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 1vkd-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkd-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkd-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkd-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/1vkd-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkd-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 19:28:07 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/1vkd-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkd-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 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-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: 86.922 101.512 254.880 90.000 90.000 90.000 Input sequence file: 1vkd-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 16224 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: 127.440 3.600 Wilson plot Bfac: 53.16 26847 reflections ( 99.71 % complete ) and 0 restraints for refining 18090 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.2885 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2518 (Rfree = 0.000) for 18090 atoms. Found 116 (116 requested) and removed 114 (58 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.16 3.12 Search for helices and strands: 0 residues in 0 chains, 18269 seeds are put forward NCS extension: 0 residues added, 18269 seeds are put forward Round 1: 994 peptides, 179 chains. Longest chain 15 peptides. Score 0.386 Round 2: 1260 peptides, 174 chains. Longest chain 23 peptides. Score 0.570 Round 3: 1309 peptides, 168 chains. Longest chain 26 peptides. Score 0.610 Round 4: 1348 peptides, 160 chains. Longest chain 30 peptides. Score 0.647 Round 5: 1397 peptides, 166 chains. Longest chain 27 peptides. Score 0.657 Taking the results from Round 5 Chains 177, Residues 1231, Estimated correctness of the model 35.6 % 17 chains (191 residues) have been docked in sequence ------------------------------------------------------ 26847 reflections ( 99.71 % complete ) and 29733 restraints for refining 14704 atoms. 24226 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2322 (Rfree = 0.000) for 14704 atoms. Found 86 (94 requested) and removed 123 (47 requested) atoms. Cycle 2: After refmac, R = 0.2137 (Rfree = 0.000) for 14505 atoms. Found 42 (94 requested) and removed 78 (47 requested) atoms. Cycle 3: After refmac, R = 0.2057 (Rfree = 0.000) for 14405 atoms. Found 30 (92 requested) and removed 60 (46 requested) atoms. Cycle 4: After refmac, R = 0.2013 (Rfree = 0.000) for 14335 atoms. Found 21 (92 requested) and removed 62 (46 requested) atoms. Cycle 5: After refmac, R = 0.1977 (Rfree = 0.000) for 14266 atoms. Found 20 (91 requested) and removed 52 (45 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.18 3.14 Search for helices and strands: 0 residues in 0 chains, 14528 seeds are put forward NCS extension: 15 residues added (5 deleted due to clashes), 14543 seeds are put forward Round 1: 1242 peptides, 186 chains. Longest chain 19 peptides. Score 0.529 Round 2: 1314 peptides, 161 chains. Longest chain 29 peptides. Score 0.628 Round 3: 1332 peptides, 155 chains. Longest chain 29 peptides. Score 0.650 Round 4: 1342 peptides, 151 chains. Longest chain 31 peptides. Score 0.664 Round 5: 1342 peptides, 151 chains. Longest chain 22 peptides. Score 0.664 Taking the results from Round 5 Chains 164, Residues 1191, Estimated correctness of the model 38.0 % 16 chains (185 residues) have been docked in sequence ------------------------------------------------------ 26847 reflections ( 99.71 % complete ) and 30476 restraints for refining 14707 atoms. 25139 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2295 (Rfree = 0.000) for 14707 atoms. Found 84 (94 requested) and removed 106 (47 requested) atoms. Cycle 7: After refmac, R = 0.2093 (Rfree = 0.000) for 14605 atoms. Found 36 (94 requested) and removed 75 (47 requested) atoms. Cycle 8: After refmac, R = 0.2004 (Rfree = 0.000) for 14538 atoms. Found 28 (93 requested) and removed 61 (46 requested) atoms. Cycle 9: After refmac, R = 0.1958 (Rfree = 0.000) for 14486 atoms. Found 21 (93 requested) and removed 55 (46 requested) atoms. Cycle 10: After refmac, R = 0.1915 (Rfree = 0.000) for 14431 atoms. Found 20 (92 requested) and removed 53 (46 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 3.16 Search for helices and strands: 0 residues in 0 chains, 14629 seeds are put forward NCS extension: 12 residues added (5 deleted due to clashes), 14641 seeds are put forward Round 1: 1227 peptides, 183 chains. Longest chain 35 peptides. Score 0.528 Round 2: 1318 peptides, 161 chains. Longest chain 29 peptides. Score 0.630 Round 3: 1318 peptides, 162 chains. Longest chain 22 peptides. Score 0.628 Round 4: 1340 peptides, 162 chains. Longest chain 29 peptides. Score 0.639 Round 5: 1328 peptides, 152 chains. Longest chain 25 peptides. Score 0.655 Taking the results from Round 5 Chains 161, Residues 1176, Estimated correctness of the model 34.9 % 13 chains (167 residues) have been docked in sequence ------------------------------------------------------ 26847 reflections ( 99.71 % complete ) and 30618 restraints for refining 14705 atoms. 25401 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2224 (Rfree = 0.000) for 14705 atoms. Found 70 (94 requested) and removed 99 (47 requested) atoms. Cycle 12: After refmac, R = 0.2024 (Rfree = 0.000) for 14558 atoms. Found 27 (94 requested) and removed 66 (47 requested) atoms. Cycle 13: After refmac, R = 0.1971 (Rfree = 0.000) for 14464 atoms. Found 28 (93 requested) and removed 60 (46 requested) atoms. Cycle 14: After refmac, R = 0.1898 (Rfree = 0.000) for 14406 atoms. Found 26 (92 requested) and removed 58 (46 requested) atoms. Cycle 15: After refmac, R = 0.1867 (Rfree = 0.000) for 14359 atoms. Found 19 (92 requested) and removed 53 (46 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.17 3.13 Search for helices and strands: 0 residues in 0 chains, 14563 seeds are put forward NCS extension: 9 residues added (7 deleted due to clashes), 14572 seeds are put forward Round 1: 1160 peptides, 176 chains. Longest chain 19 peptides. Score 0.506 Round 2: 1266 peptides, 165 chains. Longest chain 23 peptides. Score 0.595 Round 3: 1316 peptides, 161 chains. Longest chain 24 peptides. Score 0.630 Round 4: 1326 peptides, 168 chains. Longest chain 25 peptides. Score 0.619 Round 5: 1313 peptides, 165 chains. Longest chain 23 peptides. Score 0.619 Taking the results from Round 3 Chains 169, Residues 1155, Estimated correctness of the model 26.0 % 15 chains (133 residues) have been docked in sequence ------------------------------------------------------ 26847 reflections ( 99.71 % complete ) and 31180 restraints for refining 14707 atoms. 26242 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2111 (Rfree = 0.000) for 14707 atoms. Found 62 (94 requested) and removed 89 (47 requested) atoms. Cycle 17: After refmac, R = 0.1994 (Rfree = 0.000) for 14623 atoms. Found 32 (94 requested) and removed 65 (47 requested) atoms. Cycle 18: After refmac, R = 0.1922 (Rfree = 0.000) for 14560 atoms. Found 21 (93 requested) and removed 62 (46 requested) atoms. Cycle 19: After refmac, R = 0.1871 (Rfree = 0.000) for 14484 atoms. Found 23 (93 requested) and removed 55 (46 requested) atoms. Cycle 20: After refmac, R = 0.1835 (Rfree = 0.000) for 14432 atoms. Found 21 (92 requested) and removed 57 (46 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.17 3.13 Search for helices and strands: 0 residues in 0 chains, 14619 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 14634 seeds are put forward Round 1: 1189 peptides, 188 chains. Longest chain 18 peptides. Score 0.491 Round 2: 1290 peptides, 172 chains. Longest chain 27 peptides. Score 0.591 Round 3: 1250 peptides, 161 chains. Longest chain 27 peptides. Score 0.596 Round 4: 1275 peptides, 166 chains. Longest chain 26 peptides. Score 0.597 Round 5: 1261 peptides, 154 chains. Longest chain 22 peptides. Score 0.618 Taking the results from Round 5 Chains 161, Residues 1107, Estimated correctness of the model 21.6 % 11 chains (116 residues) have been docked in sequence ------------------------------------------------------ 26847 reflections ( 99.71 % complete ) and 31890 restraints for refining 14707 atoms. 27178 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2189 (Rfree = 0.000) for 14707 atoms. Found 79 (94 requested) and removed 78 (47 requested) atoms. Cycle 22: After refmac, R = 0.2035 (Rfree = 0.000) for 14665 atoms. Found 33 (94 requested) and removed 61 (47 requested) atoms. Cycle 23: After refmac, R = 0.1975 (Rfree = 0.000) for 14615 atoms. Found 25 (93 requested) and removed 61 (46 requested) atoms. Cycle 24: After refmac, R = 0.1953 (Rfree = 0.000) for 14557 atoms. Found 37 (93 requested) and removed 58 (46 requested) atoms. Cycle 25: After refmac, R = 0.1911 (Rfree = 0.000) for 14516 atoms. Found 28 (93 requested) and removed 59 (46 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.17 3.13 Search for helices and strands: 0 residues in 0 chains, 14724 seeds are put forward NCS extension: 22 residues added (4 deleted due to clashes), 14746 seeds are put forward Round 1: 1066 peptides, 177 chains. Longest chain 18 peptides. Score 0.442 Round 2: 1174 peptides, 163 chains. Longest chain 27 peptides. Score 0.548 Round 3: 1194 peptides, 155 chains. Longest chain 27 peptides. Score 0.580 Round 4: 1232 peptides, 158 chains. Longest chain 28 peptides. Score 0.593 Round 5: 1206 peptides, 152 chains. Longest chain 25 peptides. Score 0.594 Taking the results from Round 5 Chains 162, Residues 1054, Estimated correctness of the model 12.3 % 11 chains (133 residues) have been docked in sequence ------------------------------------------------------ 26847 reflections ( 99.71 % complete ) and 31731 restraints for refining 14706 atoms. 27158 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2199 (Rfree = 0.000) for 14706 atoms. Found 78 (94 requested) and removed 93 (47 requested) atoms. Cycle 27: After refmac, R = 0.2117 (Rfree = 0.000) for 14633 atoms. Found 47 (94 requested) and removed 79 (47 requested) atoms. Cycle 28: After refmac, R = 0.2013 (Rfree = 0.000) for 14569 atoms. Found 64 (93 requested) and removed 63 (46 requested) atoms. Cycle 29: After refmac, R = 0.1936 (Rfree = 0.000) for 14539 atoms. Found 44 (93 requested) and removed 67 (46 requested) atoms. Cycle 30: After refmac, R = 0.1886 (Rfree = 0.000) for 14499 atoms. Found 36 (93 requested) and removed 56 (46 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 3.13 Search for helices and strands: 0 residues in 0 chains, 14684 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 14697 seeds are put forward Round 1: 1066 peptides, 179 chains. Longest chain 17 peptides. Score 0.437 Round 2: 1146 peptides, 156 chains. Longest chain 22 peptides. Score 0.550 Round 3: 1162 peptides, 156 chains. Longest chain 30 peptides. Score 0.559 Round 4: 1163 peptides, 160 chains. Longest chain 23 peptides. Score 0.550 Round 5: 1185 peptides, 163 chains. Longest chain 25 peptides. Score 0.555 Taking the results from Round 3 Chains 157, Residues 1006, Estimated correctness of the model 0.0 % 7 chains (80 residues) have been docked in sequence ------------------------------------------------------ 26847 reflections ( 99.71 % complete ) and 32394 restraints for refining 14705 atoms. 28199 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2049 (Rfree = 0.000) for 14705 atoms. Found 74 (94 requested) and removed 82 (47 requested) atoms. Cycle 32: After refmac, R = 0.1941 (Rfree = 0.000) for 14659 atoms. Found 34 (94 requested) and removed 61 (47 requested) atoms. Cycle 33: After refmac, R = 0.1854 (Rfree = 0.000) for 14610 atoms. Found 35 (93 requested) and removed 58 (46 requested) atoms. Cycle 34: After refmac, R = 0.1831 (Rfree = 0.000) for 14571 atoms. Found 29 (93 requested) and removed 67 (46 requested) atoms. Cycle 35: After refmac, R = 0.1794 (Rfree = 0.000) for 14521 atoms. Found 33 (93 requested) and removed 53 (46 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.21 3.17 Search for helices and strands: 0 residues in 0 chains, 14732 seeds are put forward NCS extension: 35 residues added (3 deleted due to clashes), 14767 seeds are put forward Round 1: 977 peptides, 182 chains. Longest chain 13 peptides. Score 0.365 Round 2: 1080 peptides, 160 chains. Longest chain 21 peptides. Score 0.500 Round 3: 1098 peptides, 163 chains. Longest chain 21 peptides. Score 0.503 Round 4: 1113 peptides, 156 chains. Longest chain 19 peptides. Score 0.531 Round 5: 1106 peptides, 153 chains. Longest chain 27 peptides. Score 0.534 Taking the results from Round 5 Chains 157, Residues 953, Estimated correctness of the model 0.0 % 5 chains (49 residues) have been docked in sequence ------------------------------------------------------ 26847 reflections ( 99.71 % complete ) and 33162 restraints for refining 14706 atoms. 29343 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2111 (Rfree = 0.000) for 14706 atoms. Found 63 (94 requested) and removed 74 (47 requested) atoms. Cycle 37: After refmac, R = 0.2043 (Rfree = 0.000) for 14648 atoms. Found 34 (94 requested) and removed 60 (47 requested) atoms. Cycle 38: After refmac, R = 0.2016 (Rfree = 0.000) for 14609 atoms. Found 43 (93 requested) and removed 68 (46 requested) atoms. Cycle 39: After refmac, R = 0.1903 (Rfree = 0.000) for 14569 atoms. Found 41 (93 requested) and removed 59 (46 requested) atoms. Cycle 40: After refmac, R = 0.1862 (Rfree = 0.000) for 14539 atoms. Found 40 (93 requested) and removed 53 (46 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.18 3.14 Search for helices and strands: 0 residues in 0 chains, 14797 seeds are put forward NCS extension: 11 residues added (4 deleted due to clashes), 14808 seeds are put forward Round 1: 917 peptides, 167 chains. Longest chain 17 peptides. Score 0.368 Round 2: 1012 peptides, 163 chains. Longest chain 25 peptides. Score 0.447 Round 3: 1046 peptides, 156 chains. Longest chain 19 peptides. Score 0.489 Round 4: 1055 peptides, 159 chains. Longest chain 19 peptides. Score 0.486 Round 5: 1080 peptides, 161 chains. Longest chain 22 peptides. Score 0.497 Taking the results from Round 5 Chains 165, Residues 919, Estimated correctness of the model 0.0 % 13 chains (87 residues) have been docked in sequence ------------------------------------------------------ 26847 reflections ( 99.71 % complete ) and 32974 restraints for refining 14705 atoms. 29174 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2065 (Rfree = 0.000) for 14705 atoms. Found 77 (94 requested) and removed 82 (47 requested) atoms. Cycle 42: After refmac, R = 0.1940 (Rfree = 0.000) for 14670 atoms. Found 36 (94 requested) and removed 66 (47 requested) atoms. Cycle 43: After refmac, R = 0.1865 (Rfree = 0.000) for 14622 atoms. Found 41 (93 requested) and removed 56 (46 requested) atoms. Cycle 44: After refmac, R = 0.1824 (Rfree = 0.000) for 14594 atoms. Found 37 (93 requested) and removed 61 (46 requested) atoms. Cycle 45: After refmac, R = 0.1770 (Rfree = 0.000) for 14556 atoms. Found 22 (93 requested) and removed 58 (46 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.21 3.17 Search for helices and strands: 0 residues in 0 chains, 14738 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 14752 seeds are put forward Round 1: 816 peptides, 152 chains. Longest chain 12 peptides. Score 0.340 Round 2: 922 peptides, 136 chains. Longest chain 27 peptides. Score 0.466 Round 3: 917 peptides, 135 chains. Longest chain 24 peptides. Score 0.466 Round 4: 905 peptides, 139 chains. Longest chain 20 peptides. Score 0.445 Round 5: 930 peptides, 139 chains. Longest chain 25 peptides. Score 0.462 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 137, Residues 782, Estimated correctness of the model 0.0 % 5 chains (48 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 1vkd-3_warpNtrace.pdb as input Building loops using Loopy2018 137 chains (782 residues) following loop building 5 chains (48 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 26847 reflections ( 99.71 % complete ) and 33800 restraints for refining 14707 atoms. 30631 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1938 (Rfree = 0.000) for 14707 atoms. Found 0 (94 requested) and removed 47 (47 requested) atoms. Cycle 47: After refmac, R = 0.1876 (Rfree = 0.000) for 14630 atoms. Found 0 (94 requested) and removed 47 (47 requested) atoms. Cycle 48: After refmac, R = 0.1821 (Rfree = 0.000) for 14579 atoms. Found 0 (93 requested) and removed 46 (46 requested) atoms. Cycle 49: After refmac, R = 0.1690 (Rfree = 0.000) for 14526 atoms. Found 0 (93 requested) and removed 46 (46 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 22:38:00 GMT 2018 Job finished. TimeTaking 190.05 Used memory is bytes: 17485992