 14720 atoms. Found 16 (132 requested) and removed 67 (66 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1999 (Rfree = 0.000) for 14669 atoms. Found 12 (131 requested) and removed 65 (65 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.92 2.88 Search for helices and strands: 0 residues in 0 chains, 14796 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 14814 seeds are put forward Round 1: 1113 peptides, 181 chains. Longest chain 24 peptides. Score 0.462 Round 2: 1258 peptides, 169 chains. Longest chain 22 peptides. Score 0.581 Round 3: 1222 peptides, 173 chains. Longest chain 21 peptides. Score 0.551 Round 4: 1233 peptides, 155 chains. Longest chain 30 peptides. Score 0.601 Round 5: 1235 peptides, 162 chains. Longest chain 27 peptides. Score 0.585 Taking the results from Round 4 Chains 165, Residues 1078, Estimated correctness of the model 41.3 % 14 chains (140 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 37988 reflections ( 99.76 % complete ) and 4651 restraints for refining 14812 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2210 (Rfree = 0.000) for 14812 atoms. Found 87 (132 requested) and removed 93 (66 requested) atoms. Cycle 27: After refmac, R = 0.2067 (Rfree = 0.000) for 14806 atoms. Found 42 (132 requested) and removed 67 (66 requested) atoms. Cycle 28: After refmac, R = 0.1970 (Rfree = 0.000) for 14781 atoms. Found 14 (132 requested) and removed 67 (66 requested) atoms. Cycle 29: After refmac, R = 0.1934 (Rfree = 0.000) for 14728 atoms. Found 19 (132 requested) and removed 67 (66 requested) atoms. Cycle 30: After refmac, R = 0.1925 (Rfree = 0.000) for 14680 atoms. Found 16 (131 requested) and removed 65 (65 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.91 2.87 Search for helices and strands: 0 residues in 0 chains, 14788 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 14800 seeds are put forward Round 1: 1067 peptides, 174 chains. Longest chain 14 peptides. Score 0.452 Round 2: 1208 peptides, 173 chains. Longest chain 26 peptides. Score 0.542 Round 3: 1214 peptides, 167 chains. Longest chain 22 peptides. Score 0.561 Round 4: 1202 peptides, 169 chains. Longest chain 21 peptides. Score 0.549 Round 5: 1215 peptides, 162 chains. Longest chain 23 peptides. Score 0.574 Taking the results from Round 5 Chains 172, Residues 1053, Estimated correctness of the model 33.9 % 18 chains (150 residues) have been docked in sequence ------------------------------------------------------ 37988 reflections ( 99.76 % complete ) and 4603 restraints for refining 14812 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2204 (Rfree = 0.000) for 14812 atoms. Found 98 (132 requested) and removed 90 (66 requested) atoms. Cycle 32: After refmac, R = 0.2082 (Rfree = 0.000) for 14820 atoms. Found 62 (133 requested) and removed 69 (66 requested) atoms. Cycle 33: After refmac, R = 0.1971 (Rfree = 0.000) for 14813 atoms. Found 31 (132 requested) and removed 67 (66 requested) atoms. Cycle 34: After refmac, R = 0.1904 (Rfree = 0.000) for 14777 atoms. Found 29 (132 requested) and removed 70 (66 requested) atoms. Cycle 35: After refmac, R = 0.1855 (Rfree = 0.000) for 14736 atoms. Found 22 (132 requested) and removed 69 (66 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.92 2.88 Search for helices and strands: 0 residues in 0 chains, 14853 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 14871 seeds are put forward Round 1: 1060 peptides, 178 chains. Longest chain 20 peptides. Score 0.435 Round 2: 1164 peptides, 168 chains. Longest chain 26 peptides. Score 0.529 Round 3: 1158 peptides, 159 chains. Longest chain 26 peptides. Score 0.549 Round 4: 1166 peptides, 165 chains. Longest chain 26 peptides. Score 0.538 Round 5: 1213 peptides, 164 chains. Longest chain 30 peptides. Score 0.568 Taking the results from Round 5 Chains 172, Residues 1049, Estimated correctness of the model 32.1 % 15 chains (148 residues) have been docked in sequence ------------------------------------------------------ 37988 reflections ( 99.76 % complete ) and 4617 restraints for refining 14812 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2191 (Rfree = 0.000) for 14812 atoms. Found 91 (132 requested) and removed 98 (66 requested) atoms. Cycle 37: After refmac, R = 0.2042 (Rfree = 0.000) for 14805 atoms. Found 59 (132 requested) and removed 71 (66 requested) atoms. Cycle 38: After refmac, R = 0.1977 (Rfree = 0.000) for 14793 atoms. Found 37 (132 requested) and removed 68 (66 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1936 (Rfree = 0.000) for 14762 atoms. Found 29 (132 requested) and removed 69 (66 requested) atoms. Cycle 40: After refmac, R = 0.1920 (Rfree = 0.000) for 14722 atoms. Found 20 (132 requested) and removed 68 (66 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.91 2.87 Search for helices and strands: 0 residues in 0 chains, 14817 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 14835 seeds are put forward Round 1: 995 peptides, 166 chains. Longest chain 18 peptides. Score 0.426 Round 2: 1093 peptides, 155 chains. Longest chain 22 peptides. Score 0.521 Round 3: 1132 peptides, 163 chains. Longest chain 27 peptides. Score 0.523 Round 4: 1122 peptides, 155 chains. Longest chain 17 peptides. Score 0.539 Round 5: 1112 peptides, 157 chains. Longest chain 27 peptides. Score 0.527 Taking the results from Round 4 Chains 162, Residues 967, Estimated correctness of the model 23.6 % 10 chains (96 residues) have been docked in sequence ------------------------------------------------------ 37988 reflections ( 99.76 % complete ) and 4077 restraints for refining 14812 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2098 (Rfree = 0.000) for 14812 atoms. Found 67 (132 requested) and removed 92 (66 requested) atoms. Cycle 42: After refmac, R = 0.1946 (Rfree = 0.000) for 14787 atoms. Found 53 (132 requested) and removed 69 (66 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1922 (Rfree = 0.000) for 14771 atoms. Found 37 (132 requested) and removed 70 (66 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1925 (Rfree = 0.000) for 14738 atoms. Found 35 (132 requested) and removed 69 (66 requested) atoms. Cycle 45: After refmac, R = 0.1871 (Rfree = 0.000) for 14704 atoms. Found 33 (131 requested) and removed 68 (65 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.91 2.87 Search for helices and strands: 0 residues in 0 chains, 14782 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 14798 seeds are put forward Round 1: 930 peptides, 166 chains. Longest chain 15 peptides. Score 0.380 Round 2: 1078 peptides, 173 chains. Longest chain 27 peptides. Score 0.462 Round 3: 1064 peptides, 166 chains. Longest chain 27 peptides. Score 0.473 Round 4: 1039 peptides, 159 chains. Longest chain 27 peptides. Score 0.476 Round 5: 1059 peptides, 158 chains. Longest chain 24 peptides. Score 0.492 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 167, Residues 901, Estimated correctness of the model 8.7 % 9 chains (83 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 1vkd-3_warpNtrace.pdb as input Building loops using Loopy2018 167 chains (901 residues) following loop building 9 chains (83 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 37988 reflections ( 99.76 % complete ) and 3778 restraints for refining 14812 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2122 (Rfree = 0.000) for 14812 atoms. Found 0 (132 requested) and removed 55 (66 requested) atoms. Cycle 47: After refmac, R = 0.2018 (Rfree = 0.000) for 14757 atoms. Found 0 (132 requested) and removed 54 (66 requested) atoms. Cycle 48: After refmac, R = 0.1897 (Rfree = 0.000) for 14703 atoms. Found 0 (131 requested) and removed 65 (65 requested) atoms. Cycle 49: After refmac, R = 0.1895 (Rfree = 0.000) for 14638 atoms. TimeTaking 139.53