null Mon 24 Dec 08:00:03 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-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2prr-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2prr-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prr-3.4-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-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prr-3.4-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 08:00:08 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-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prr-3.4-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 1882 and 0 Target number of residues in the AU: 1882 Target solvent content: 0.6429 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-3.4-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-3.4-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 3.400 Wilson plot Bfac: 73.79 37049 reflections ( 97.55 % complete ) and 0 restraints for refining 20860 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3140 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2618 (Rfree = 0.000) for 20860 atoms. Found 156 (157 requested) and removed 167 (78 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.40 3.18 Search for helices and strands: 0 residues in 0 chains, 21466 seeds are put forward NCS extension: 0 residues added, 21466 seeds are put forward Round 1: 1112 peptides, 212 chains. Longest chain 13 peptides. Score 0.337 Round 2: 1285 peptides, 201 chains. Longest chain 14 peptides. Score 0.461 Round 3: 1344 peptides, 198 chains. Longest chain 20 peptides. Score 0.498 Round 4: 1354 peptides, 187 chains. Longest chain 24 peptides. Score 0.526 Round 5: 1385 peptides, 182 chains. Longest chain 24 peptides. Score 0.551 Taking the results from Round 5 Chains 189, Residues 1203, Estimated correctness of the model 11.9 % 13 chains (117 residues) have been docked in sequence ------------------------------------------------------ 37049 reflections ( 97.55 % complete ) and 5075 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2019 (Rfree = 0.000) for 17196 atoms. Found 50 (129 requested) and removed 98 (64 requested) atoms. Cycle 2: After refmac, R = 0.1843 (Rfree = 0.000) for 17148 atoms. Found 26 (129 requested) and removed 78 (64 requested) atoms. Cycle 3: After refmac, R = 0.1605 (Rfree = 0.000) for 17096 atoms. Found 17 (129 requested) and removed 75 (64 requested) atoms. Cycle 4: After refmac, R = 0.1544 (Rfree = 0.000) for 17038 atoms. Found 10 (128 requested) and removed 70 (64 requested) atoms. Cycle 5: After refmac, R = 0.1506 (Rfree = 0.000) for 16978 atoms. Found 5 (128 requested) and removed 64 (64 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.39 3.17 Search for helices and strands: 0 residues in 0 chains, 17720 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 17737 seeds are put forward Round 1: 1224 peptides, 209 chains. Longest chain 16 peptides. Score 0.409 Round 2: 1325 peptides, 186 chains. Longest chain 26 peptides. Score 0.514 Round 3: 1397 peptides, 185 chains. Longest chain 27 peptides. Score 0.551 Round 4: 1360 peptides, 175 chains. Longest chain 24 peptides. Score 0.554 Round 5: 1353 peptides, 187 chains. Longest chain 26 peptides. Score 0.526 Taking the results from Round 4 Chains 181, Residues 1185, Estimated correctness of the model 13.0 % 10 chains (95 residues) have been docked in sequence ------------------------------------------------------ 37049 reflections ( 97.55 % complete ) and 4909 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1870 (Rfree = 0.000) for 17196 atoms. Found 41 (129 requested) and removed 88 (64 requested) atoms. Cycle 7: After refmac, R = 0.1800 (Rfree = 0.000) for 17149 atoms. Found 47 (129 requested) and removed 87 (64 requested) atoms. Cycle 8: After refmac, R = 0.1716 (Rfree = 0.000) for 17109 atoms. Found 47 (129 requested) and removed 77 (64 requested) atoms. Cycle 9: After refmac, R = 0.1714 (Rfree = 0.000) for 17079 atoms. Found 34 (128 requested) and removed 83 (64 requested) atoms. Cycle 10: After refmac, R = 0.1604 (Rfree = 0.000) for 17030 atoms. Found 31 (128 requested) and removed 88 (64 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.15 Search for helices and strands: 0 residues in 0 chains, 17709 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 17729 seeds are put forward Round 1: 1230 peptides, 196 chains. Longest chain 24 peptides. Score 0.443 Round 2: 1339 peptides, 189 chains. Longest chain 26 peptides. Score 0.515 Round 3: 1349 peptides, 189 chains. Longest chain 30 peptides. Score 0.520 Round 4: 1347 peptides, 177 chains. Longest chain 29 peptides. Score 0.544 Round 5: 1390 peptides, 178 chains. Longest chain 23 peptides. Score 0.562 Taking the results from Round 5 Chains 185, Residues 1212, Estimated correctness of the model 15.8 % 10 chains (83 residues) have been docked in sequence ------------------------------------------------------ 37049 reflections ( 97.55 % complete ) and 4975 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1824 (Rfree = 0.000) for 17196 atoms. Found 52 (129 requested) and removed 87 (64 requested) atoms. Cycle 12: After refmac, R = 0.1693 (Rfree = 0.000) for 17161 atoms. Found 42 (129 requested) and removed 72 (64 requested) atoms. Cycle 13: After refmac, R = 0.1626 (Rfree = 0.000) for 17131 atoms. Found 29 (129 requested) and removed 85 (64 requested) atoms. Cycle 14: After refmac, R = 0.1590 (Rfree = 0.000) for 17075 atoms. Found 27 (128 requested) and removed 70 (64 requested) atoms. Cycle 15: After refmac, R = 0.1579 (Rfree = 0.000) for 17032 atoms. Found 36 (128 requested) and removed 72 (64 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 3.17 Search for helices and strands: 0 residues in 0 chains, 17714 seeds are put forward NCS extension: 8 residues added (9 deleted due to clashes), 17722 seeds are put forward Round 1: 1195 peptides, 201 chains. Longest chain 18 peptides. Score 0.412 Round 2: 1334 peptides, 189 chains. Longest chain 21 peptides. Score 0.512 Round 3: 1369 peptides, 190 chains. Longest chain 22 peptides. Score 0.527 Round 4: 1365 peptides, 183 chains. Longest chain 33 peptides. Score 0.540 Round 5: 1380 peptides, 188 chains. Longest chain 20 peptides. Score 0.537 Taking the results from Round 4 Chains 189, Residues 1182, Estimated correctness of the model 7.9 % 8 chains (86 residues) have been docked in sequence ------------------------------------------------------ 37049 reflections ( 97.55 % complete ) and 4846 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1768 (Rfree = 0.000) for 17196 atoms. Found 45 (129 requested) and removed 87 (64 requested) atoms. Cycle 17: After refmac, R = 0.1720 (Rfree = 0.000) for 17154 atoms. Found 54 (129 requested) and removed 79 (64 requested) atoms. Cycle 18: After refmac, R = 0.1668 (Rfree = 0.000) for 17129 atoms. Found 45 (129 requested) and removed 70 (64 requested) atoms. Cycle 19: After refmac, R = 0.1619 (Rfree = 0.000) for 17104 atoms. Found 27 (129 requested) and removed 71 (64 requested) atoms. Cycle 20: After refmac, R = 0.1413 (Rfree = 0.000) for 17060 atoms. Found 9 (128 requested) and removed 71 (64 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.17 Search for helices and strands: 0 residues in 0 chains, 17718 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 17740 seeds are put forward Round 1: 1159 peptides, 193 chains. Longest chain 35 peptides. Score 0.411 Round 2: 1285 peptides, 183 chains. Longest chain 19 peptides. Score 0.501 Round 3: 1338 peptides, 190 chains. Longest chain 23 peptides. Score 0.512 Round 4: 1314 peptides, 186 chains. Longest chain 30 peptides. Score 0.509 Round 5: 1320 peptides, 185 chains. Longest chain 21 peptides. Score 0.514 Taking the results from Round 5 Chains 187, Residues 1135, Estimated correctness of the model 0.0 % 8 chains (58 residues) have been docked in sequence ------------------------------------------------------ 37049 reflections ( 97.55 % complete ) and 4581 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1743 (Rfree = 0.000) for 17196 atoms. Found 41 (129 requested) and removed 76 (64 requested) atoms. Cycle 22: After refmac, R = 0.1703 (Rfree = 0.000) for 17161 atoms. Found 49 (129 requested) and removed 68 (64 requested) atoms. Cycle 23: After refmac, R = 0.1623 (Rfree = 0.000) for 17142 atoms. Found 37 (129 requested) and removed 72 (64 requested) atoms. Cycle 24: After refmac, R = 0.1590 (Rfree = 0.000) for 17107 atoms. Found 33 (129 requested) and removed 70 (64 requested) atoms. Cycle 25: After refmac, R = 0.1539 (Rfree = 0.000) for 17070 atoms. Found 33 (128 requested) and removed 69 (64 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.38 3.16 Search for helices and strands: 0 residues in 0 chains, 17724 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 17746 seeds are put forward Round 1: 1069 peptides, 195 chains. Longest chain 12 peptides. Score 0.355 Round 2: 1276 peptides, 194 chains. Longest chain 18 peptides. Score 0.472 Round 3: 1301 peptides, 191 chains. Longest chain 23 peptides. Score 0.492 Round 4: 1239 peptides, 181 chains. Longest chain 22 peptides. Score 0.482 Round 5: 1222 peptides, 183 chains. Longest chain 17 peptides. Score 0.469 Taking the results from Round 3 Chains 202, Residues 1110, Estimated correctness of the model 0.0 % 18 chains (150 residues) have been docked in sequence ------------------------------------------------------ 37049 reflections ( 97.55 % complete ) and 4807 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1741 (Rfree = 0.000) for 17196 atoms. Found 55 (129 requested) and removed 100 (64 requested) atoms. Cycle 27: After refmac, R = 0.1627 (Rfree = 0.000) for 17151 atoms. Found 25 (129 requested) and removed 73 (64 requested) atoms. Cycle 28: After refmac, R = 0.1593 (Rfree = 0.000) for 17103 atoms. Found 30 (129 requested) and removed 76 (64 requested) atoms. Cycle 29: After refmac, R = 0.1558 (Rfree = 0.000) for 17057 atoms. Found 18 (128 requested) and removed 68 (64 requested) atoms. Cycle 30: After refmac, R = 0.1550 (Rfree = 0.000) for 17007 atoms. Found 31 (128 requested) and removed 72 (64 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.39 3.17 Search for helices and strands: 0 residues in 0 chains, 17609 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 17626 seeds are put forward Round 1: 1048 peptides, 201 chains. Longest chain 14 peptides. Score 0.327 Round 2: 1199 peptides, 200 chains. Longest chain 15 peptides. Score 0.417 Round 3: 1210 peptides, 189 chains. Longest chain 18 peptides. Score 0.449 Round 4: 1196 peptides, 187 chains. Longest chain 17 peptides. Score 0.446 Round 5: 1201 peptides, 179 chains. Longest chain 17 peptides. Score 0.467 Taking the results from Round 5 Chains 181, Residues 1022, Estimated correctness of the model 0.0 % 11 chains (63 residues) have been docked in sequence ------------------------------------------------------ 37049 reflections ( 97.55 % complete ) and 4108 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1682 (Rfree = 0.000) for 17196 atoms. Found 50 (129 requested) and removed 80 (64 requested) atoms. Cycle 32: After refmac, R = 0.1563 (Rfree = 0.000) for 17166 atoms. Found 31 (129 requested) and removed 70 (64 requested) atoms. Cycle 33: After refmac, R = 0.1547 (Rfree = 0.000) for 17127 atoms. Found 36 (129 requested) and removed 65 (64 requested) atoms. Cycle 34: After refmac, R = 0.1500 (Rfree = 0.000) for 17098 atoms. Found 29 (129 requested) and removed 66 (64 requested) atoms. Cycle 35: After refmac, R = 0.1469 (Rfree = 0.000) for 17061 atoms. Found 31 (128 requested) and removed 72 (64 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 3.15 Search for helices and strands: 0 residues in 0 chains, 17675 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 17688 seeds are put forward Round 1: 989 peptides, 190 chains. Longest chain 12 peptides. Score 0.319 Round 2: 1173 peptides, 196 chains. Longest chain 18 peptides. Score 0.412 Round 3: 1128 peptides, 183 chains. Longest chain 17 peptides. Score 0.419 Round 4: 1184 peptides, 185 chains. Longest chain 20 peptides. Score 0.444 Round 5: 1175 peptides, 173 chains. Longest chain 20 peptides. Score 0.468 Taking the results from Round 5 Chains 175, Residues 1002, Estimated correctness of the model 0.0 % 7 chains (62 residues) have been docked in sequence ------------------------------------------------------ 37049 reflections ( 97.55 % complete ) and 4053 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1606 (Rfree = 0.000) for 17196 atoms. Found 49 (129 requested) and removed 76 (64 requested) atoms. Cycle 37: After refmac, R = 0.1494 (Rfree = 0.000) for 17169 atoms. Found 22 (129 requested) and removed 70 (64 requested) atoms. Cycle 38: After refmac, R = 0.1472 (Rfree = 0.000) for 17121 atoms. Found 32 (129 requested) and removed 68 (64 requested) atoms. Cycle 39: After refmac, R = 0.1425 (Rfree = 0.000) for 17085 atoms. Found 25 (129 requested) and removed 69 (64 requested) atoms. Cycle 40: After refmac, R = 0.1396 (Rfree = 0.000) for 17041 atoms. Found 24 (128 requested) and removed 69 (64 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 3.17 Search for helices and strands: 0 residues in 0 chains, 17640 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 17658 seeds are put forward Round 1: 951 peptides, 183 chains. Longest chain 15 peptides. Score 0.314 Round 2: 1095 peptides, 187 chains. Longest chain 18 peptides. Score 0.390 Round 3: 1132 peptides, 183 chains. Longest chain 21 peptides. Score 0.421 Round 4: 1139 peptides, 185 chains. Longest chain 23 peptides. Score 0.420 Round 5: 1077 peptides, 168 chains. Longest chain 19 peptides. Score 0.427 Taking the results from Round 5 Chains 172, Residues 909, Estimated correctness of the model 0.0 % 6 chains (52 residues) have been docked in sequence ------------------------------------------------------ 37049 reflections ( 97.55 % complete ) and 3655 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1588 (Rfree = 0.000) for 17196 atoms. Found 43 (129 requested) and removed 75 (64 requested) atoms. Cycle 42: After refmac, R = 0.1538 (Rfree = 0.000) for 17164 atoms. Found 31 (129 requested) and removed 68 (64 requested) atoms. Cycle 43: After refmac, R = 0.1487 (Rfree = 0.000) for 17126 atoms. Found 35 (129 requested) and removed 69 (64 requested) atoms. Cycle 44: After refmac, R = 0.1435 (Rfree = 0.000) for 17091 atoms. Found 32 (129 requested) and removed 76 (64 requested) atoms. Cycle 45: After refmac, R = 0.1371 (Rfree = 0.000) for 17046 atoms. Found 26 (128 requested) and removed 78 (64 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.39 3.17 Search for helices and strands: 0 residues in 0 chains, 17608 seeds are put forward NCS extension: 32 residues added (3 deleted due to clashes), 17640 seeds are put forward Round 1: 898 peptides, 179 chains. Longest chain 12 peptides. Score 0.291 Round 2: 1017 peptides, 173 chains. Longest chain 16 peptides. Score 0.380 Round 3: 1033 peptides, 171 chains. Longest chain 16 peptides. Score 0.394 Round 4: 1067 peptides, 166 chains. Longest chain 15 peptides. Score 0.426 Round 5: 1044 peptides, 174 chains. Longest chain 21 peptides. Score 0.393 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 167, Residues 901, Estimated correctness of the model 0.0 % 6 chains (50 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2prr-3_warpNtrace.pdb as input Building loops using Loopy2018 167 chains (901 residues) following loop building 6 chains (50 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 37049 reflections ( 97.55 % complete ) and 3628 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1542 (Rfree = 0.000) for 17196 atoms. Found 0 (129 requested) and removed 34 (64 requested) atoms. Cycle 47: After refmac, R = 0.1480 (Rfree = 0.000) for 17162 atoms. Found 0 (129 requested) and removed 49 (64 requested) atoms. Cycle 48: After refmac, R = 0.1452 (Rfree = 0.000) for 17113 atoms. Found 0 (129 requested) and removed 64 (64 requested) atoms. Cycle 49: After refmac, R = 0.1374 (Rfree = 0.000) for 17049 atoms. Found 0 (128 requested) and removed 64 (64 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 10:49:06 GMT 2018 Job finished. TimeTaking 169.05 Used memory is bytes: 13857584