Mon 24 Dec 00:46:25 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2prr-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2prr-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2prr-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prr-3.4-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2prr-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prr-3.4-parrot-mrncs ############### 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 00:46:30 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/mrncs/ArpWArp/wArpResults/WorkingDir/2prr-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prr-3.4-parrot-mrncs/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-mrncs.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-mrncs.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 21022 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.2940 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2384 (Rfree = 0.000) for 21022 atoms. Found 123 (158 requested) and removed 132 (79 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.40 3.18 Search for helices and strands: 0 residues in 0 chains, 21551 seeds are put forward NCS extension: 0 residues added, 21551 seeds are put forward Round 1: 1266 peptides, 234 chains. Longest chain 17 peptides. Score 0.373 Round 2: 1438 peptides, 197 chains. Longest chain 31 peptides. Score 0.545 Round 3: 1473 peptides, 192 chains. Longest chain 29 peptides. Score 0.571 Round 4: 1485 peptides, 183 chains. Longest chain 23 peptides. Score 0.594 Round 5: 1523 peptides, 183 chains. Longest chain 26 peptides. Score 0.610 Taking the results from Round 5 Chains 192, Residues 1340, Estimated correctness of the model 31.9 % 10 chains (98 residues) have been docked in sequence ------------------------------------------------------ 37049 reflections ( 97.55 % complete ) and 5522 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2010 (Rfree = 0.000) for 17196 atoms. Found 70 (129 requested) and removed 89 (64 requested) atoms. Cycle 2: After refmac, R = 0.1816 (Rfree = 0.000) for 17177 atoms. Found 43 (129 requested) and removed 77 (64 requested) atoms. Cycle 3: After refmac, R = 0.1735 (Rfree = 0.000) for 17143 atoms. Found 39 (129 requested) and removed 87 (64 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.1642 (Rfree = 0.000) for 17095 atoms. Found 41 (129 requested) and removed 88 (64 requested) atoms. Cycle 5: After refmac, R = 0.1608 (Rfree = 0.000) for 17048 atoms. Found 52 (128 requested) and removed 97 (64 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.39 3.17 Search for helices and strands: 0 residues in 0 chains, 17787 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 17803 seeds are put forward Round 1: 1405 peptides, 212 chains. Longest chain 18 peptides. Score 0.497 Round 2: 1538 peptides, 206 chains. Longest chain 27 peptides. Score 0.572 Round 3: 1486 peptides, 178 chains. Longest chain 30 peptides. Score 0.604 Round 4: 1525 peptides, 177 chains. Longest chain 32 peptides. Score 0.622 Round 5: 1523 peptides, 187 chains. Longest chain 26 peptides. Score 0.602 Taking the results from Round 4 Chains 190, Residues 1348, Estimated correctness of the model 35.7 % 13 chains (188 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 37049 reflections ( 97.55 % complete ) and 5950 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1853 (Rfree = 0.000) for 17196 atoms. Found 63 (129 requested) and removed 108 (64 requested) atoms. Cycle 7: After refmac, R = 0.1747 (Rfree = 0.000) for 17151 atoms. Found 48 (129 requested) and removed 84 (64 requested) atoms. Cycle 8: After refmac, R = 0.1660 (Rfree = 0.000) for 17115 atoms. Found 41 (129 requested) and removed 81 (64 requested) atoms. Cycle 9: After refmac, R = 0.1592 (Rfree = 0.000) for 17075 atoms. Found 31 (128 requested) and removed 87 (64 requested) atoms. Cycle 10: After refmac, R = 0.1562 (Rfree = 0.000) for 17019 atoms. Found 27 (128 requested) and removed 76 (64 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.38 3.16 Search for helices and strands: 0 residues in 0 chains, 17766 seeds are put forward NCS extension: 21 residues added (13 deleted due to clashes), 17787 seeds are put forward Round 1: 1314 peptides, 206 chains. Longest chain 17 peptides. Score 0.464 Round 2: 1494 peptides, 200 chains. Longest chain 22 peptides. Score 0.564 Round 3: 1489 peptides, 189 chains. Longest chain 27 peptides. Score 0.584 Round 4: 1499 peptides, 195 chains. Longest chain 18 peptides. Score 0.576 Round 5: 1472 peptides, 194 chains. Longest chain 22 peptides. Score 0.566 Taking the results from Round 3 Chains 194, Residues 1300, Estimated correctness of the model 23.4 % 6 chains (59 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 37049 reflections ( 97.55 % complete ) and 5244 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1748 (Rfree = 0.000) for 17196 atoms. Found 46 (129 requested) and removed 82 (64 requested) atoms. Cycle 12: After refmac, R = 0.1643 (Rfree = 0.000) for 17160 atoms. Found 34 (129 requested) and removed 71 (64 requested) atoms. Cycle 13: After refmac, R = 0.1604 (Rfree = 0.000) for 17123 atoms. Found 29 (129 requested) and removed 71 (64 requested) atoms. Cycle 14: After refmac, R = 0.1543 (Rfree = 0.000) for 17081 atoms. Found 26 (128 requested) and removed 69 (64 requested) atoms. Cycle 15: After refmac, R = 0.1495 (Rfree = 0.000) for 17038 atoms. Found 26 (128 requested) and removed 68 (64 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 3.17 Search for helices and strands: 0 residues in 0 chains, 17720 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 17742 seeds are put forward Round 1: 1303 peptides, 202 chains. Longest chain 24 peptides. Score 0.468 Round 2: 1454 peptides, 192 chains. Longest chain 32 peptides. Score 0.562 Round 3: 1467 peptides, 180 chains. Longest chain 29 peptides. Score 0.592 Round 4: 1467 peptides, 174 chains. Longest chain 25 peptides. Score 0.603 Round 5: 1458 peptides, 185 chains. Longest chain 21 peptides. Score 0.578 Taking the results from Round 4 Chains 184, Residues 1293, Estimated correctness of the model 29.7 % 14 chains (195 residues) have been docked in sequence ------------------------------------------------------ 37049 reflections ( 97.55 % complete ) and 5807 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1790 (Rfree = 0.000) for 17196 atoms. Found 54 (129 requested) and removed 94 (64 requested) atoms. Cycle 17: After refmac, R = 0.1646 (Rfree = 0.000) for 17156 atoms. Found 23 (129 requested) and removed 78 (64 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1611 (Rfree = 0.000) for 17101 atoms. Found 32 (129 requested) and removed 71 (64 requested) atoms. Cycle 19: After refmac, R = 0.1593 (Rfree = 0.000) for 17062 atoms. Found 23 (128 requested) and removed 71 (64 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1588 (Rfree = 0.000) for 17014 atoms. Found 25 (128 requested) and removed 70 (64 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.40 3.18 Search for helices and strands: 0 residues in 0 chains, 17683 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 17700 seeds are put forward Round 1: 1280 peptides, 199 chains. Longest chain 21 peptides. Score 0.463 Round 2: 1358 peptides, 174 chains. Longest chain 37 peptides. Score 0.555 Round 3: 1382 peptides, 178 chains. Longest chain 37 peptides. Score 0.558 Round 4: 1411 peptides, 182 chains. Longest chain 22 peptides. Score 0.563 Round 5: 1412 peptides, 181 chains. Longest chain 25 peptides. Score 0.566 Taking the results from Round 5 Chains 187, Residues 1231, Estimated correctness of the model 17.2 % 12 chains (93 residues) have been docked in sequence ------------------------------------------------------ 37049 reflections ( 97.55 % complete ) and 5056 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1818 (Rfree = 0.000) for 17196 atoms. Found 49 (129 requested) and removed 89 (64 requested) atoms. Cycle 22: After refmac, R = 0.1720 (Rfree = 0.000) for 17156 atoms. Found 65 (129 requested) and removed 72 (64 requested) atoms. Cycle 23: After refmac, R = 0.1636 (Rfree = 0.000) for 17149 atoms. Found 37 (129 requested) and removed 69 (64 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.1583 (Rfree = 0.000) for 17117 atoms. Found 48 (129 requested) and removed 75 (64 requested) atoms. Cycle 25: After refmac, R = 0.1554 (Rfree = 0.000) for 17090 atoms. Found 37 (129 requested) and removed 74 (64 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.39 3.17 Search for helices and strands: 0 residues in 0 chains, 17757 seeds are put forward NCS extension: 21 residues added (6 deleted due to clashes), 17778 seeds are put forward Round 1: 1229 peptides, 197 chains. Longest chain 21 peptides. Score 0.440 Round 2: 1332 peptides, 189 chains. Longest chain 32 peptides. Score 0.511 Round 3: 1334 peptides, 186 chains. Longest chain 33 peptides. Score 0.519 Round 4: 1309 peptides, 178 chains. Longest chain 23 peptides. Score 0.524 Round 5: 1283 peptides, 186 chains. Longest chain 23 peptides. Score 0.494 Taking the results from Round 4 Chains 179, Residues 1131, Estimated correctness of the model 1.9 % 8 chains (60 residues) have been docked in sequence ------------------------------------------------------ 37049 reflections ( 97.55 % complete ) and 4564 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1738 (Rfree = 0.000) for 17196 atoms. Found 75 (129 requested) and removed 89 (64 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1636 (Rfree = 0.000) for 17182 atoms. Found 39 (129 requested) and removed 75 (64 requested) atoms. Cycle 28: After refmac, R = 0.1632 (Rfree = 0.000) for 17146 atoms. Found 54 (129 requested) and removed 68 (64 requested) atoms. Cycle 29: After refmac, R = 0.1612 (Rfree = 0.000) for 17132 atoms. Found 40 (129 requested) and removed 71 (64 requested) atoms. Cycle 30: After refmac, R = 0.1455 (Rfree = 0.000) for 17101 atoms. Found 16 (129 requested) and removed 72 (64 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.18 Search for helices and strands: 0 residues in 0 chains, 17710 seeds are put forward NCS extension: 16 residues added (5 deleted due to clashes), 17726 seeds are put forward Round 1: 1128 peptides, 200 chains. Longest chain 17 peptides. Score 0.377 Round 2: 1297 peptides, 192 chains. Longest chain 22 peptides. Score 0.487 Round 3: 1237 peptides, 171 chains. Longest chain 21 peptides. Score 0.504 Round 4: 1238 peptides, 175 chains. Longest chain 21 peptides. Score 0.496 Round 5: 1264 peptides, 184 chains. Longest chain 19 peptides. Score 0.488 Taking the results from Round 3 Chains 175, Residues 1066, Estimated correctness of the model 0.0 % 5 chains (47 residues) have been docked in sequence ------------------------------------------------------ 37049 reflections ( 97.55 % complete ) and 4290 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1673 (Rfree = 0.000) for 17196 atoms. Found 49 (129 requested) and removed 82 (64 requested) atoms. Cycle 32: After refmac, R = 0.1614 (Rfree = 0.000) for 17163 atoms. Found 23 (129 requested) and removed 66 (64 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1603 (Rfree = 0.000) for 17120 atoms. Found 51 (129 requested) and removed 68 (64 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1570 (Rfree = 0.000) for 17103 atoms. Found 36 (129 requested) and removed 70 (64 requested) atoms. Cycle 35: After refmac, R = 0.1385 (Rfree = 0.000) for 17069 atoms. Found 12 (128 requested) and removed 66 (64 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.39 3.17 Search for helices and strands: 0 residues in 0 chains, 17679 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 17696 seeds are put forward Round 1: 1070 peptides, 186 chains. Longest chain 17 peptides. Score 0.378 Round 2: 1202 peptides, 182 chains. Longest chain 19 peptides. Score 0.461 Round 3: 1229 peptides, 174 chains. Longest chain 24 peptides. Score 0.493 Round 4: 1191 peptides, 171 chains. Longest chain 23 peptides. Score 0.481 Round 5: 1244 peptides, 183 chains. Longest chain 30 peptides. Score 0.481 Taking the results from Round 3 Chains 179, Residues 1055, Estimated correctness of the model 0.0 % 11 chains (105 residues) have been docked in sequence ------------------------------------------------------ 37049 reflections ( 97.55 % complete ) and 4433 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1640 (Rfree = 0.000) for 17196 atoms. Found 41 (129 requested) and removed 90 (64 requested) atoms. Cycle 37: After refmac, R = 0.1569 (Rfree = 0.000) for 17147 atoms. Found 30 (129 requested) and removed 67 (64 requested) atoms. Cycle 38: After refmac, R = 0.1582 (Rfree = 0.000) for 17110 atoms. Found 35 (129 requested) and removed 68 (64 requested) atoms. Cycle 39: After refmac, R = 0.1555 (Rfree = 0.000) for 17077 atoms. Found 37 (128 requested) and removed 70 (64 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1520 (Rfree = 0.000) for 17044 atoms. Found 30 (128 requested) and removed 65 (64 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.38 3.16 Search for helices and strands: 0 residues in 0 chains, 17684 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 17706 seeds are put forward Round 1: 1048 peptides, 187 chains. Longest chain 16 peptides. Score 0.363 Round 2: 1179 peptides, 176 chains. Longest chain 24 peptides. Score 0.463 Round 3: 1157 peptides, 171 chains. Longest chain 18 peptides. Score 0.463 Round 4: 1203 peptides, 171 chains. Longest chain 21 peptides. Score 0.487 Round 5: 1200 peptides, 175 chains. Longest chain 18 peptides. Score 0.476 Taking the results from Round 4 Chains 172, Residues 1032, Estimated correctness of the model 0.0 % 6 chains (63 residues) have been docked in sequence ------------------------------------------------------ 37049 reflections ( 97.55 % complete ) and 4191 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1606 (Rfree = 0.000) for 17196 atoms. Found 29 (129 requested) and removed 76 (64 requested) atoms. Cycle 42: After refmac, R = 0.1552 (Rfree = 0.000) for 17149 atoms. Found 40 (129 requested) and removed 72 (64 requested) atoms. Cycle 43: After refmac, R = 0.1544 (Rfree = 0.000) for 17117 atoms. Found 29 (129 requested) and removed 71 (64 requested) atoms. Cycle 44: After refmac, R = 0.1497 (Rfree = 0.000) for 17075 atoms. Found 36 (128 requested) and removed 66 (64 requested) atoms. Cycle 45: After refmac, R = 0.1477 (Rfree = 0.000) for 17045 atoms. Found 17 (128 requested) and removed 66 (64 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.40 3.18 Search for helices and strands: 0 residues in 0 chains, 17604 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 17621 seeds are put forward Round 1: 976 peptides, 174 chains. Longest chain 17 peptides. Score 0.353 Round 2: 1135 peptides, 185 chains. Longest chain 20 peptides. Score 0.418 Round 3: 1153 peptides, 173 chains. Longest chain 20 peptides. Score 0.456 Round 4: 1133 peptides, 183 chains. Longest chain 19 peptides. Score 0.421 Round 5: 1159 peptides, 189 chains. Longest chain 18 peptides. Score 0.421 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 177, Residues 980, Estimated correctness of the model 0.0 % 9 chains (75 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2prr-3_warpNtrace.pdb as input Building loops using Loopy2018 177 chains (980 residues) following loop building 9 chains (75 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 37049 reflections ( 97.55 % complete ) and 4035 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1603 (Rfree = 0.000) for 17196 atoms. Found 0 (129 requested) and removed 30 (64 requested) atoms. Cycle 47: After refmac, R = 0.1587 (Rfree = 0.000) for 17166 atoms. Found 0 (129 requested) and removed 44 (64 requested) atoms. Cycle 48: After refmac, R = 0.1524 (Rfree = 0.000) for 17122 atoms. Found 0 (129 requested) and removed 44 (64 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.1488 (Rfree = 0.000) for 17078 atoms. TimeTaking 180.02