Sun 23 Dec 22:23:13 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 2o2x-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o2x-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o2x-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2x-4.0-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/2o2x-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2x-4.0-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 ============================================================ Sun 23 Dec 22:23:22 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/2o2x-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2x-4.0-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 118 and 0 Target number of residues in the AU: 118 Target solvent content: 0.6601 Checking the provided sequence file Detected sequence length: 218 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 218 Adjusted target solvent content: 0.37 Input MTZ file: 2o2x-4.0-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: 4 Cell parameters: 36.470 66.250 41.010 90.000 108.540 90.000 Input sequence file: 2o2x-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1744 target number of atoms Had to go as low as 0.65 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 Loops will be built when appropriate and at the last cycle Resolution range: 38.882 4.001 Wilson plot Bfac: 83.60 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 1591 reflections ( 99.13 % complete ) and 0 restraints for refining 1929 atoms. Observations/parameters ratio is 0.21 ------------------------------------------------------ Starting model: R = 0.3234 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.1950 (Rfree = 0.000) for 1929 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.73 4.45 Search for helices and strands: 0 residues in 0 chains, 1962 seeds are put forward Round 1: 65 peptides, 13 chains. Longest chain 7 peptides. Score 0.298 Round 2: 87 peptides, 15 chains. Longest chain 10 peptides. Score 0.418 Round 3: 92 peptides, 15 chains. Longest chain 10 peptides. Score 0.458 Round 4: 102 peptides, 17 chains. Longest chain 11 peptides. Score 0.469 Round 5: 106 peptides, 15 chains. Longest chain 11 peptides. Score 0.560 Taking the results from Round 5 Chains 15, Residues 91, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 1591 reflections ( 99.13 % complete ) and 3670 restraints for refining 1561 atoms. 3296 conditional restraints added. Observations/parameters ratio is 0.25 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2324 (Rfree = 0.000) for 1561 atoms. Found 5 (7 requested) and removed 9 (3 requested) atoms. Cycle 2: After refmac, R = 0.2348 (Rfree = 0.000) for 1534 atoms. Found 3 (7 requested) and removed 23 (3 requested) atoms. Cycle 3: After refmac, R = 0.2135 (Rfree = 0.000) for 1504 atoms. Found 3 (7 requested) and removed 11 (3 requested) atoms. Cycle 4: After refmac, R = 0.1887 (Rfree = 0.000) for 1491 atoms. Found 0 (7 requested) and removed 8 (3 requested) atoms. Cycle 5: After refmac, R = 0.2164 (Rfree = 0.000) for 1479 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.73 4.45 Search for helices and strands: 0 residues in 0 chains, 1521 seeds are put forward Round 1: 80 peptides, 15 chains. Longest chain 9 peptides. Score 0.358 Round 2: 93 peptides, 15 chains. Longest chain 13 peptides. Score 0.466 Round 3: 97 peptides, 15 chains. Longest chain 16 peptides. Score 0.496 Round 4: 94 peptides, 16 chains. Longest chain 14 peptides. Score 0.440 Round 5: 98 peptides, 15 chains. Longest chain 15 peptides. Score 0.504 Taking the results from Round 5 Chains 15, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1591 reflections ( 99.13 % complete ) and 3521 restraints for refining 1471 atoms. 3204 conditional restraints added. Observations/parameters ratio is 0.27 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1988 (Rfree = 0.000) for 1471 atoms. Found 3 (6 requested) and removed 10 (3 requested) atoms. Cycle 7: After refmac, R = 0.1815 (Rfree = 0.000) for 1459 atoms. Found 0 (6 requested) and removed 9 (3 requested) atoms. Cycle 8: After refmac, R = 0.2217 (Rfree = 0.000) for 1445 atoms. Found 1 (6 requested) and removed 10 (3 requested) atoms. Cycle 9: After refmac, R = 0.1703 (Rfree = 0.000) for 1435 atoms. Found 0 (6 requested) and removed 6 (3 requested) atoms. Cycle 10: After refmac, R = 0.1786 (Rfree = 0.000) for 1427 atoms. Found 0 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.63 4.33 Search for helices and strands: 0 residues in 0 chains, 1479 seeds are put forward Round 1: 69 peptides, 14 chains. Longest chain 8 peptides. Score 0.296 Round 2: 88 peptides, 16 chains. Longest chain 10 peptides. Score 0.391 Round 3: 87 peptides, 13 chains. Longest chain 12 peptides. Score 0.487 Round 4: 88 peptides, 15 chains. Longest chain 11 peptides. Score 0.426 Round 5: 82 peptides, 13 chains. Longest chain 11 peptides. Score 0.448 Taking the results from Round 3 Chains 13, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1591 reflections ( 99.13 % complete ) and 3590 restraints for refining 1470 atoms. 3307 conditional restraints added. Observations/parameters ratio is 0.27 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1634 (Rfree = 0.000) for 1470 atoms. Found 0 (6 requested) and removed 10 (3 requested) atoms. Cycle 12: After refmac, R = 0.1469 (Rfree = 0.000) for 1452 atoms. Found 3 (6 requested) and removed 8 (3 requested) atoms. Cycle 13: After refmac, R = 0.1322 (Rfree = 0.000) for 1443 atoms. Found 2 (6 requested) and removed 9 (3 requested) atoms. Cycle 14: After refmac, R = 0.1232 (Rfree = 0.000) for 1435 atoms. Found 1 (6 requested) and removed 6 (3 requested) atoms. Cycle 15: After refmac, R = 0.1250 (Rfree = 0.000) for 1427 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.67 4.38 Search for helices and strands: 0 residues in 0 chains, 1465 seeds are put forward Round 1: 71 peptides, 15 chains. Longest chain 7 peptides. Score 0.276 Round 2: 75 peptides, 15 chains. Longest chain 7 peptides. Score 0.313 Round 3: 96 peptides, 18 chains. Longest chain 10 peptides. Score 0.387 Round 4: 88 peptides, 15 chains. Longest chain 22 peptides. Score 0.426 Round 5: 99 peptides, 18 chains. Longest chain 11 peptides. Score 0.412 Taking the results from Round 4 Chains 15, Residues 73, Estimated correctness of the model 0.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 1591 reflections ( 99.13 % complete ) and 3298 restraints for refining 1476 atoms. 2930 conditional restraints added. Observations/parameters ratio is 0.27 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1748 (Rfree = 0.000) for 1476 atoms. Found 4 (7 requested) and removed 43 (3 requested) atoms. Cycle 17: After refmac, R = 0.1473 (Rfree = 0.000) for 1430 atoms. Found 1 (6 requested) and removed 11 (3 requested) atoms. Cycle 18: After refmac, R = 0.1367 (Rfree = 0.000) for 1414 atoms. Found 0 (6 requested) and removed 7 (3 requested) atoms. Cycle 19: After refmac, R = 0.1362 (Rfree = 0.000) for 1405 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 20: After refmac, R = 0.1345 (Rfree = 0.000) for 1399 atoms. Found 0 (6 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.65 4.36 Search for helices and strands: 0 residues in 0 chains, 1449 seeds are put forward Round 1: 62 peptides, 13 chains. Longest chain 7 peptides. Score 0.269 Round 2: 76 peptides, 14 chains. Longest chain 8 peptides. Score 0.360 Round 3: 96 peptides, 16 chains. Longest chain 9 peptides. Score 0.456 Round 4: 91 peptides, 14 chains. Longest chain 9 peptides. Score 0.484 Round 5: 92 peptides, 14 chains. Longest chain 10 peptides. Score 0.492 Taking the results from Round 5 Chains 14, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1591 reflections ( 99.13 % complete ) and 3440 restraints for refining 1451 atoms. 3142 conditional restraints added. Observations/parameters ratio is 0.27 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1531 (Rfree = 0.000) for 1451 atoms. Found 2 (6 requested) and removed 7 (3 requested) atoms. Cycle 22: After refmac, R = 0.1513 (Rfree = 0.000) for 1444 atoms. Found 0 (6 requested) and removed 6 (3 requested) atoms. Cycle 23: After refmac, R = 0.1517 (Rfree = 0.000) for 1437 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. Cycle 24: After refmac, R = 0.1512 (Rfree = 0.000) for 1433 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 25: After refmac, R = 0.1477 (Rfree = 0.000) for 1430 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.65 4.36 Search for helices and strands: 0 residues in 0 chains, 1479 seeds are put forward Round 1: 74 peptides, 15 chains. Longest chain 8 peptides. Score 0.304 Round 2: 80 peptides, 13 chains. Longest chain 10 peptides. Score 0.431 Round 3: 75 peptides, 14 chains. Longest chain 10 peptides. Score 0.351 Round 4: 86 peptides, 15 chains. Longest chain 10 peptides. Score 0.410 Round 5: 89 peptides, 15 chains. Longest chain 9 peptides. Score 0.434 Taking the results from Round 5 Chains 15, Residues 74, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 1591 reflections ( 99.13 % complete ) and 3603 restraints for refining 1510 atoms. 3305 conditional restraints added. Observations/parameters ratio is 0.26 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1521 (Rfree = 0.000) for 1510 atoms. Found 2 (7 requested) and removed 14 (3 requested) atoms. Cycle 27: After refmac, R = 0.1217 (Rfree = 0.000) for 1493 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 28: After refmac, R = 0.1160 (Rfree = 0.000) for 1484 atoms. Found 0 (7 requested) and removed 6 (3 requested) atoms. Cycle 29: After refmac, R = 0.1176 (Rfree = 0.000) for 1477 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. Cycle 30: After refmac, R = 0.1164 (Rfree = 0.000) for 1475 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.72 4.44 Search for helices and strands: 0 residues in 0 chains, 1523 seeds are put forward Round 1: 63 peptides, 13 chains. Longest chain 8 peptides. Score 0.279 Round 2: 79 peptides, 15 chains. Longest chain 8 peptides. Score 0.349 Round 3: 85 peptides, 16 chains. Longest chain 9 peptides. Score 0.365 Round 4: 84 peptides, 14 chains. Longest chain 8 peptides. Score 0.429 Round 5: 75 peptides, 14 chains. Longest chain 7 peptides. Score 0.351 Taking the results from Round 4 Chains 14, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1591 reflections ( 99.13 % complete ) and 3689 restraints for refining 1518 atoms. 3423 conditional restraints added. Observations/parameters ratio is 0.26 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1472 (Rfree = 0.000) for 1518 atoms. Found 1 (7 requested) and removed 12 (3 requested) atoms. Cycle 32: After refmac, R = 0.1349 (Rfree = 0.000) for 1505 atoms. Found 0 (7 requested) and removed 6 (3 requested) atoms. Cycle 33: After refmac, R = 0.1278 (Rfree = 0.000) for 1498 atoms. Found 0 (7 requested) and removed 5 (3 requested) atoms. Cycle 34: After refmac, R = 0.1313 (Rfree = 0.000) for 1493 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 35: After refmac, R = 0.1163 (Rfree = 0.000) for 1490 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.70 4.42 Search for helices and strands: 0 residues in 0 chains, 1520 seeds are put forward Round 1: 63 peptides, 13 chains. Longest chain 7 peptides. Score 0.279 Round 2: 63 peptides, 12 chains. Longest chain 8 peptides. Score 0.320 Round 3: 64 peptides, 12 chains. Longest chain 8 peptides. Score 0.329 Round 4: 65 peptides, 11 chains. Longest chain 10 peptides. Score 0.377 Round 5: 63 peptides, 11 chains. Longest chain 9 peptides. Score 0.359 Taking the results from Round 4 Chains 11, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1591 reflections ( 99.13 % complete ) and 3806 restraints for refining 1535 atoms. 3601 conditional restraints added. Observations/parameters ratio is 0.26 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1533 (Rfree = 0.000) for 1535 atoms. Found 0 (7 requested) and removed 9 (3 requested) atoms. Cycle 37: After refmac, R = 0.2320 (Rfree = 0.000) for 1523 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 38: After refmac, R = 0.1545 (Rfree = 0.000) for 1513 atoms. Found 1 (7 requested) and removed 6 (3 requested) atoms. Cycle 39: After refmac, R = 0.1247 (Rfree = 0.000) for 1500 atoms. Found 2 (7 requested) and removed 7 (3 requested) atoms. Cycle 40: After refmac, R = 0.1516 (Rfree = 0.000) for 1494 atoms. Found 4 (7 requested) and removed 12 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.78 4.51 Search for helices and strands: 0 residues in 0 chains, 1549 seeds are put forward Round 1: 46 peptides, 11 chains. Longest chain 5 peptides. Score 0.189 Round 2: 60 peptides, 12 chains. Longest chain 8 peptides. Score 0.291 Round 3: 67 peptides, 13 chains. Longest chain 7 peptides. Score 0.317 Round 4: 73 peptides, 12 chains. Longest chain 13 peptides. Score 0.409 Round 5: 69 peptides, 11 chains. Longest chain 13 peptides. Score 0.413 Taking the results from Round 5 Chains 11, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1591 reflections ( 99.13 % complete ) and 3501 restraints for refining 1476 atoms. 3280 conditional restraints added. Observations/parameters ratio is 0.27 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1217 (Rfree = 0.000) for 1476 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. Cycle 42: After refmac, R = 0.1066 (Rfree = 0.000) for 1472 atoms. Found 3 (7 requested) and removed 6 (3 requested) atoms. Cycle 43: After refmac, R = 0.0985 (Rfree = 0.000) for 1469 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 44: After refmac, R = 0.0949 (Rfree = 0.000) for 1468 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 45: After refmac, R = 0.0910 (Rfree = 0.000) for 1466 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 4.39 Search for helices and strands: 0 residues in 0 chains, 1503 seeds are put forward Round 1: 50 peptides, 11 chains. Longest chain 6 peptides. Score 0.232 Round 2: 50 peptides, 9 chains. Longest chain 14 peptides. Score 0.319 Round 3: 59 peptides, 9 chains. Longest chain 14 peptides. Score 0.403 Round 4: 63 peptides, 10 chains. Longest chain 14 peptides. Score 0.399 Round 5: 58 peptides, 9 chains. Longest chain 14 peptides. Score 0.394 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2o2x-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1591 reflections ( 99.13 % complete ) and 3605 restraints for refining 1496 atoms. 3414 conditional restraints added. Observations/parameters ratio is 0.27 ------------------------------------------------------ Cycle 46: After refmac, R = 0.0969 (Rfree = 0.000) for 1496 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.0926 (Rfree = 0.000) for 1492 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1014 (Rfree = 0.000) for 1489 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1121 (Rfree = 0.000) for 1483 atoms. TimeTaking 27.9