null Sun 23 Dec 22:23:08 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 2obn-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2obn-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2obn-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obn-3.6-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/2obn-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obn-3.6-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 22:23:18 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/2obn-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obn-3.6-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 879 and 0 Target number of residues in the AU: 879 Target solvent content: 0.6480 Checking the provided sequence file Detected sequence length: 349 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1396 Adjusted target solvent content: 0.44 Input MTZ file: 2obn-3.6-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: 75.040 122.990 75.170 90.000 103.099 90.000 Input sequence file: 2obn-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 11168 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 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: 73.214 3.600 Wilson plot Bfac: 76.69 15421 reflections ( 99.62 % complete ) and 0 restraints for refining 12374 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3061 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2946 (Rfree = 0.000) for 12374 atoms. Found 72 (79 requested) and removed 289 (39 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.55 3.85 Search for helices and strands: 0 residues in 0 chains, 12341 seeds are put forward NCS extension: 0 residues added, 12341 seeds are put forward Round 1: 441 peptides, 96 chains. Longest chain 8 peptides. Score 0.248 Round 2: 582 peptides, 107 chains. Longest chain 14 peptides. Score 0.371 Round 3: 622 peptides, 104 chains. Longest chain 17 peptides. Score 0.433 Round 4: 643 peptides, 108 chains. Longest chain 14 peptides. Score 0.437 Round 5: 656 peptides, 107 chains. Longest chain 17 peptides. Score 0.456 Taking the results from Round 5 Chains 107, Residues 549, Estimated correctness of the model 0.0 % 9 chains (46 residues) have been docked in sequence ------------------------------------------------------ 15421 reflections ( 99.62 % complete ) and 23875 restraints for refining 10121 atoms. 21658 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2325 (Rfree = 0.000) for 10121 atoms. Found 43 (64 requested) and removed 89 (32 requested) atoms. Cycle 2: After refmac, R = 0.2151 (Rfree = 0.000) for 9997 atoms. Found 30 (64 requested) and removed 57 (32 requested) atoms. Cycle 3: After refmac, R = 0.2011 (Rfree = 0.000) for 9919 atoms. Found 31 (63 requested) and removed 48 (31 requested) atoms. Cycle 4: After refmac, R = 0.1881 (Rfree = 0.000) for 9870 atoms. Found 13 (63 requested) and removed 48 (31 requested) atoms. Cycle 5: After refmac, R = 0.1581 (Rfree = 0.000) for 9805 atoms. Found 18 (63 requested) and removed 40 (31 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 3.74 Search for helices and strands: 0 residues in 0 chains, 10125 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 10137 seeds are put forward Round 1: 604 peptides, 114 chains. Longest chain 11 peptides. Score 0.362 Round 2: 710 peptides, 116 chains. Longest chain 17 peptides. Score 0.473 Round 3: 699 peptides, 111 chains. Longest chain 18 peptides. Score 0.484 Round 4: 713 peptides, 100 chains. Longest chain 21 peptides. Score 0.547 Round 5: 710 peptides, 106 chains. Longest chain 21 peptides. Score 0.518 Taking the results from Round 4 Chains 103, Residues 613, Estimated correctness of the model 0.0 % 14 chains (73 residues) have been docked in sequence ------------------------------------------------------ 15421 reflections ( 99.62 % complete ) and 23149 restraints for refining 10100 atoms. 20633 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2011 (Rfree = 0.000) for 10100 atoms. Found 31 (64 requested) and removed 77 (32 requested) atoms. Cycle 7: After refmac, R = 0.1903 (Rfree = 0.000) for 9992 atoms. Found 34 (64 requested) and removed 60 (32 requested) atoms. Cycle 8: After refmac, R = 0.1804 (Rfree = 0.000) for 9943 atoms. Found 28 (63 requested) and removed 52 (31 requested) atoms. Cycle 9: After refmac, R = 0.1761 (Rfree = 0.000) for 9903 atoms. Found 31 (63 requested) and removed 45 (31 requested) atoms. Cycle 10: After refmac, R = 0.1626 (Rfree = 0.000) for 9873 atoms. Found 26 (63 requested) and removed 40 (31 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.44 3.73 Search for helices and strands: 0 residues in 0 chains, 10217 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 10245 seeds are put forward Round 1: 628 peptides, 111 chains. Longest chain 17 peptides. Score 0.405 Round 2: 736 peptides, 108 chains. Longest chain 19 peptides. Score 0.535 Round 3: 761 peptides, 109 chains. Longest chain 22 peptides. Score 0.555 Round 4: 757 peptides, 102 chains. Longest chain 21 peptides. Score 0.580 Round 5: 749 peptides, 102 chains. Longest chain 27 peptides. Score 0.572 Taking the results from Round 4 Chains 107, Residues 655, Estimated correctness of the model 6.7 % 10 chains (75 residues) have been docked in sequence ------------------------------------------------------ 15421 reflections ( 99.62 % complete ) and 22533 restraints for refining 10124 atoms. 19786 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1980 (Rfree = 0.000) for 10124 atoms. Found 38 (64 requested) and removed 64 (32 requested) atoms. Cycle 12: After refmac, R = 0.1788 (Rfree = 0.000) for 10043 atoms. Found 26 (64 requested) and removed 45 (32 requested) atoms. Cycle 13: After refmac, R = 0.1718 (Rfree = 0.000) for 9999 atoms. Found 26 (64 requested) and removed 50 (32 requested) atoms. Cycle 14: After refmac, R = 0.1615 (Rfree = 0.000) for 9960 atoms. Found 18 (63 requested) and removed 46 (31 requested) atoms. Cycle 15: After refmac, R = 0.1586 (Rfree = 0.000) for 9920 atoms. Found 22 (63 requested) and removed 35 (31 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 3.73 Search for helices and strands: 0 residues in 0 chains, 10275 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 10299 seeds are put forward Round 1: 616 peptides, 118 chains. Longest chain 15 peptides. Score 0.356 Round 2: 696 peptides, 107 chains. Longest chain 17 peptides. Score 0.499 Round 3: 665 peptides, 93 chains. Longest chain 26 peptides. Score 0.530 Round 4: 671 peptides, 98 chains. Longest chain 23 peptides. Score 0.514 Round 5: 657 peptides, 92 chains. Longest chain 17 peptides. Score 0.527 Taking the results from Round 3 Chains 97, Residues 572, Estimated correctness of the model 0.0 % 9 chains (67 residues) have been docked in sequence ------------------------------------------------------ 15421 reflections ( 99.62 % complete ) and 23076 restraints for refining 10121 atoms. 20670 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1907 (Rfree = 0.000) for 10121 atoms. Found 50 (64 requested) and removed 49 (32 requested) atoms. Cycle 17: After refmac, R = 0.1767 (Rfree = 0.000) for 10059 atoms. Found 34 (64 requested) and removed 43 (32 requested) atoms. Cycle 18: After refmac, R = 0.1696 (Rfree = 0.000) for 10020 atoms. Found 34 (64 requested) and removed 43 (32 requested) atoms. Cycle 19: After refmac, R = 0.1658 (Rfree = 0.000) for 9992 atoms. Found 36 (64 requested) and removed 36 (32 requested) atoms. Cycle 20: After refmac, R = 0.1600 (Rfree = 0.000) for 9977 atoms. Found 20 (64 requested) and removed 45 (32 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 3.76 Search for helices and strands: 0 residues in 0 chains, 10266 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 10290 seeds are put forward Round 1: 542 peptides, 102 chains. Longest chain 14 peptides. Score 0.348 Round 2: 626 peptides, 102 chains. Longest chain 15 peptides. Score 0.447 Round 3: 640 peptides, 97 chains. Longest chain 21 peptides. Score 0.486 Round 4: 642 peptides, 98 chains. Longest chain 19 peptides. Score 0.484 Round 5: 650 peptides, 93 chains. Longest chain 20 peptides. Score 0.515 Taking the results from Round 5 Chains 96, Residues 557, Estimated correctness of the model 0.0 % 10 chains (77 residues) have been docked in sequence ------------------------------------------------------ 15421 reflections ( 99.62 % complete ) and 22924 restraints for refining 10124 atoms. 20517 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1910 (Rfree = 0.000) for 10124 atoms. Found 57 (64 requested) and removed 48 (32 requested) atoms. Cycle 22: After refmac, R = 0.1748 (Rfree = 0.000) for 10078 atoms. Found 26 (65 requested) and removed 41 (32 requested) atoms. Cycle 23: After refmac, R = 0.1612 (Rfree = 0.000) for 10024 atoms. Found 25 (64 requested) and removed 37 (32 requested) atoms. Cycle 24: After refmac, R = 0.1540 (Rfree = 0.000) for 9992 atoms. Found 19 (64 requested) and removed 41 (32 requested) atoms. Cycle 25: After refmac, R = 0.1495 (Rfree = 0.000) for 9952 atoms. Found 28 (63 requested) and removed 36 (31 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.45 3.74 Search for helices and strands: 0 residues in 0 chains, 10263 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 10287 seeds are put forward Round 1: 519 peptides, 105 chains. Longest chain 13 peptides. Score 0.303 Round 2: 623 peptides, 101 chains. Longest chain 16 peptides. Score 0.449 Round 3: 626 peptides, 103 chains. Longest chain 14 peptides. Score 0.442 Round 4: 635 peptides, 94 chains. Longest chain 20 peptides. Score 0.495 Round 5: 628 peptides, 98 chains. Longest chain 18 peptides. Score 0.468 Taking the results from Round 4 Chains 94, Residues 541, Estimated correctness of the model 0.0 % 5 chains (25 residues) have been docked in sequence ------------------------------------------------------ 15421 reflections ( 99.62 % complete ) and 23460 restraints for refining 10124 atoms. 21311 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1745 (Rfree = 0.000) for 10124 atoms. Found 45 (64 requested) and removed 47 (32 requested) atoms. Cycle 27: After refmac, R = 0.1647 (Rfree = 0.000) for 10085 atoms. Found 34 (64 requested) and removed 39 (32 requested) atoms. Cycle 28: After refmac, R = 0.1619 (Rfree = 0.000) for 10062 atoms. Found 28 (64 requested) and removed 40 (32 requested) atoms. Cycle 29: After refmac, R = 0.1526 (Rfree = 0.000) for 10035 atoms. Found 27 (64 requested) and removed 36 (32 requested) atoms. Cycle 30: After refmac, R = 0.1563 (Rfree = 0.000) for 10014 atoms. Found 32 (64 requested) and removed 40 (32 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.47 3.76 Search for helices and strands: 0 residues in 0 chains, 10288 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 10318 seeds are put forward Round 1: 475 peptides, 91 chains. Longest chain 11 peptides. Score 0.322 Round 2: 559 peptides, 95 chains. Longest chain 14 peptides. Score 0.405 Round 3: 596 peptides, 98 chains. Longest chain 14 peptides. Score 0.433 Round 4: 600 peptides, 96 chains. Longest chain 16 peptides. Score 0.447 Round 5: 590 peptides, 94 chains. Longest chain 17 peptides. Score 0.446 Taking the results from Round 4 Chains 97, Residues 504, Estimated correctness of the model 0.0 % 6 chains (33 residues) have been docked in sequence ------------------------------------------------------ 15421 reflections ( 99.62 % complete ) and 23601 restraints for refining 10123 atoms. 21590 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1686 (Rfree = 0.000) for 10123 atoms. Found 38 (64 requested) and removed 50 (32 requested) atoms. Cycle 32: After refmac, R = 0.1602 (Rfree = 0.000) for 10083 atoms. Found 36 (64 requested) and removed 40 (32 requested) atoms. Cycle 33: After refmac, R = 0.1540 (Rfree = 0.000) for 10070 atoms. Found 36 (64 requested) and removed 38 (32 requested) atoms. Cycle 34: After refmac, R = 0.1449 (Rfree = 0.000) for 10058 atoms. Found 27 (64 requested) and removed 39 (32 requested) atoms. Cycle 35: After refmac, R = 0.1407 (Rfree = 0.000) for 10038 atoms. Found 37 (64 requested) and removed 39 (32 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.44 3.73 Search for helices and strands: 0 residues in 0 chains, 10319 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 10337 seeds are put forward Round 1: 498 peptides, 101 chains. Longest chain 11 peptides. Score 0.297 Round 2: 543 peptides, 91 chains. Longest chain 16 peptides. Score 0.406 Round 3: 518 peptides, 84 chains. Longest chain 16 peptides. Score 0.413 Round 4: 506 peptides, 83 chains. Longest chain 14 peptides. Score 0.404 Round 5: 508 peptides, 79 chains. Longest chain 16 peptides. Score 0.427 Taking the results from Round 5 Chains 79, Residues 429, Estimated correctness of the model 0.0 % 9 chains (56 residues) have been docked in sequence ------------------------------------------------------ 15421 reflections ( 99.62 % complete ) and 23768 restraints for refining 10124 atoms. 21965 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1648 (Rfree = 0.000) for 10124 atoms. Found 44 (64 requested) and removed 46 (32 requested) atoms. Cycle 37: After refmac, R = 0.1545 (Rfree = 0.000) for 10101 atoms. Found 34 (64 requested) and removed 42 (32 requested) atoms. Cycle 38: After refmac, R = 0.1491 (Rfree = 0.000) for 10078 atoms. Found 34 (64 requested) and removed 35 (32 requested) atoms. Cycle 39: After refmac, R = 0.1446 (Rfree = 0.000) for 10064 atoms. Found 35 (64 requested) and removed 40 (32 requested) atoms. Cycle 40: After refmac, R = 0.1411 (Rfree = 0.000) for 10050 atoms. Found 32 (64 requested) and removed 35 (32 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.45 3.74 Search for helices and strands: 0 residues in 0 chains, 10328 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 10353 seeds are put forward Round 1: 417 peptides, 87 chains. Longest chain 9 peptides. Score 0.267 Round 2: 484 peptides, 87 chains. Longest chain 18 peptides. Score 0.356 Round 3: 476 peptides, 82 chains. Longest chain 13 peptides. Score 0.373 Round 4: 450 peptides, 72 chains. Longest chain 14 peptides. Score 0.395 Round 5: 462 peptides, 75 chains. Longest chain 13 peptides. Score 0.393 Taking the results from Round 4 Chains 72, Residues 378, Estimated correctness of the model 0.0 % 5 chains (34 residues) have been docked in sequence ------------------------------------------------------ 15421 reflections ( 99.62 % complete ) and 24248 restraints for refining 10123 atoms. 22706 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1617 (Rfree = 0.000) for 10123 atoms. Found 37 (64 requested) and removed 40 (32 requested) atoms. Cycle 42: After refmac, R = 0.1504 (Rfree = 0.000) for 10101 atoms. Found 38 (64 requested) and removed 35 (32 requested) atoms. Cycle 43: After refmac, R = 0.1475 (Rfree = 0.000) for 10084 atoms. Found 40 (64 requested) and removed 35 (32 requested) atoms. Cycle 44: After refmac, R = 0.1459 (Rfree = 0.000) for 10078 atoms. Found 47 (64 requested) and removed 34 (32 requested) atoms. Cycle 45: After refmac, R = 0.1407 (Rfree = 0.000) for 10082 atoms. Found 41 (64 requested) and removed 40 (32 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.45 3.74 Search for helices and strands: 0 residues in 0 chains, 10335 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 10348 seeds are put forward Round 1: 419 peptides, 87 chains. Longest chain 10 peptides. Score 0.270 Round 2: 480 peptides, 91 chains. Longest chain 11 peptides. Score 0.329 Round 3: 501 peptides, 89 chains. Longest chain 16 peptides. Score 0.366 Round 4: 495 peptides, 83 chains. Longest chain 17 peptides. Score 0.391 Round 5: 491 peptides, 88 chains. Longest chain 16 peptides. Score 0.359 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 83, Residues 412, Estimated correctness of the model 0.0 % 4 chains (31 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2obn-3_warpNtrace.pdb as input Building loops using Loopy2018 83 chains (412 residues) following loop building 4 chains (31 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 15421 reflections ( 99.62 % complete ) and 24290 restraints for refining 10123 atoms. 22637 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1534 (Rfree = 0.000) for 10123 atoms. Found 0 (64 requested) and removed 32 (32 requested) atoms. Cycle 47: After refmac, R = 0.1489 (Rfree = 0.000) for 10066 atoms. Found 0 (64 requested) and removed 32 (32 requested) atoms. Cycle 48: After refmac, R = 0.1447 (Rfree = 0.000) for 10021 atoms. Found 0 (64 requested) and removed 32 (32 requested) atoms. Cycle 49: After refmac, R = 0.1414 (Rfree = 0.000) for 9979 atoms. Found 0 (64 requested) and removed 32 (32 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:15:43 GMT 2018 Job finished. TimeTaking 112.59 Used memory is bytes: 22447368