null Sun 23 Dec 22:22:46 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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o2x-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o2x-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2x-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/2o2x-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2x-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 ============================================================ Sun 23 Dec 22:22:56 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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2x-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 122 and 0 Target number of residues in the AU: 122 Target solvent content: 0.6486 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-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: 4 Cell parameters: 36.470 66.250 41.010 90.000 108.540 90.000 Input sequence file: 2o2x-3.8-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 3.800 Wilson plot Bfac: 76.02 1858 reflections ( 99.25 % complete ) and 0 restraints for refining 1927 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.3195 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2699 (Rfree = 0.000) for 1927 atoms. Found 6 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.56 4.25 Search for helices and strands: 0 residues in 0 chains, 1962 seeds are put forward Round 1: 71 peptides, 15 chains. Longest chain 7 peptides. Score 0.276 Round 2: 90 peptides, 16 chains. Longest chain 9 peptides. Score 0.407 Round 3: 109 peptides, 16 chains. Longest chain 11 peptides. Score 0.551 Round 4: 118 peptides, 16 chains. Longest chain 13 peptides. Score 0.609 Round 5: 109 peptides, 14 chains. Longest chain 15 peptides. Score 0.608 Taking the results from Round 4 Chains 16, Residues 102, Estimated correctness of the model 3.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 1858 reflections ( 99.25 % complete ) and 3541 restraints for refining 1577 atoms. 3101 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2212 (Rfree = 0.000) for 1577 atoms. Found 6 (8 requested) and removed 31 (4 requested) atoms. Cycle 2: After refmac, R = 0.1963 (Rfree = 0.000) for 1529 atoms. Found 1 (8 requested) and removed 7 (4 requested) atoms. Cycle 3: After refmac, R = 0.1856 (Rfree = 0.000) for 1519 atoms. Found 3 (8 requested) and removed 11 (4 requested) atoms. Cycle 4: After refmac, R = 0.2091 (Rfree = 0.000) for 1504 atoms. Found 6 (8 requested) and removed 11 (4 requested) atoms. Cycle 5: After refmac, R = 0.1672 (Rfree = 0.000) for 1488 atoms. Found 5 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.51 4.19 Search for helices and strands: 0 residues in 0 chains, 1545 seeds are put forward Round 1: 73 peptides, 16 chains. Longest chain 8 peptides. Score 0.256 Round 2: 108 peptides, 19 chains. Longest chain 11 peptides. Score 0.450 Round 3: 108 peptides, 16 chains. Longest chain 20 peptides. Score 0.544 Round 4: 120 peptides, 16 chains. Longest chain 13 peptides. Score 0.621 Round 5: 118 peptides, 17 chains. Longest chain 21 peptides. Score 0.582 Taking the results from Round 4 Chains 16, Residues 104, Estimated correctness of the model 8.4 % 4 chains (31 residues) have been docked in sequence ------------------------------------------------------ 1858 reflections ( 99.25 % complete ) and 3204 restraints for refining 1528 atoms. 2706 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2019 (Rfree = 0.000) for 1528 atoms. Found 6 (8 requested) and removed 21 (4 requested) atoms. Cycle 7: After refmac, R = 0.1809 (Rfree = 0.000) for 1490 atoms. Found 3 (8 requested) and removed 9 (4 requested) atoms. Cycle 8: After refmac, R = 0.1841 (Rfree = 0.000) for 1480 atoms. Found 4 (8 requested) and removed 9 (4 requested) atoms. Cycle 9: After refmac, R = 0.1635 (Rfree = 0.000) for 1469 atoms. Found 2 (8 requested) and removed 8 (4 requested) atoms. Cycle 10: After refmac, R = 0.1807 (Rfree = 0.000) for 1463 atoms. Found 1 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.57 4.26 Search for helices and strands: 0 residues in 0 chains, 1505 seeds are put forward Round 1: 87 peptides, 19 chains. Longest chain 7 peptides. Score 0.271 Round 2: 108 peptides, 20 chains. Longest chain 12 peptides. Score 0.416 Round 3: 103 peptides, 19 chains. Longest chain 10 peptides. Score 0.410 Round 4: 101 peptides, 18 chains. Longest chain 13 peptides. Score 0.428 Round 5: 99 peptides, 17 chains. Longest chain 10 peptides. Score 0.446 Taking the results from Round 5 Chains 17, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1858 reflections ( 99.25 % complete ) and 3844 restraints for refining 1556 atoms. 3533 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1922 (Rfree = 0.000) for 1556 atoms. Found 2 (8 requested) and removed 14 (4 requested) atoms. Cycle 12: After refmac, R = 0.1640 (Rfree = 0.000) for 1541 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. Cycle 13: After refmac, R = 0.1613 (Rfree = 0.000) for 1538 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 14: After refmac, R = 0.1639 (Rfree = 0.000) for 1533 atoms. Found 2 (8 requested) and removed 7 (4 requested) atoms. Cycle 15: After refmac, R = 0.1680 (Rfree = 0.000) for 1525 atoms. Found 2 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.49 4.17 Search for helices and strands: 0 residues in 0 chains, 1568 seeds are put forward Round 1: 87 peptides, 19 chains. Longest chain 8 peptides. Score 0.271 Round 2: 105 peptides, 18 chains. Longest chain 13 peptides. Score 0.459 Round 3: 104 peptides, 18 chains. Longest chain 9 peptides. Score 0.451 Round 4: 94 peptides, 15 chains. Longest chain 13 peptides. Score 0.474 Round 5: 89 peptides, 15 chains. Longest chain 10 peptides. Score 0.434 Taking the results from Round 4 Chains 16, Residues 79, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 1858 reflections ( 99.25 % complete ) and 3694 restraints for refining 1576 atoms. 3371 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1925 (Rfree = 0.000) for 1576 atoms. Found 4 (8 requested) and removed 12 (4 requested) atoms. Cycle 17: After refmac, R = 0.1544 (Rfree = 0.000) for 1562 atoms. Found 0 (8 requested) and removed 5 (4 requested) atoms. Cycle 18: After refmac, R = 0.1476 (Rfree = 0.000) for 1554 atoms. Found 1 (8 requested) and removed 7 (4 requested) atoms. Cycle 19: After refmac, R = 0.1746 (Rfree = 0.000) for 1545 atoms. Found 3 (8 requested) and removed 9 (4 requested) atoms. Cycle 20: After refmac, R = 0.1433 (Rfree = 0.000) for 1537 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.52 4.20 Search for helices and strands: 0 residues in 0 chains, 1589 seeds are put forward Round 1: 68 peptides, 15 chains. Longest chain 6 peptides. Score 0.247 Round 2: 94 peptides, 18 chains. Longest chain 10 peptides. Score 0.370 Round 3: 85 peptides, 16 chains. Longest chain 11 peptides. Score 0.365 Round 4: 79 peptides, 15 chains. Longest chain 10 peptides. Score 0.349 Round 5: 81 peptides, 14 chains. Longest chain 12 peptides. Score 0.404 Taking the results from Round 5 Chains 14, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1858 reflections ( 99.25 % complete ) and 3818 restraints for refining 1555 atoms. 3564 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1522 (Rfree = 0.000) for 1555 atoms. Found 2 (8 requested) and removed 8 (4 requested) atoms. Cycle 22: After refmac, R = 0.1871 (Rfree = 0.000) for 1545 atoms. Found 5 (8 requested) and removed 7 (4 requested) atoms. Cycle 23: After refmac, R = 0.1424 (Rfree = 0.000) for 1537 atoms. Found 1 (8 requested) and removed 9 (4 requested) atoms. Cycle 24: After refmac, R = 0.1144 (Rfree = 0.000) for 1525 atoms. Found 0 (8 requested) and removed 6 (4 requested) atoms. Cycle 25: After refmac, R = 0.1024 (Rfree = 0.000) for 1516 atoms. Found 1 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.52 4.20 Search for helices and strands: 0 residues in 0 chains, 1586 seeds are put forward Round 1: 66 peptides, 14 chains. Longest chain 6 peptides. Score 0.268 Round 2: 80 peptides, 13 chains. Longest chain 12 peptides. Score 0.431 Round 3: 82 peptides, 14 chains. Longest chain 10 peptides. Score 0.412 Round 4: 85 peptides, 13 chains. Longest chain 11 peptides. Score 0.472 Round 5: 82 peptides, 13 chains. Longest chain 12 peptides. Score 0.448 Taking the results from Round 4 Chains 13, Residues 72, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 1858 reflections ( 99.25 % complete ) and 3643 restraints for refining 1577 atoms. 3329 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1380 (Rfree = 0.000) for 1577 atoms. Found 5 (8 requested) and removed 10 (4 requested) atoms. Cycle 27: After refmac, R = 0.1250 (Rfree = 0.000) for 1568 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 28: After refmac, R = 0.1222 (Rfree = 0.000) for 1567 atoms. Found 2 (8 requested) and removed 7 (4 requested) atoms. Cycle 29: After refmac, R = 0.1080 (Rfree = 0.000) for 1562 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. Cycle 30: After refmac, R = 0.1134 (Rfree = 0.000) for 1559 atoms. Found 0 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.53 4.21 Search for helices and strands: 0 residues in 0 chains, 1596 seeds are put forward Round 1: 67 peptides, 14 chains. Longest chain 8 peptides. Score 0.277 Round 2: 80 peptides, 12 chains. Longest chain 9 peptides. Score 0.467 Round 3: 88 peptides, 15 chains. Longest chain 9 peptides. Score 0.426 Round 4: 84 peptides, 12 chains. Longest chain 11 peptides. Score 0.498 Round 5: 85 peptides, 13 chains. Longest chain 14 peptides. Score 0.472 Taking the results from Round 4 Chains 12, Residues 72, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 1858 reflections ( 99.25 % complete ) and 3743 restraints for refining 1576 atoms. 3443 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1770 (Rfree = 0.000) for 1576 atoms. Found 3 (8 requested) and removed 21 (4 requested) atoms. Cycle 32: After refmac, R = 0.1509 (Rfree = 0.000) for 1558 atoms. Found 3 (8 requested) and removed 7 (4 requested) atoms. Cycle 33: After refmac, R = 0.1317 (Rfree = 0.000) for 1553 atoms. Found 4 (8 requested) and removed 8 (4 requested) atoms. Cycle 34: After refmac, R = 0.1161 (Rfree = 0.000) for 1549 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 35: After refmac, R = 0.1278 (Rfree = 0.000) for 1546 atoms. Found 2 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 4.29 Search for helices and strands: 0 residues in 0 chains, 1577 seeds are put forward Round 1: 75 peptides, 17 chains. Longest chain 7 peptides. Score 0.235 Round 2: 81 peptides, 15 chains. Longest chain 10 peptides. Score 0.367 Round 3: 87 peptides, 15 chains. Longest chain 12 peptides. Score 0.418 Round 4: 87 peptides, 14 chains. Longest chain 12 peptides. Score 0.453 Round 5: 83 peptides, 14 chains. Longest chain 10 peptides. Score 0.420 Taking the results from Round 4 Chains 14, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1858 reflections ( 99.25 % complete ) and 3759 restraints for refining 1557 atoms. 3481 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1604 (Rfree = 0.000) for 1557 atoms. Found 2 (8 requested) and removed 11 (4 requested) atoms. Cycle 37: After refmac, R = 0.1320 (Rfree = 0.000) for 1545 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 38: After refmac, R = 0.1280 (Rfree = 0.000) for 1541 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 39: After refmac, R = 0.1277 (Rfree = 0.000) for 1537 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.1201 (Rfree = 0.000) for 1535 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.55 4.24 Search for helices and strands: 0 residues in 0 chains, 1586 seeds are put forward Round 1: 54 peptides, 12 chains. Longest chain 9 peptides. Score 0.231 Round 2: 59 peptides, 11 chains. Longest chain 8 peptides. Score 0.322 Round 3: 55 peptides, 10 chains. Longest chain 10 peptides. Score 0.325 Round 4: 65 peptides, 12 chains. Longest chain 9 peptides. Score 0.338 Round 5: 68 peptides, 12 chains. Longest chain 11 peptides. Score 0.365 Taking the results from Round 5 Chains 12, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1858 reflections ( 99.25 % complete ) and 3875 restraints for refining 1577 atoms. 3663 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1320 (Rfree = 0.000) for 1577 atoms. Found 6 (8 requested) and removed 5 (4 requested) atoms. Cycle 42: After refmac, R = 0.1056 (Rfree = 0.000) for 1572 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. Cycle 43: After refmac, R = 0.1098 (Rfree = 0.000) for 1569 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. Cycle 44: After refmac, R = 0.0958 (Rfree = 0.000) for 1565 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 45: After refmac, R = 0.0900 (Rfree = 0.000) for 1560 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 4.23 Search for helices and strands: 0 residues in 0 chains, 1621 seeds are put forward Round 1: 45 peptides, 10 chains. Longest chain 6 peptides. Score 0.223 Round 2: 58 peptides, 11 chains. Longest chain 7 peptides. Score 0.313 Round 3: 57 peptides, 9 chains. Longest chain 11 peptides. Score 0.385 Round 4: 51 peptides, 9 chains. Longest chain 10 peptides. Score 0.329 Round 5: 57 peptides, 10 chains. Longest chain 9 peptides. Score 0.344 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 48, 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-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1858 reflections ( 99.25 % complete ) and 3906 restraints for refining 1563 atoms. 3723 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1196 (Rfree = 0.000) for 1563 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.1455 (Rfree = 0.000) for 1557 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1719 (Rfree = 0.000) for 1551 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.0950 (Rfree = 0.000) for 1544 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:50:39 GMT 2018 Job finished. TimeTaking 27.88 Used memory is bytes: 11004016