Mon 24 Dec 07:55:34 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 1vl4-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vl4-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vl4-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl4-3.4-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/1vl4-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl4-3.4-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 07:55:38 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/1vl4-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl4-3.4-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 734 and 0 Target number of residues in the AU: 734 Target solvent content: 0.6140 Checking the provided sequence file Detected sequence length: 447 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 894 Adjusted target solvent content: 0.53 Input MTZ file: 1vl4-3.4-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: 19 Cell parameters: 80.171 107.117 119.834 90.000 90.000 90.000 Input sequence file: 1vl4-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 7152 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: 79.862 3.400 Wilson plot Bfac: 58.63 14660 reflections ( 99.46 % complete ) and 0 restraints for refining 7937 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3058 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2905 (Rfree = 0.000) for 7937 atoms. Found 59 (59 requested) and removed 63 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.17 3.05 Search for helices and strands: 0 residues in 0 chains, 8058 seeds are put forward NCS extension: 0 residues added, 8058 seeds are put forward Round 1: 472 peptides, 77 chains. Longest chain 20 peptides. Score 0.444 Round 2: 553 peptides, 76 chains. Longest chain 26 peptides. Score 0.560 Round 3: 581 peptides, 67 chains. Longest chain 33 peptides. Score 0.639 Round 4: 593 peptides, 65 chains. Longest chain 33 peptides. Score 0.661 Round 5: 616 peptides, 68 chains. Longest chain 27 peptides. Score 0.671 Taking the results from Round 5 Chains 75, Residues 548, Estimated correctness of the model 50.1 % 6 chains (70 residues) have been docked in sequence ------------------------------------------------------ 14660 reflections ( 99.46 % complete ) and 13413 restraints for refining 6498 atoms. 11044 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2593 (Rfree = 0.000) for 6498 atoms. Found 49 (49 requested) and removed 62 (24 requested) atoms. Cycle 2: After refmac, R = 0.2381 (Rfree = 0.000) for 6413 atoms. Found 25 (48 requested) and removed 47 (24 requested) atoms. Cycle 3: After refmac, R = 0.2263 (Rfree = 0.000) for 6370 atoms. Found 25 (48 requested) and removed 43 (24 requested) atoms. Cycle 4: After refmac, R = 0.2180 (Rfree = 0.000) for 6339 atoms. Found 11 (47 requested) and removed 31 (23 requested) atoms. Cycle 5: After refmac, R = 0.2320 (Rfree = 0.000) for 6315 atoms. Found 22 (47 requested) and removed 31 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.18 3.06 Search for helices and strands: 0 residues in 0 chains, 6506 seeds are put forward NCS extension: 16 residues added (7 deleted due to clashes), 6522 seeds are put forward Round 1: 550 peptides, 74 chains. Longest chain 21 peptides. Score 0.568 Round 2: 576 peptides, 63 chains. Longest chain 33 peptides. Score 0.653 Round 3: 601 peptides, 62 chains. Longest chain 34 peptides. Score 0.683 Round 4: 625 peptides, 62 chains. Longest chain 35 peptides. Score 0.705 Round 5: 614 peptides, 62 chains. Longest chain 36 peptides. Score 0.695 Taking the results from Round 4 Chains 69, Residues 563, Estimated correctness of the model 59.1 % 8 chains (114 residues) have been docked in sequence Building loops using Loopy2018 69 chains (563 residues) following loop building 8 chains (114 residues) in sequence following loop building ------------------------------------------------------ 14660 reflections ( 99.46 % complete ) and 13015 restraints for refining 6503 atoms. 10402 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2534 (Rfree = 0.000) for 6503 atoms. Found 41 (49 requested) and removed 53 (24 requested) atoms. Cycle 7: After refmac, R = 0.2565 (Rfree = 0.000) for 6451 atoms. Found 21 (48 requested) and removed 35 (24 requested) atoms. Cycle 8: After refmac, R = 0.2525 (Rfree = 0.000) for 6423 atoms. Found 22 (46 requested) and removed 42 (24 requested) atoms. Cycle 9: After refmac, R = 0.2423 (Rfree = 0.000) for 6395 atoms. Found 12 (45 requested) and removed 36 (24 requested) atoms. Cycle 10: After refmac, R = 0.2405 (Rfree = 0.000) for 6368 atoms. Found 20 (44 requested) and removed 31 (24 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.18 3.06 Search for helices and strands: 0 residues in 0 chains, 6555 seeds are put forward NCS extension: 12 residues added (16 deleted due to clashes), 6567 seeds are put forward Round 1: 557 peptides, 73 chains. Longest chain 23 peptides. Score 0.582 Round 2: 591 peptides, 65 chains. Longest chain 31 peptides. Score 0.659 Round 3: 621 peptides, 67 chains. Longest chain 46 peptides. Score 0.680 Round 4: 596 peptides, 60 chains. Longest chain 32 peptides. Score 0.687 Round 5: 621 peptides, 68 chains. Longest chain 30 peptides. Score 0.675 Taking the results from Round 4 Chains 63, Residues 536, Estimated correctness of the model 54.5 % 10 chains (135 residues) have been docked in sequence ------------------------------------------------------ 14660 reflections ( 99.46 % complete ) and 12847 restraints for refining 6502 atoms. 10227 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2628 (Rfree = 0.000) for 6502 atoms. Found 29 (44 requested) and removed 56 (24 requested) atoms. Cycle 12: After refmac, R = 0.2450 (Rfree = 0.000) for 6444 atoms. Found 17 (43 requested) and removed 34 (24 requested) atoms. Cycle 13: After refmac, R = 0.2308 (Rfree = 0.000) for 6407 atoms. Found 16 (43 requested) and removed 31 (24 requested) atoms. Cycle 14: After refmac, R = 0.2327 (Rfree = 0.000) for 6378 atoms. Found 21 (43 requested) and removed 28 (24 requested) atoms. Cycle 15: After refmac, R = 0.2367 (Rfree = 0.000) for 6361 atoms. Found 34 (43 requested) and removed 33 (24 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.17 3.05 Search for helices and strands: 0 residues in 0 chains, 6515 seeds are put forward NCS extension: 29 residues added (10 deleted due to clashes), 6544 seeds are put forward Round 1: 535 peptides, 73 chains. Longest chain 24 peptides. Score 0.555 Round 2: 580 peptides, 66 chains. Longest chain 32 peptides. Score 0.643 Round 3: 578 peptides, 63 chains. Longest chain 35 peptides. Score 0.656 Round 4: 576 peptides, 64 chains. Longest chain 32 peptides. Score 0.649 Round 5: 578 peptides, 60 chains. Longest chain 29 peptides. Score 0.670 Taking the results from Round 5 Chains 67, Residues 518, Estimated correctness of the model 49.8 % 11 chains (137 residues) have been docked in sequence ------------------------------------------------------ 14660 reflections ( 99.46 % complete ) and 12931 restraints for refining 6501 atoms. 10410 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2492 (Rfree = 0.000) for 6501 atoms. Found 44 (44 requested) and removed 55 (24 requested) atoms. Cycle 17: After refmac, R = 0.2272 (Rfree = 0.000) for 6446 atoms. Found 24 (44 requested) and removed 36 (24 requested) atoms. Cycle 18: After refmac, R = 0.2207 (Rfree = 0.000) for 6411 atoms. Found 13 (43 requested) and removed 31 (24 requested) atoms. Cycle 19: After refmac, R = 0.2150 (Rfree = 0.000) for 6378 atoms. Found 13 (43 requested) and removed 32 (24 requested) atoms. Cycle 20: After refmac, R = 0.2049 (Rfree = 0.000) for 6353 atoms. Found 15 (43 requested) and removed 27 (24 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.21 3.08 Search for helices and strands: 0 residues in 0 chains, 6502 seeds are put forward NCS extension: 23 residues added (4 deleted due to clashes), 6525 seeds are put forward Round 1: 516 peptides, 72 chains. Longest chain 24 peptides. Score 0.536 Round 2: 568 peptides, 71 chains. Longest chain 23 peptides. Score 0.605 Round 3: 561 peptides, 67 chains. Longest chain 25 peptides. Score 0.618 Round 4: 549 peptides, 63 chains. Longest chain 25 peptides. Score 0.625 Round 5: 544 peptides, 62 chains. Longest chain 27 peptides. Score 0.624 Taking the results from Round 4 Chains 66, Residues 486, Estimated correctness of the model 36.6 % 6 chains (90 residues) have been docked in sequence ------------------------------------------------------ 14660 reflections ( 99.46 % complete ) and 13542 restraints for refining 6502 atoms. 11323 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2631 (Rfree = 0.000) for 6502 atoms. Found 44 (44 requested) and removed 52 (24 requested) atoms. Cycle 22: After refmac, R = 0.2377 (Rfree = 0.000) for 6460 atoms. Found 43 (44 requested) and removed 39 (24 requested) atoms. Cycle 23: After refmac, R = 0.2394 (Rfree = 0.000) for 6443 atoms. Found 43 (43 requested) and removed 35 (24 requested) atoms. Cycle 24: After refmac, R = 0.2505 (Rfree = 0.000) for 6431 atoms. Found 43 (43 requested) and removed 39 (24 requested) atoms. Cycle 25: After refmac, R = 0.2376 (Rfree = 0.000) for 6416 atoms. Found 43 (43 requested) and removed 34 (24 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.23 3.10 Search for helices and strands: 0 residues in 0 chains, 6589 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 6618 seeds are put forward Round 1: 465 peptides, 72 chains. Longest chain 21 peptides. Score 0.466 Round 2: 519 peptides, 69 chains. Longest chain 22 peptides. Score 0.557 Round 3: 525 peptides, 66 chains. Longest chain 25 peptides. Score 0.581 Round 4: 534 peptides, 67 chains. Longest chain 24 peptides. Score 0.586 Round 5: 523 peptides, 64 chains. Longest chain 21 peptides. Score 0.589 Taking the results from Round 5 Chains 66, Residues 459, Estimated correctness of the model 25.0 % 5 chains (61 residues) have been docked in sequence ------------------------------------------------------ 14660 reflections ( 99.46 % complete ) and 14044 restraints for refining 6502 atoms. 12020 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2466 (Rfree = 0.000) for 6502 atoms. Found 44 (44 requested) and removed 43 (24 requested) atoms. Cycle 27: After refmac, R = 0.2249 (Rfree = 0.000) for 6468 atoms. Found 24 (44 requested) and removed 38 (24 requested) atoms. Cycle 28: After refmac, R = 0.2122 (Rfree = 0.000) for 6447 atoms. Found 25 (43 requested) and removed 36 (24 requested) atoms. Cycle 29: After refmac, R = 0.2063 (Rfree = 0.000) for 6430 atoms. Found 19 (43 requested) and removed 30 (24 requested) atoms. Cycle 30: After refmac, R = 0.2041 (Rfree = 0.000) for 6414 atoms. Found 12 (43 requested) and removed 33 (24 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.14 3.02 Search for helices and strands: 0 residues in 0 chains, 6539 seeds are put forward NCS extension: 33 residues added (3 deleted due to clashes), 6572 seeds are put forward Round 1: 483 peptides, 73 chains. Longest chain 21 peptides. Score 0.485 Round 2: 520 peptides, 69 chains. Longest chain 21 peptides. Score 0.558 Round 3: 525 peptides, 65 chains. Longest chain 22 peptides. Score 0.586 Round 4: 517 peptides, 72 chains. Longest chain 22 peptides. Score 0.537 Round 5: 525 peptides, 68 chains. Longest chain 22 peptides. Score 0.570 Taking the results from Round 3 Chains 69, Residues 460, Estimated correctness of the model 24.0 % 6 chains (50 residues) have been docked in sequence ------------------------------------------------------ 14660 reflections ( 99.46 % complete ) and 14015 restraints for refining 6503 atoms. 12082 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2335 (Rfree = 0.000) for 6503 atoms. Found 25 (44 requested) and removed 37 (24 requested) atoms. Cycle 32: After refmac, R = 0.2097 (Rfree = 0.000) for 6460 atoms. Found 23 (44 requested) and removed 35 (24 requested) atoms. Cycle 33: After refmac, R = 0.2036 (Rfree = 0.000) for 6435 atoms. Found 25 (43 requested) and removed 33 (24 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.2015 (Rfree = 0.000) for 6420 atoms. Found 23 (43 requested) and removed 37 (24 requested) atoms. Cycle 35: After refmac, R = 0.2000 (Rfree = 0.000) for 6400 atoms. Found 25 (43 requested) and removed 31 (24 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.13 3.01 Search for helices and strands: 0 residues in 0 chains, 6539 seeds are put forward NCS extension: 37 residues added (0 deleted due to clashes), 6576 seeds are put forward Round 1: 445 peptides, 75 chains. Longest chain 22 peptides. Score 0.417 Round 2: 489 peptides, 68 chains. Longest chain 22 peptides. Score 0.524 Round 3: 472 peptides, 69 chains. Longest chain 23 peptides. Score 0.495 Round 4: 482 peptides, 68 chains. Longest chain 21 peptides. Score 0.514 Round 5: 489 peptides, 71 chains. Longest chain 25 peptides. Score 0.506 Taking the results from Round 2 Chains 72, Residues 421, Estimated correctness of the model 1.9 % 9 chains (54 residues) have been docked in sequence ------------------------------------------------------ 14660 reflections ( 99.46 % complete ) and 14208 restraints for refining 6503 atoms. 12400 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2234 (Rfree = 0.000) for 6503 atoms. Found 26 (44 requested) and removed 33 (24 requested) atoms. Cycle 37: After refmac, R = 0.2139 (Rfree = 0.000) for 6474 atoms. Found 36 (44 requested) and removed 26 (24 requested) atoms. Cycle 38: After refmac, R = 0.2077 (Rfree = 0.000) for 6471 atoms. Found 26 (43 requested) and removed 29 (24 requested) atoms. Cycle 39: After refmac, R = 0.1953 (Rfree = 0.000) for 6456 atoms. Found 19 (43 requested) and removed 27 (24 requested) atoms. Cycle 40: After refmac, R = 0.1983 (Rfree = 0.000) for 6442 atoms. Found 31 (43 requested) and removed 29 (24 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.14 3.02 Search for helices and strands: 0 residues in 0 chains, 6587 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 6621 seeds are put forward Round 1: 397 peptides, 69 chains. Longest chain 16 peptides. Score 0.383 Round 2: 471 peptides, 69 chains. Longest chain 22 peptides. Score 0.493 Round 3: 467 peptides, 70 chains. Longest chain 17 peptides. Score 0.481 Round 4: 491 peptides, 66 chains. Longest chain 23 peptides. Score 0.538 Round 5: 464 peptides, 67 chains. Longest chain 19 peptides. Score 0.496 Taking the results from Round 4 Chains 70, Residues 425, Estimated correctness of the model 7.2 % 5 chains (40 residues) have been docked in sequence ------------------------------------------------------ 14660 reflections ( 99.46 % complete ) and 14324 restraints for refining 6501 atoms. 12558 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2190 (Rfree = 0.000) for 6501 atoms. Found 34 (44 requested) and removed 33 (24 requested) atoms. Cycle 42: After refmac, R = 0.2131 (Rfree = 0.000) for 6476 atoms. Found 43 (44 requested) and removed 28 (24 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1904 (Rfree = 0.000) for 6480 atoms. Found 26 (44 requested) and removed 26 (24 requested) atoms. Cycle 44: After refmac, R = 0.1868 (Rfree = 0.000) for 6475 atoms. Found 26 (43 requested) and removed 28 (24 requested) atoms. Cycle 45: After refmac, R = 0.1833 (Rfree = 0.000) for 6464 atoms. Found 21 (43 requested) and removed 25 (24 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.13 3.01 Search for helices and strands: 0 residues in 0 chains, 6602 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 6623 seeds are put forward Round 1: 417 peptides, 75 chains. Longest chain 23 peptides. Score 0.373 Round 2: 449 peptides, 70 chains. Longest chain 20 peptides. Score 0.456 Round 3: 462 peptides, 67 chains. Longest chain 23 peptides. Score 0.493 Round 4: 461 peptides, 72 chains. Longest chain 16 peptides. Score 0.460 Round 5: 465 peptides, 68 chains. Longest chain 23 peptides. Score 0.491 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 69, Residues 395, Estimated correctness of the model 0.0 % 5 chains (32 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 1vl4-3_warpNtrace.pdb as input Building loops using Loopy2018 69 chains (395 residues) following loop building 5 chains (32 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14660 reflections ( 99.46 % complete ) and 14608 restraints for refining 6503 atoms. 13002 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2035 (Rfree = 0.000) for 6503 atoms. Found 0 (44 requested) and removed 24 (24 requested) atoms. Cycle 47: After refmac, R = 0.2089 (Rfree = 0.000) for 6456 atoms. Found 0 (43 requested) and removed 24 (24 requested) atoms. Cycle 48: After refmac, R = 0.2297 (Rfree = 0.000) for 6421 atoms. Found 0 (43 requested) and removed 24 (24 requested) atoms. Cycle 49: After refmac, R = 0.1985 (Rfree = 0.000) for 6379 atoms. Found 0 (43 requested) and removed 24 (24 requested) atoms. Writing output files ... TimeTaking 68.58