null Mon 24 Dec 07:41:33 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 2prr-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2prr-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2prr-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prr-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/2prr-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prr-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 07:41:37 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/2prr-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prr-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 1816 and 0 Target number of residues in the AU: 1816 Target solvent content: 0.6555 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-3.6-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: 1 Cell parameters: 65.105 93.953 120.898 84.262 81.638 77.734 Input sequence file: 2prr-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 18912 target number of atoms Had to go as low as 0.80 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 3.600 Wilson plot Bfac: 81.74 31226 reflections ( 97.59 % complete ) and 0 restraints for refining 20993 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3202 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2808 (Rfree = 0.000) for 20993 atoms. Found 134 (134 requested) and removed 151 (67 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.59 3.36 Search for helices and strands: 0 residues in 0 chains, 21576 seeds are put forward NCS extension: 0 residues added, 21576 seeds are put forward Round 1: 1058 peptides, 207 chains. Longest chain 17 peptides. Score 0.317 Round 2: 1235 peptides, 193 chains. Longest chain 17 peptides. Score 0.453 Round 3: 1302 peptides, 188 chains. Longest chain 21 peptides. Score 0.499 Round 4: 1346 peptides, 177 chains. Longest chain 23 peptides. Score 0.544 Round 5: 1329 peptides, 172 chains. Longest chain 30 peptides. Score 0.546 Taking the results from Round 5 Chains 176, Residues 1157, Estimated correctness of the model 0.0 % 8 chains (57 residues) have been docked in sequence ------------------------------------------------------ 31226 reflections ( 97.59 % complete ) and 4607 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2181 (Rfree = 0.000) for 17144 atoms. Found 99 (109 requested) and removed 74 (54 requested) atoms. Cycle 2: After refmac, R = 0.2016 (Rfree = 0.000) for 17169 atoms. Found 61 (110 requested) and removed 91 (55 requested) atoms. Cycle 3: After refmac, R = 0.1893 (Rfree = 0.000) for 17139 atoms. Found 76 (109 requested) and removed 90 (54 requested) atoms. Cycle 4: After refmac, R = 0.1828 (Rfree = 0.000) for 17125 atoms. Found 99 (109 requested) and removed 87 (54 requested) atoms. Cycle 5: After refmac, R = 0.1759 (Rfree = 0.000) for 17137 atoms. Found 72 (109 requested) and removed 84 (54 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.56 3.33 Search for helices and strands: 0 residues in 0 chains, 18052 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 18068 seeds are put forward Round 1: 1070 peptides, 189 chains. Longest chain 16 peptides. Score 0.370 Round 2: 1275 peptides, 183 chains. Longest chain 22 peptides. Score 0.496 Round 3: 1310 peptides, 176 chains. Longest chain 21 peptides. Score 0.529 Round 4: 1296 peptides, 175 chains. Longest chain 27 peptides. Score 0.524 Round 5: 1328 peptides, 172 chains. Longest chain 25 peptides. Score 0.546 Taking the results from Round 5 Chains 177, Residues 1156, Estimated correctness of the model 0.0 % 9 chains (86 residues) have been docked in sequence ------------------------------------------------------ 31226 reflections ( 97.59 % complete ) and 4734 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1808 (Rfree = 0.000) for 17144 atoms. Found 65 (109 requested) and removed 108 (54 requested) atoms. Cycle 7: After refmac, R = 0.1690 (Rfree = 0.000) for 17101 atoms. Found 55 (109 requested) and removed 101 (54 requested) atoms. Cycle 8: After refmac, R = 0.1580 (Rfree = 0.000) for 17055 atoms. Found 32 (109 requested) and removed 107 (54 requested) atoms. Cycle 9: After refmac, R = 0.1529 (Rfree = 0.000) for 16980 atoms. Found 36 (108 requested) and removed 97 (54 requested) atoms. Cycle 10: After refmac, R = 0.1532 (Rfree = 0.000) for 16919 atoms. Found 60 (108 requested) and removed 102 (54 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.54 3.31 Search for helices and strands: 0 residues in 0 chains, 17642 seeds are put forward NCS extension: 20 residues added (5 deleted due to clashes), 17662 seeds are put forward Round 1: 1168 peptides, 203 chains. Longest chain 15 peptides. Score 0.392 Round 2: 1315 peptides, 181 chains. Longest chain 23 peptides. Score 0.520 Round 3: 1321 peptides, 171 chains. Longest chain 26 peptides. Score 0.545 Round 4: 1303 peptides, 170 chains. Longest chain 25 peptides. Score 0.538 Round 5: 1355 peptides, 175 chains. Longest chain 26 peptides. Score 0.552 Taking the results from Round 5 Chains 181, Residues 1180, Estimated correctness of the model 0.0 % 9 chains (80 residues) have been docked in sequence ------------------------------------------------------ 31226 reflections ( 97.59 % complete ) and 4837 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1682 (Rfree = 0.000) for 17144 atoms. Found 30 (109 requested) and removed 92 (54 requested) atoms. Cycle 12: After refmac, R = 0.1595 (Rfree = 0.000) for 17082 atoms. Found 55 (109 requested) and removed 90 (54 requested) atoms. Cycle 13: After refmac, R = 0.1532 (Rfree = 0.000) for 17047 atoms. Found 42 (109 requested) and removed 81 (54 requested) atoms. Cycle 14: After refmac, R = 0.1234 (Rfree = 0.000) for 17008 atoms. Found 6 (109 requested) and removed 79 (54 requested) atoms. Cycle 15: After refmac, R = 0.1195 (Rfree = 0.000) for 16935 atoms. Found 9 (108 requested) and removed 71 (54 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.55 3.32 Search for helices and strands: 0 residues in 0 chains, 17564 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 17581 seeds are put forward Round 1: 1152 peptides, 198 chains. Longest chain 19 peptides. Score 0.395 Round 2: 1278 peptides, 174 chains. Longest chain 28 peptides. Score 0.518 Round 3: 1271 peptides, 175 chains. Longest chain 18 peptides. Score 0.512 Round 4: 1306 peptides, 172 chains. Longest chain 27 peptides. Score 0.535 Round 5: 1317 peptides, 169 chains. Longest chain 28 peptides. Score 0.547 Taking the results from Round 5 Chains 172, Residues 1148, Estimated correctness of the model 0.0 % 7 chains (74 residues) have been docked in sequence ------------------------------------------------------ 31226 reflections ( 97.59 % complete ) and 4719 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1686 (Rfree = 0.000) for 17144 atoms. Found 33 (109 requested) and removed 70 (54 requested) atoms. Cycle 17: After refmac, R = 0.1656 (Rfree = 0.000) for 17107 atoms. Found 79 (109 requested) and removed 68 (54 requested) atoms. Cycle 18: After refmac, R = 0.1597 (Rfree = 0.000) for 17118 atoms. Found 50 (109 requested) and removed 79 (54 requested) atoms. Cycle 19: After refmac, R = 0.1524 (Rfree = 0.000) for 17089 atoms. Found 58 (109 requested) and removed 76 (54 requested) atoms. Cycle 20: After refmac, R = 0.1482 (Rfree = 0.000) for 17071 atoms. Found 45 (109 requested) and removed 75 (54 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.57 3.34 Search for helices and strands: 0 residues in 0 chains, 17728 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 17745 seeds are put forward Round 1: 1081 peptides, 193 chains. Longest chain 14 peptides. Score 0.367 Round 2: 1219 peptides, 173 chains. Longest chain 29 peptides. Score 0.490 Round 3: 1234 peptides, 179 chains. Longest chain 22 peptides. Score 0.484 Round 4: 1240 peptides, 164 chains. Longest chain 26 peptides. Score 0.521 Round 5: 1243 peptides, 178 chains. Longest chain 17 peptides. Score 0.491 Taking the results from Round 4 Chains 166, Residues 1076, Estimated correctness of the model 0.0 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 31226 reflections ( 97.59 % complete ) and 4257 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1713 (Rfree = 0.000) for 17144 atoms. Found 67 (109 requested) and removed 84 (54 requested) atoms. Cycle 22: After refmac, R = 0.1687 (Rfree = 0.000) for 17127 atoms. Found 98 (109 requested) and removed 73 (54 requested) atoms. Cycle 23: After refmac, R = 0.1599 (Rfree = 0.000) for 17152 atoms. Found 79 (110 requested) and removed 77 (55 requested) atoms. Cycle 24: After refmac, R = 0.1523 (Rfree = 0.000) for 17154 atoms. Found 79 (110 requested) and removed 87 (55 requested) atoms. Cycle 25: After refmac, R = 0.1176 (Rfree = 0.000) for 17146 atoms. Found 12 (110 requested) and removed 71 (55 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 3.33 Search for helices and strands: 0 residues in 0 chains, 17724 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 17745 seeds are put forward Round 1: 1046 peptides, 191 chains. Longest chain 16 peptides. Score 0.351 Round 2: 1175 peptides, 180 chains. Longest chain 18 peptides. Score 0.451 Round 3: 1196 peptides, 172 chains. Longest chain 20 peptides. Score 0.481 Round 4: 1204 peptides, 175 chains. Longest chain 16 peptides. Score 0.478 Round 5: 1191 peptides, 177 chains. Longest chain 18 peptides. Score 0.467 Taking the results from Round 3 Chains 174, Residues 1024, Estimated correctness of the model 0.0 % 10 chains (77 residues) have been docked in sequence ------------------------------------------------------ 31226 reflections ( 97.59 % complete ) and 4248 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1567 (Rfree = 0.000) for 17144 atoms. Found 49 (109 requested) and removed 84 (54 requested) atoms. Cycle 27: After refmac, R = 0.1553 (Rfree = 0.000) for 17109 atoms. Found 72 (109 requested) and removed 71 (54 requested) atoms. Cycle 28: After refmac, R = 0.1527 (Rfree = 0.000) for 17110 atoms. Found 85 (109 requested) and removed 67 (54 requested) atoms. Cycle 29: After refmac, R = 0.1176 (Rfree = 0.000) for 17128 atoms. Found 6 (109 requested) and removed 62 (54 requested) atoms. Cycle 30: After refmac, R = 0.1137 (Rfree = 0.000) for 17072 atoms. Found 4 (109 requested) and removed 67 (54 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.57 3.34 Search for helices and strands: 0 residues in 0 chains, 17607 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 17629 seeds are put forward Round 1: 1043 peptides, 192 chains. Longest chain 19 peptides. Score 0.347 Round 2: 1136 peptides, 180 chains. Longest chain 20 peptides. Score 0.430 Round 3: 1160 peptides, 181 chains. Longest chain 19 peptides. Score 0.441 Round 4: 1154 peptides, 173 chains. Longest chain 23 peptides. Score 0.457 Round 5: 1158 peptides, 170 chains. Longest chain 18 peptides. Score 0.466 Taking the results from Round 5 Chains 173, Residues 988, Estimated correctness of the model 0.0 % 6 chains (39 residues) have been docked in sequence ------------------------------------------------------ 31226 reflections ( 97.59 % complete ) and 3941 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1622 (Rfree = 0.000) for 17144 atoms. Found 84 (109 requested) and removed 74 (54 requested) atoms. Cycle 32: After refmac, R = 0.1633 (Rfree = 0.000) for 17154 atoms. Found 96 (110 requested) and removed 77 (55 requested) atoms. Cycle 33: After refmac, R = 0.1605 (Rfree = 0.000) for 17173 atoms. Found 99 (110 requested) and removed 74 (55 requested) atoms. Cycle 34: After refmac, R = 0.1512 (Rfree = 0.000) for 17198 atoms. Found 81 (110 requested) and removed 88 (55 requested) atoms. Cycle 35: After refmac, R = 0.1164 (Rfree = 0.000) for 17191 atoms. Found 13 (110 requested) and removed 68 (55 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.56 3.33 Search for helices and strands: 0 residues in 0 chains, 17693 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 17707 seeds are put forward Round 1: 966 peptides, 184 chains. Longest chain 15 peptides. Score 0.321 Round 2: 1091 peptides, 174 chains. Longest chain 17 peptides. Score 0.420 Round 3: 1078 peptides, 163 chains. Longest chain 22 peptides. Score 0.440 Round 4: 1071 peptides, 165 chains. Longest chain 20 peptides. Score 0.431 Round 5: 1111 peptides, 166 chains. Longest chain 17 peptides. Score 0.450 Taking the results from Round 5 Chains 166, Residues 945, Estimated correctness of the model 0.0 % 5 chains (38 residues) have been docked in sequence ------------------------------------------------------ 31226 reflections ( 97.59 % complete ) and 3747 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1584 (Rfree = 0.000) for 17144 atoms. Found 75 (109 requested) and removed 71 (54 requested) atoms. Cycle 37: After refmac, R = 0.1259 (Rfree = 0.000) for 17148 atoms. Found 17 (110 requested) and removed 73 (55 requested) atoms. Cycle 38: After refmac, R = 0.1195 (Rfree = 0.000) for 17092 atoms. Found 11 (109 requested) and removed 59 (54 requested) atoms. Cycle 39: After refmac, R = 0.1163 (Rfree = 0.000) for 17044 atoms. Found 10 (109 requested) and removed 56 (54 requested) atoms. Cycle 40: After refmac, R = 0.1137 (Rfree = 0.000) for 16998 atoms. Found 8 (109 requested) and removed 55 (54 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.57 3.34 Search for helices and strands: 0 residues in 0 chains, 17511 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 17523 seeds are put forward Round 1: 927 peptides, 174 chains. Longest chain 12 peptides. Score 0.323 Round 2: 1041 peptides, 166 chains. Longest chain 19 peptides. Score 0.412 Round 3: 1045 peptides, 173 chains. Longest chain 16 peptides. Score 0.396 Round 4: 1044 peptides, 163 chains. Longest chain 23 peptides. Score 0.421 Round 5: 1039 peptides, 158 chains. Longest chain 16 peptides. Score 0.430 Taking the results from Round 5 Chains 159, Residues 881, Estimated correctness of the model 0.0 % 4 chains (31 residues) have been docked in sequence ------------------------------------------------------ 31226 reflections ( 97.59 % complete ) and 3480 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1623 (Rfree = 0.000) for 17144 atoms. Found 85 (109 requested) and removed 64 (54 requested) atoms. Cycle 42: After refmac, R = 0.1596 (Rfree = 0.000) for 17165 atoms. Found 106 (110 requested) and removed 72 (55 requested) atoms. Cycle 43: After refmac, R = 0.1213 (Rfree = 0.000) for 17199 atoms. Found 11 (110 requested) and removed 65 (55 requested) atoms. Cycle 44: After refmac, R = 0.1136 (Rfree = 0.000) for 17145 atoms. Found 15 (109 requested) and removed 57 (54 requested) atoms. Cycle 45: After refmac, R = 0.1112 (Rfree = 0.000) for 17103 atoms. Found 12 (109 requested) and removed 55 (54 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.57 3.34 Search for helices and strands: 0 residues in 0 chains, 17611 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 17629 seeds are put forward Round 1: 834 peptides, 163 chains. Longest chain 13 peptides. Score 0.294 Round 2: 967 peptides, 156 chains. Longest chain 17 peptides. Score 0.394 Round 3: 942 peptides, 154 chains. Longest chain 16 peptides. Score 0.385 Round 4: 982 peptides, 157 chains. Longest chain 17 peptides. Score 0.401 Round 5: 943 peptides, 155 chains. Longest chain 19 peptides. Score 0.383 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 159, Residues 825, Estimated correctness of the model 0.0 % 7 chains (52 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2prr-3_warpNtrace.pdb as input Building loops using Loopy2018 159 chains (825 residues) following loop building 7 chains (52 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 31226 reflections ( 97.59 % complete ) and 3336 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1589 (Rfree = 0.000) for 17144 atoms. Found 0 (109 requested) and removed 54 (54 requested) atoms. Cycle 47: After refmac, R = 0.1680 (Rfree = 0.000) for 17090 atoms. Found 0 (109 requested) and removed 54 (54 requested) atoms. Cycle 48: After refmac, R = 0.1654 (Rfree = 0.000) for 17036 atoms. Found 0 (109 requested) and removed 54 (54 requested) atoms. Cycle 49: After refmac, R = 0.1591 (Rfree = 0.000) for 16982 atoms. Found 0 (108 requested) and removed 54 (54 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 10:07:55 GMT 2018 Job finished. TimeTaking 146.37 Used memory is bytes: 7892904