Mon 24 Dec 07:46:00 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 1vqy-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vqy-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vqy-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqy-4.0-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/1vqy-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqy-4.0-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 07:46:04 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/1vqy-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqy-4.0-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 703 and 0 Target number of residues in the AU: 703 Target solvent content: 0.6116 Checking the provided sequence file Detected sequence length: 116 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 8 Adjusted target number of residues: 928 Adjusted target solvent content: 0.49 Input MTZ file: 1vqy-4.0-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: 68.026 110.931 129.804 90.000 90.000 90.000 Input sequence file: 1vqy-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 7424 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: 29.074 4.000 Wilson plot Bfac: 57.43 8602 reflections ( 98.34 % complete ) and 0 restraints for refining 8204 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3204 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3371 (Rfree = 0.000) for 8204 atoms. Found 38 (38 requested) and removed 72 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.49 3.54 Search for helices and strands: 0 residues in 0 chains, 8341 seeds are put forward NCS extension: 0 residues added, 8341 seeds are put forward Round 1: 317 peptides, 61 chains. Longest chain 16 peptides. Score 0.311 Round 2: 406 peptides, 65 chains. Longest chain 13 peptides. Score 0.433 Round 3: 438 peptides, 62 chains. Longest chain 20 peptides. Score 0.502 Round 4: 447 peptides, 63 chains. Longest chain 23 peptides. Score 0.509 Round 5: 462 peptides, 65 chains. Longest chain 26 peptides. Score 0.517 Taking the results from Round 5 Chains 65, Residues 397, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8602 reflections ( 98.34 % complete ) and 15943 restraints for refining 6703 atoms. 14420 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2531 (Rfree = 0.000) for 6703 atoms. Found 31 (31 requested) and removed 50 (15 requested) atoms. Cycle 2: After refmac, R = 0.2418 (Rfree = 0.000) for 6592 atoms. Found 31 (31 requested) and removed 45 (15 requested) atoms. Cycle 3: After refmac, R = 0.1884 (Rfree = 0.000) for 6526 atoms. Found 18 (31 requested) and removed 46 (15 requested) atoms. Cycle 4: After refmac, R = 0.1757 (Rfree = 0.000) for 6459 atoms. Found 10 (30 requested) and removed 29 (15 requested) atoms. Cycle 5: After refmac, R = 0.1726 (Rfree = 0.000) for 6411 atoms. Found 11 (30 requested) and removed 29 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.42 3.47 Search for helices and strands: 0 residues in 0 chains, 6620 seeds are put forward NCS extension: 8 residues added (7 deleted due to clashes), 6628 seeds are put forward Round 1: 428 peptides, 80 chains. Longest chain 15 peptides. Score 0.364 Round 2: 480 peptides, 75 chains. Longest chain 20 peptides. Score 0.480 Round 3: 500 peptides, 76 chains. Longest chain 17 peptides. Score 0.502 Round 4: 503 peptides, 66 chains. Longest chain 24 peptides. Score 0.567 Round 5: 508 peptides, 70 chains. Longest chain 28 peptides. Score 0.550 Taking the results from Round 4 Chains 66, Residues 437, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8602 reflections ( 98.34 % complete ) and 15511 restraints for refining 6704 atoms. 13829 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2299 (Rfree = 0.000) for 6704 atoms. Found 31 (31 requested) and removed 80 (15 requested) atoms. Cycle 7: After refmac, R = 0.2338 (Rfree = 0.000) for 6610 atoms. Found 31 (31 requested) and removed 89 (15 requested) atoms. Cycle 8: After refmac, R = 0.1794 (Rfree = 0.000) for 6521 atoms. Found 15 (31 requested) and removed 51 (15 requested) atoms. Cycle 9: After refmac, R = 0.1702 (Rfree = 0.000) for 6473 atoms. Found 10 (30 requested) and removed 30 (15 requested) atoms. Cycle 10: After refmac, R = 0.1676 (Rfree = 0.000) for 6449 atoms. Found 2 (30 requested) and removed 29 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.48 Search for helices and strands: 0 residues in 0 chains, 6645 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 6668 seeds are put forward Round 1: 400 peptides, 67 chains. Longest chain 17 peptides. Score 0.410 Round 2: 441 peptides, 64 chains. Longest chain 19 peptides. Score 0.493 Round 3: 458 peptides, 63 chains. Longest chain 21 peptides. Score 0.524 Round 4: 470 peptides, 70 chains. Longest chain 15 peptides. Score 0.497 Round 5: 464 peptides, 69 chains. Longest chain 15 peptides. Score 0.495 Taking the results from Round 3 Chains 64, Residues 395, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 8602 reflections ( 98.34 % complete ) and 15592 restraints for refining 6705 atoms. 14013 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2327 (Rfree = 0.000) for 6705 atoms. Found 31 (31 requested) and removed 64 (15 requested) atoms. Cycle 12: After refmac, R = 0.2238 (Rfree = 0.000) for 6640 atoms. Found 31 (31 requested) and removed 55 (15 requested) atoms. Cycle 13: After refmac, R = 0.2205 (Rfree = 0.000) for 6590 atoms. Found 31 (31 requested) and removed 57 (15 requested) atoms. Cycle 14: After refmac, R = 0.1763 (Rfree = 0.000) for 6545 atoms. Found 16 (31 requested) and removed 41 (15 requested) atoms. Cycle 15: After refmac, R = 0.1674 (Rfree = 0.000) for 6510 atoms. Found 9 (30 requested) and removed 29 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 3.43 Search for helices and strands: 0 residues in 0 chains, 6691 seeds are put forward NCS extension: 14 residues added (4 deleted due to clashes), 6705 seeds are put forward Round 1: 442 peptides, 82 chains. Longest chain 14 peptides. Score 0.373 Round 2: 489 peptides, 77 chains. Longest chain 27 peptides. Score 0.480 Round 3: 485 peptides, 71 chains. Longest chain 17 peptides. Score 0.512 Round 4: 475 peptides, 74 chains. Longest chain 14 peptides. Score 0.479 Round 5: 489 peptides, 75 chains. Longest chain 16 peptides. Score 0.493 Taking the results from Round 3 Chains 71, Residues 414, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8602 reflections ( 98.34 % complete ) and 15593 restraints for refining 6704 atoms. 14008 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2287 (Rfree = 0.000) for 6704 atoms. Found 31 (31 requested) and removed 57 (15 requested) atoms. Cycle 17: After refmac, R = 0.2111 (Rfree = 0.000) for 6635 atoms. Found 31 (31 requested) and removed 39 (15 requested) atoms. Cycle 18: After refmac, R = 0.2021 (Rfree = 0.000) for 6612 atoms. Found 31 (31 requested) and removed 43 (15 requested) atoms. Cycle 19: After refmac, R = 0.1612 (Rfree = 0.000) for 6587 atoms. Found 11 (31 requested) and removed 28 (15 requested) atoms. Cycle 20: After refmac, R = 0.1572 (Rfree = 0.000) for 6560 atoms. Found 7 (31 requested) and removed 29 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.44 Search for helices and strands: 0 residues in 0 chains, 6750 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 6766 seeds are put forward Round 1: 392 peptides, 76 chains. Longest chain 12 peptides. Score 0.331 Round 2: 421 peptides, 67 chains. Longest chain 17 peptides. Score 0.443 Round 3: 440 peptides, 71 chains. Longest chain 13 peptides. Score 0.446 Round 4: 455 peptides, 70 chains. Longest chain 14 peptides. Score 0.475 Round 5: 461 peptides, 65 chains. Longest chain 17 peptides. Score 0.516 Taking the results from Round 5 Chains 65, Residues 396, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8602 reflections ( 98.34 % complete ) and 15371 restraints for refining 6705 atoms. 13852 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2109 (Rfree = 0.000) for 6705 atoms. Found 31 (31 requested) and removed 40 (15 requested) atoms. Cycle 22: After refmac, R = 0.2108 (Rfree = 0.000) for 6666 atoms. Found 31 (31 requested) and removed 40 (15 requested) atoms. Cycle 23: After refmac, R = 0.1628 (Rfree = 0.000) for 6638 atoms. Found 20 (31 requested) and removed 28 (15 requested) atoms. Cycle 24: After refmac, R = 0.1529 (Rfree = 0.000) for 6613 atoms. Found 10 (31 requested) and removed 22 (15 requested) atoms. Cycle 25: After refmac, R = 0.1495 (Rfree = 0.000) for 6596 atoms. Found 15 (31 requested) and removed 28 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.40 3.45 Search for helices and strands: 0 residues in 0 chains, 6793 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 6812 seeds are put forward Round 1: 373 peptides, 74 chains. Longest chain 12 peptides. Score 0.313 Round 2: 423 peptides, 69 chains. Longest chain 16 peptides. Score 0.433 Round 3: 422 peptides, 62 chains. Longest chain 15 peptides. Score 0.478 Round 4: 443 peptides, 65 chains. Longest chain 21 peptides. Score 0.490 Round 5: 433 peptides, 66 chains. Longest chain 17 peptides. Score 0.468 Taking the results from Round 4 Chains 66, Residues 378, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 8602 reflections ( 98.34 % complete ) and 15402 restraints for refining 6704 atoms. 13904 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2040 (Rfree = 0.000) for 6704 atoms. Found 31 (31 requested) and removed 46 (15 requested) atoms. Cycle 27: After refmac, R = 0.2017 (Rfree = 0.000) for 6651 atoms. Found 31 (31 requested) and removed 47 (15 requested) atoms. Cycle 28: After refmac, R = 0.1621 (Rfree = 0.000) for 6607 atoms. Found 15 (31 requested) and removed 27 (15 requested) atoms. Cycle 29: After refmac, R = 0.1524 (Rfree = 0.000) for 6577 atoms. Found 10 (31 requested) and removed 25 (15 requested) atoms. Cycle 30: After refmac, R = 0.1537 (Rfree = 0.000) for 6559 atoms. Found 3 (31 requested) and removed 23 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.45 Search for helices and strands: 0 residues in 0 chains, 6743 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 6759 seeds are put forward Round 1: 369 peptides, 68 chains. Longest chain 11 peptides. Score 0.350 Round 2: 410 peptides, 66 chains. Longest chain 15 peptides. Score 0.433 Round 3: 429 peptides, 66 chains. Longest chain 18 peptides. Score 0.462 Round 4: 418 peptides, 65 chains. Longest chain 13 peptides. Score 0.452 Round 5: 437 peptides, 62 chains. Longest chain 17 peptides. Score 0.500 Taking the results from Round 5 Chains 62, Residues 375, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8602 reflections ( 98.34 % complete ) and 15684 restraints for refining 6704 atoms. 14246 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2195 (Rfree = 0.000) for 6704 atoms. Found 31 (31 requested) and removed 50 (15 requested) atoms. Cycle 32: After refmac, R = 0.2150 (Rfree = 0.000) for 6654 atoms. Found 31 (31 requested) and removed 45 (15 requested) atoms. Cycle 33: After refmac, R = 0.2060 (Rfree = 0.000) for 6618 atoms. Found 31 (31 requested) and removed 32 (15 requested) atoms. Cycle 34: After refmac, R = 0.1583 (Rfree = 0.000) for 6593 atoms. Found 16 (31 requested) and removed 23 (15 requested) atoms. Cycle 35: After refmac, R = 0.1505 (Rfree = 0.000) for 6570 atoms. Found 11 (31 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.42 3.47 Search for helices and strands: 0 residues in 0 chains, 6750 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 6772 seeds are put forward Round 1: 365 peptides, 76 chains. Longest chain 11 peptides. Score 0.283 Round 2: 391 peptides, 65 chains. Longest chain 15 peptides. Score 0.409 Round 3: 387 peptides, 62 chains. Longest chain 12 peptides. Score 0.424 Round 4: 412 peptides, 67 chains. Longest chain 15 peptides. Score 0.429 Round 5: 412 peptides, 67 chains. Longest chain 15 peptides. Score 0.429 Taking the results from Round 5 Chains 67, Residues 345, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8602 reflections ( 98.34 % complete ) and 15630 restraints for refining 6704 atoms. 14317 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2187 (Rfree = 0.000) for 6704 atoms. Found 31 (31 requested) and removed 45 (15 requested) atoms. Cycle 37: After refmac, R = 0.2090 (Rfree = 0.000) for 6653 atoms. Found 31 (31 requested) and removed 33 (15 requested) atoms. Cycle 38: After refmac, R = 0.1702 (Rfree = 0.000) for 6616 atoms. Found 12 (31 requested) and removed 24 (15 requested) atoms. Cycle 39: After refmac, R = 0.1626 (Rfree = 0.000) for 6585 atoms. Found 13 (31 requested) and removed 21 (15 requested) atoms. Cycle 40: After refmac, R = 0.1618 (Rfree = 0.000) for 6570 atoms. Found 14 (31 requested) and removed 26 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.43 3.48 Search for helices and strands: 0 residues in 0 chains, 6722 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 6750 seeds are put forward Round 1: 340 peptides, 66 chains. Longest chain 11 peptides. Score 0.314 Round 2: 359 peptides, 66 chains. Longest chain 12 peptides. Score 0.348 Round 3: 361 peptides, 58 chains. Longest chain 14 peptides. Score 0.410 Round 4: 381 peptides, 62 chains. Longest chain 13 peptides. Score 0.414 Round 5: 382 peptides, 62 chains. Longest chain 12 peptides. Score 0.416 Taking the results from Round 5 Chains 62, Residues 320, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8602 reflections ( 98.34 % complete ) and 16087 restraints for refining 6705 atoms. 14869 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2308 (Rfree = 0.000) for 6705 atoms. Found 31 (31 requested) and removed 50 (15 requested) atoms. Cycle 42: After refmac, R = 0.2289 (Rfree = 0.000) for 6660 atoms. Found 31 (31 requested) and removed 52 (15 requested) atoms. Cycle 43: After refmac, R = 0.2265 (Rfree = 0.000) for 6620 atoms. Found 31 (31 requested) and removed 37 (15 requested) atoms. Cycle 44: After refmac, R = 0.2068 (Rfree = 0.000) for 6589 atoms. Found 31 (31 requested) and removed 35 (15 requested) atoms. Cycle 45: After refmac, R = 0.1649 (Rfree = 0.000) for 6565 atoms. Found 16 (31 requested) and removed 22 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.39 3.44 Search for helices and strands: 0 residues in 0 chains, 6712 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 6725 seeds are put forward Round 1: 315 peptides, 66 chains. Longest chain 9 peptides. Score 0.268 Round 2: 361 peptides, 64 chains. Longest chain 13 peptides. Score 0.366 Round 3: 369 peptides, 65 chains. Longest chain 16 peptides. Score 0.372 Round 4: 365 peptides, 64 chains. Longest chain 12 peptides. Score 0.373 Round 5: 370 peptides, 65 chains. Longest chain 13 peptides. Score 0.374 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 65, Residues 305, 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 1vqy-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8602 reflections ( 98.34 % complete ) and 16167 restraints for refining 6704 atoms. 15012 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2372 (Rfree = 0.000) for 6704 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2400 (Rfree = 0.000) for 6653 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.2083 (Rfree = 0.000) for 6608 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.1628 (Rfree = 0.000) for 6575 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Writing output files ... TimeTaking 68.15