null Tue 25 Dec 19:27:55 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 2prr-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2prr-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2prr-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prr-3.8-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/2prr-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prr-3.8-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 19:28:04 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/2prr-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prr-3.8-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 1752 and 0 Target number of residues in the AU: 1752 Target solvent content: 0.6676 Target number of residues exceeds 1700, conditional restraints are disabled Checking the provided sequence file Detected sequence length: 197 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 12 Adjusted target number of residues: 2364 Adjusted target solvent content: 0.55 Input MTZ file: 2prr-3.8-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: 1 Cell parameters: 65.105 93.953 120.898 84.262 81.638 77.734 Input sequence file: 2prr-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 18912 target number of atoms Had to go as low as 0.85 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: 119.307 3.800 Wilson plot Bfac: 90.62 26567 reflections ( 97.64 % complete ) and 0 restraints for refining 21043 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3173 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2816 (Rfree = 0.000) for 21043 atoms. Found 115 (115 requested) and removed 124 (57 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.76 3.52 Search for helices and strands: 0 residues in 0 chains, 21676 seeds are put forward NCS extension: 0 residues added, 21676 seeds are put forward Round 1: 1062 peptides, 205 chains. Longest chain 11 peptides. Score 0.325 Round 2: 1234 peptides, 180 chains. Longest chain 17 peptides. Score 0.482 Round 3: 1304 peptides, 174 chains. Longest chain 20 peptides. Score 0.530 Round 4: 1300 peptides, 156 chains. Longest chain 25 peptides. Score 0.566 Round 5: 1306 peptides, 152 chains. Longest chain 26 peptides. Score 0.577 Taking the results from Round 5 Chains 159, Residues 1154, Estimated correctness of the model 0.0 % 10 chains (129 residues) have been docked in sequence ------------------------------------------------------ 26567 reflections ( 97.64 % complete ) and 4961 restraints for refining 17106 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2058 (Rfree = 0.000) for 17106 atoms. Found 48 (94 requested) and removed 89 (47 requested) atoms. Cycle 2: After refmac, R = 0.1983 (Rfree = 0.000) for 17065 atoms. Found 58 (93 requested) and removed 83 (46 requested) atoms. Cycle 3: After refmac, R = 0.1473 (Rfree = 0.000) for 17040 atoms. Found 17 (93 requested) and removed 88 (46 requested) atoms. Cycle 4: After refmac, R = 0.1371 (Rfree = 0.000) for 16969 atoms. Found 13 (93 requested) and removed 75 (46 requested) atoms. Cycle 5: After refmac, R = 0.1358 (Rfree = 0.000) for 16907 atoms. Found 12 (92 requested) and removed 69 (46 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.71 3.47 Search for helices and strands: 0 residues in 0 chains, 17610 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 17626 seeds are put forward Round 1: 1102 peptides, 188 chains. Longest chain 16 peptides. Score 0.392 Round 2: 1277 peptides, 177 chains. Longest chain 20 peptides. Score 0.511 Round 3: 1254 peptides, 168 chains. Longest chain 22 peptides. Score 0.519 Round 4: 1284 peptides, 169 chains. Longest chain 22 peptides. Score 0.531 Round 5: 1239 peptides, 157 chains. Longest chain 24 peptides. Score 0.536 Taking the results from Round 5 Chains 161, Residues 1082, Estimated correctness of the model 0.0 % 6 chains (59 residues) have been docked in sequence ------------------------------------------------------ 26567 reflections ( 97.64 % complete ) and 4368 restraints for refining 17106 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1885 (Rfree = 0.000) for 17106 atoms. Found 90 (94 requested) and removed 103 (47 requested) atoms. Cycle 7: After refmac, R = 0.1873 (Rfree = 0.000) for 17093 atoms. Found 94 (94 requested) and removed 112 (47 requested) atoms. Cycle 8: After refmac, R = 0.1745 (Rfree = 0.000) for 17075 atoms. Found 91 (93 requested) and removed 100 (46 requested) atoms. Cycle 9: After refmac, R = 0.1660 (Rfree = 0.000) for 17066 atoms. Found 93 (93 requested) and removed 86 (46 requested) atoms. Cycle 10: After refmac, R = 0.1163 (Rfree = 0.000) for 17073 atoms. Found 20 (93 requested) and removed 83 (46 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.70 3.46 Search for helices and strands: 0 residues in 0 chains, 17700 seeds are put forward NCS extension: 13 residues added (4 deleted due to clashes), 17713 seeds are put forward Round 1: 1085 peptides, 193 chains. Longest chain 13 peptides. Score 0.369 Round 2: 1284 peptides, 193 chains. Longest chain 17 peptides. Score 0.478 Round 3: 1281 peptides, 181 chains. Longest chain 22 peptides. Score 0.504 Round 4: 1248 peptides, 172 chains. Longest chain 17 peptides. Score 0.507 Round 5: 1258 peptides, 179 chains. Longest chain 21 peptides. Score 0.497 Taking the results from Round 4 Chains 176, Residues 1076, Estimated correctness of the model 0.0 % 7 chains (48 residues) have been docked in sequence ------------------------------------------------------ 26567 reflections ( 97.64 % complete ) and 4297 restraints for refining 17106 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1738 (Rfree = 0.000) for 17106 atoms. Found 77 (94 requested) and removed 97 (47 requested) atoms. Cycle 12: After refmac, R = 0.1692 (Rfree = 0.000) for 17086 atoms. Found 93 (93 requested) and removed 102 (46 requested) atoms. Cycle 13: After refmac, R = 0.1194 (Rfree = 0.000) for 17077 atoms. Found 11 (93 requested) and removed 67 (46 requested) atoms. Cycle 14: After refmac, R = 0.1092 (Rfree = 0.000) for 17021 atoms. Found 7 (93 requested) and removed 67 (46 requested) atoms. Cycle 15: After refmac, R = 0.1072 (Rfree = 0.000) for 16961 atoms. Found 9 (93 requested) and removed 65 (46 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.71 3.47 Search for helices and strands: 0 residues in 0 chains, 17593 seeds are put forward NCS extension: 9 residues added (5 deleted due to clashes), 17602 seeds are put forward Round 1: 1109 peptides, 204 chains. Longest chain 17 peptides. Score 0.356 Round 2: 1235 peptides, 181 chains. Longest chain 29 peptides. Score 0.480 Round 3: 1277 peptides, 183 chains. Longest chain 23 peptides. Score 0.497 Round 4: 1281 peptides, 176 chains. Longest chain 18 peptides. Score 0.515 Round 5: 1281 peptides, 174 chains. Longest chain 27 peptides. Score 0.519 Taking the results from Round 5 Chains 178, Residues 1107, Estimated correctness of the model 0.0 % 5 chains (55 residues) have been docked in sequence ------------------------------------------------------ 26567 reflections ( 97.64 % complete ) and 4444 restraints for refining 17106 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1677 (Rfree = 0.000) for 17106 atoms. Found 69 (94 requested) and removed 97 (47 requested) atoms. Cycle 17: After refmac, R = 0.1700 (Rfree = 0.000) for 17078 atoms. Found 89 (93 requested) and removed 68 (46 requested) atoms. Cycle 18: After refmac, R = 0.1180 (Rfree = 0.000) for 17099 atoms. Found 9 (94 requested) and removed 82 (47 requested) atoms. Cycle 19: After refmac, R = 0.1097 (Rfree = 0.000) for 17026 atoms. Found 11 (93 requested) and removed 60 (46 requested) atoms. Cycle 20: After refmac, R = 0.1073 (Rfree = 0.000) for 16977 atoms. Found 4 (93 requested) and removed 60 (46 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.73 3.49 Search for helices and strands: 0 residues in 0 chains, 17568 seeds are put forward NCS extension: 11 residues added (3 deleted due to clashes), 17579 seeds are put forward Round 1: 1060 peptides, 185 chains. Longest chain 16 peptides. Score 0.375 Round 2: 1180 peptides, 172 chains. Longest chain 21 peptides. Score 0.473 Round 3: 1196 peptides, 167 chains. Longest chain 23 peptides. Score 0.492 Round 4: 1219 peptides, 173 chains. Longest chain 23 peptides. Score 0.490 Round 5: 1204 peptides, 170 chains. Longest chain 23 peptides. Score 0.490 Taking the results from Round 3 Chains 171, Residues 1029, Estimated correctness of the model 0.0 % 9 chains (110 residues) have been docked in sequence ------------------------------------------------------ 26567 reflections ( 97.64 % complete ) and 4384 restraints for refining 17106 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1655 (Rfree = 0.000) for 17106 atoms. Found 46 (94 requested) and removed 96 (47 requested) atoms. Cycle 22: After refmac, R = 0.1652 (Rfree = 0.000) for 17056 atoms. Found 93 (93 requested) and removed 81 (46 requested) atoms. Cycle 23: After refmac, R = 0.1165 (Rfree = 0.000) for 17068 atoms. Found 8 (93 requested) and removed 65 (46 requested) atoms. Cycle 24: After refmac, R = 0.1099 (Rfree = 0.000) for 17011 atoms. Found 9 (93 requested) and removed 57 (46 requested) atoms. Cycle 25: After refmac, R = 0.1078 (Rfree = 0.000) for 16963 atoms. Found 4 (93 requested) and removed 53 (46 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.73 3.49 Search for helices and strands: 0 residues in 0 chains, 17542 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 17559 seeds are put forward Round 1: 987 peptides, 177 chains. Longest chain 13 peptides. Score 0.352 Round 2: 1145 peptides, 178 chains. Longest chain 22 peptides. Score 0.440 Round 3: 1153 peptides, 160 chains. Longest chain 24 peptides. Score 0.486 Round 4: 1173 peptides, 162 chains. Longest chain 27 peptides. Score 0.492 Round 5: 1207 peptides, 166 chains. Longest chain 25 peptides. Score 0.500 Taking the results from Round 5 Chains 167, Residues 1041, Estimated correctness of the model 0.0 % 4 chains (27 residues) have been docked in sequence ------------------------------------------------------ 26567 reflections ( 97.64 % complete ) and 4100 restraints for refining 17106 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1645 (Rfree = 0.000) for 17106 atoms. Found 59 (94 requested) and removed 73 (47 requested) atoms. Cycle 27: After refmac, R = 0.1225 (Rfree = 0.000) for 17092 atoms. Found 10 (93 requested) and removed 65 (46 requested) atoms. Cycle 28: After refmac, R = 0.1152 (Rfree = 0.000) for 17037 atoms. Found 7 (93 requested) and removed 63 (46 requested) atoms. Cycle 29: After refmac, R = 0.1150 (Rfree = 0.000) for 16981 atoms. Found 7 (93 requested) and removed 50 (46 requested) atoms. Cycle 30: After refmac, R = 0.1158 (Rfree = 0.000) for 16938 atoms. Found 10 (93 requested) and removed 47 (46 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.74 3.50 Search for helices and strands: 0 residues in 0 chains, 17491 seeds are put forward NCS extension: 31 residues added (7 deleted due to clashes), 17522 seeds are put forward Round 1: 995 peptides, 177 chains. Longest chain 16 peptides. Score 0.357 Round 2: 1164 peptides, 174 chains. Longest chain 24 peptides. Score 0.460 Round 3: 1175 peptides, 169 chains. Longest chain 19 peptides. Score 0.477 Round 4: 1147 peptides, 163 chains. Longest chain 26 peptides. Score 0.476 Round 5: 1151 peptides, 164 chains. Longest chain 25 peptides. Score 0.476 Taking the results from Round 3 Chains 172, Residues 1006, Estimated correctness of the model 0.0 % 8 chains (72 residues) have been docked in sequence ------------------------------------------------------ 26567 reflections ( 97.64 % complete ) and 4141 restraints for refining 17106 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1634 (Rfree = 0.000) for 17106 atoms. Found 78 (94 requested) and removed 86 (47 requested) atoms. Cycle 32: After refmac, R = 0.1642 (Rfree = 0.000) for 17098 atoms. Found 94 (94 requested) and removed 80 (47 requested) atoms. Cycle 33: After refmac, R = 0.1133 (Rfree = 0.000) for 17112 atoms. Found 7 (94 requested) and removed 73 (47 requested) atoms. Cycle 34: After refmac, R = 0.1054 (Rfree = 0.000) for 17046 atoms. Found 13 (93 requested) and removed 63 (46 requested) atoms. Cycle 35: After refmac, R = 0.1037 (Rfree = 0.000) for 16996 atoms. Found 6 (93 requested) and removed 50 (46 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.73 3.49 Search for helices and strands: 0 residues in 0 chains, 17587 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 17610 seeds are put forward Round 1: 941 peptides, 173 chains. Longest chain 12 peptides. Score 0.334 Round 2: 1127 peptides, 175 chains. Longest chain 17 peptides. Score 0.437 Round 3: 1140 peptides, 169 chains. Longest chain 18 peptides. Score 0.459 Round 4: 1150 peptides, 167 chains. Longest chain 29 peptides. Score 0.469 Round 5: 1165 peptides, 165 chains. Longest chain 19 peptides. Score 0.481 Taking the results from Round 5 Chains 168, Residues 1000, Estimated correctness of the model 0.0 % 6 chains (56 residues) have been docked in sequence ------------------------------------------------------ 26567 reflections ( 97.64 % complete ) and 4049 restraints for refining 17106 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1726 (Rfree = 0.000) for 17106 atoms. Found 84 (94 requested) and removed 82 (47 requested) atoms. Cycle 37: After refmac, R = 0.1633 (Rfree = 0.000) for 17108 atoms. Found 75 (94 requested) and removed 64 (47 requested) atoms. Cycle 38: After refmac, R = 0.1171 (Rfree = 0.000) for 17119 atoms. Found 5 (94 requested) and removed 67 (47 requested) atoms. Cycle 39: After refmac, R = 0.1069 (Rfree = 0.000) for 17057 atoms. Found 5 (93 requested) and removed 57 (46 requested) atoms. Cycle 40: After refmac, R = 0.1064 (Rfree = 0.000) for 17005 atoms. Found 3 (93 requested) and removed 53 (46 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.74 3.50 Search for helices and strands: 0 residues in 0 chains, 17551 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 17569 seeds are put forward Round 1: 967 peptides, 182 chains. Longest chain 12 peptides. Score 0.327 Round 2: 1058 peptides, 167 chains. Longest chain 21 peptides. Score 0.419 Round 3: 1060 peptides, 170 chains. Longest chain 17 peptides. Score 0.412 Round 4: 1069 peptides, 162 chains. Longest chain 20 peptides. Score 0.437 Round 5: 1077 peptides, 161 chains. Longest chain 16 peptides. Score 0.444 Taking the results from Round 5 Chains 165, Residues 916, Estimated correctness of the model 0.0 % 6 chains (43 residues) have been docked in sequence ------------------------------------------------------ 26567 reflections ( 97.64 % complete ) and 3668 restraints for refining 17106 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1657 (Rfree = 0.000) for 17106 atoms. Found 65 (94 requested) and removed 82 (47 requested) atoms. Cycle 42: After refmac, R = 0.1656 (Rfree = 0.000) for 17089 atoms. Found 93 (93 requested) and removed 73 (46 requested) atoms. Cycle 43: After refmac, R = 0.1652 (Rfree = 0.000) for 17109 atoms. Found 87 (94 requested) and removed 88 (47 requested) atoms. Cycle 44: After refmac, R = 0.1548 (Rfree = 0.000) for 17108 atoms. Found 81 (94 requested) and removed 83 (47 requested) atoms. Cycle 45: After refmac, R = 0.1124 (Rfree = 0.000) for 17106 atoms. Found 9 (94 requested) and removed 64 (47 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.73 3.49 Search for helices and strands: 0 residues in 0 chains, 17666 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 17685 seeds are put forward Round 1: 861 peptides, 171 chains. Longest chain 11 peptides. Score 0.289 Round 2: 1006 peptides, 170 chains. Longest chain 15 peptides. Score 0.381 Round 3: 1025 peptides, 169 chains. Longest chain 16 peptides. Score 0.395 Round 4: 1009 peptides, 164 chains. Longest chain 15 peptides. Score 0.398 Round 5: 1019 peptides, 162 chains. Longest chain 18 peptides. Score 0.409 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 162, Residues 857, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 2prr-3_warpNtrace.pdb as input Building loops using Loopy2018 162 chains (857 residues) following loop building 3 chains (20 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 26567 reflections ( 97.64 % complete ) and 3337 restraints for refining 17106 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1680 (Rfree = 0.000) for 17106 atoms. Found 0 (94 requested) and removed 47 (47 requested) atoms. Cycle 47: After refmac, R = 0.1658 (Rfree = 0.000) for 17059 atoms. Found 0 (93 requested) and removed 46 (46 requested) atoms. Cycle 48: After refmac, R = 0.1626 (Rfree = 0.000) for 17013 atoms. Found 0 (93 requested) and removed 46 (46 requested) atoms. Cycle 49: After refmac, R = 0.1544 (Rfree = 0.000) for 16967 atoms. Found 0 (93 requested) and removed 46 (46 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 22:39:05 GMT 2018 Job finished. TimeTaking 191.18 Used memory is bytes: 13240280