Sun 23 Dec 22:22:41 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 1vl5-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vl5-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vl5-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl5-3.4-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/1vl5-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl5-3.4-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 22:22:50 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/1vl5-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl5-3.4-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 813 and 0 Target number of residues in the AU: 813 Target solvent content: 0.6202 Checking the provided sequence file Detected sequence length: 260 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1040 Adjusted target solvent content: 0.51 Input MTZ file: 1vl5-3.4-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: 64.006 87.475 105.236 90.000 100.573 90.000 Input sequence file: 1vl5-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 8320 target number of atoms Had to go as low as 0.70 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: 49.849 3.400 Wilson plot Bfac: 61.39 15845 reflections ( 99.92 % complete ) and 0 restraints for refining 9198 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3061 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2582 (Rfree = 0.000) for 9198 atoms. Found 69 (69 requested) and removed 64 (34 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.25 3.21 Search for helices and strands: 0 residues in 0 chains, 9371 seeds are put forward NCS extension: 0 residues added, 9371 seeds are put forward Round 1: 521 peptides, 89 chains. Longest chain 17 peptides. Score 0.418 Round 2: 616 peptides, 86 chains. Longest chain 28 peptides. Score 0.551 Round 3: 634 peptides, 86 chains. Longest chain 23 peptides. Score 0.571 Round 4: 647 peptides, 75 chains. Longest chain 28 peptides. Score 0.635 Round 5: 648 peptides, 75 chains. Longest chain 29 peptides. Score 0.636 Taking the results from Round 5 Chains 78, Residues 573, Estimated correctness of the model 40.0 % 7 chains (123 residues) have been docked in sequence ------------------------------------------------------ 15845 reflections ( 99.92 % complete ) and 15459 restraints for refining 7562 atoms. 12738 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2371 (Rfree = 0.000) for 7562 atoms. Found 40 (57 requested) and removed 66 (28 requested) atoms. Cycle 2: After refmac, R = 0.2192 (Rfree = 0.000) for 7413 atoms. Found 30 (56 requested) and removed 35 (28 requested) atoms. Cycle 3: After refmac, R = 0.2136 (Rfree = 0.000) for 7360 atoms. Found 19 (55 requested) and removed 40 (27 requested) atoms. Cycle 4: After refmac, R = 0.2090 (Rfree = 0.000) for 7308 atoms. Found 13 (55 requested) and removed 36 (27 requested) atoms. Cycle 5: After refmac, R = 0.2027 (Rfree = 0.000) for 7257 atoms. Found 20 (55 requested) and removed 33 (27 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.21 3.17 Search for helices and strands: 0 residues in 0 chains, 7526 seeds are put forward NCS extension: 19 residues added (9 deleted due to clashes), 7545 seeds are put forward Round 1: 588 peptides, 84 chains. Longest chain 21 peptides. Score 0.529 Round 2: 631 peptides, 73 chains. Longest chain 30 peptides. Score 0.628 Round 3: 641 peptides, 75 chains. Longest chain 38 peptides. Score 0.629 Round 4: 640 peptides, 70 chains. Longest chain 36 peptides. Score 0.650 Round 5: 633 peptides, 73 chains. Longest chain 33 peptides. Score 0.630 Taking the results from Round 4 Chains 72, Residues 570, Estimated correctness of the model 44.1 % 6 chains (98 residues) have been docked in sequence ------------------------------------------------------ 15845 reflections ( 99.92 % complete ) and 15952 restraints for refining 7563 atoms. 13293 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2331 (Rfree = 0.000) for 7563 atoms. Found 42 (57 requested) and removed 60 (28 requested) atoms. Cycle 7: After refmac, R = 0.2175 (Rfree = 0.000) for 7494 atoms. Found 25 (56 requested) and removed 40 (28 requested) atoms. Cycle 8: After refmac, R = 0.2109 (Rfree = 0.000) for 7437 atoms. Found 19 (56 requested) and removed 41 (28 requested) atoms. Cycle 9: After refmac, R = 0.2050 (Rfree = 0.000) for 7379 atoms. Found 14 (55 requested) and removed 33 (27 requested) atoms. Cycle 10: After refmac, R = 0.2015 (Rfree = 0.000) for 7341 atoms. Found 19 (55 requested) and removed 31 (27 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 3.16 Search for helices and strands: 0 residues in 0 chains, 7573 seeds are put forward NCS extension: 16 residues added (5 deleted due to clashes), 7589 seeds are put forward Round 1: 552 peptides, 85 chains. Longest chain 17 peptides. Score 0.480 Round 2: 633 peptides, 75 chains. Longest chain 31 peptides. Score 0.621 Round 3: 636 peptides, 73 chains. Longest chain 24 peptides. Score 0.633 Round 4: 643 peptides, 73 chains. Longest chain 30 peptides. Score 0.640 Round 5: 633 peptides, 65 chains. Longest chain 24 peptides. Score 0.665 Taking the results from Round 5 Chains 70, Residues 568, Estimated correctness of the model 48.4 % 5 chains (83 residues) have been docked in sequence ------------------------------------------------------ 15845 reflections ( 99.92 % complete ) and 15911 restraints for refining 7564 atoms. 13358 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2287 (Rfree = 0.000) for 7564 atoms. Found 36 (57 requested) and removed 53 (28 requested) atoms. Cycle 12: After refmac, R = 0.2142 (Rfree = 0.000) for 7495 atoms. Found 16 (56 requested) and removed 42 (28 requested) atoms. Cycle 13: After refmac, R = 0.2047 (Rfree = 0.000) for 7436 atoms. Found 17 (56 requested) and removed 38 (28 requested) atoms. Cycle 14: After refmac, R = 0.1973 (Rfree = 0.000) for 7395 atoms. Found 14 (55 requested) and removed 30 (27 requested) atoms. Cycle 15: After refmac, R = 0.1928 (Rfree = 0.000) for 7362 atoms. Found 27 (55 requested) and removed 35 (27 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.21 3.17 Search for helices and strands: 0 residues in 0 chains, 7609 seeds are put forward NCS extension: 22 residues added (10 deleted due to clashes), 7631 seeds are put forward Round 1: 577 peptides, 91 chains. Longest chain 19 peptides. Score 0.479 Round 2: 614 peptides, 80 chains. Longest chain 17 peptides. Score 0.578 Round 3: 618 peptides, 76 chains. Longest chain 31 peptides. Score 0.601 Round 4: 625 peptides, 69 chains. Longest chain 24 peptides. Score 0.640 Round 5: 630 peptides, 76 chains. Longest chain 23 peptides. Score 0.614 Taking the results from Round 4 Chains 70, Residues 556, Estimated correctness of the model 41.2 % 10 chains (93 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 15845 reflections ( 99.92 % complete ) and 16032 restraints for refining 7563 atoms. 13528 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2277 (Rfree = 0.000) for 7563 atoms. Found 44 (57 requested) and removed 48 (28 requested) atoms. Cycle 17: After refmac, R = 0.2145 (Rfree = 0.000) for 7517 atoms. Found 27 (57 requested) and removed 42 (28 requested) atoms. Cycle 18: After refmac, R = 0.2077 (Rfree = 0.000) for 7477 atoms. Found 15 (56 requested) and removed 35 (28 requested) atoms. Cycle 19: After refmac, R = 0.1997 (Rfree = 0.000) for 7443 atoms. Found 12 (56 requested) and removed 33 (28 requested) atoms. Cycle 20: After refmac, R = 0.1963 (Rfree = 0.000) for 7408 atoms. Found 12 (56 requested) and removed 31 (28 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.21 3.17 Search for helices and strands: 0 residues in 0 chains, 7622 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 7638 seeds are put forward Round 1: 572 peptides, 87 chains. Longest chain 18 peptides. Score 0.494 Round 2: 607 peptides, 78 chains. Longest chain 23 peptides. Score 0.580 Round 3: 627 peptides, 78 chains. Longest chain 33 peptides. Score 0.601 Round 4: 638 peptides, 77 chains. Longest chain 33 peptides. Score 0.617 Round 5: 622 peptides, 78 chains. Longest chain 41 peptides. Score 0.596 Taking the results from Round 4 Chains 81, Residues 561, Estimated correctness of the model 34.1 % 6 chains (88 residues) have been docked in sequence ------------------------------------------------------ 15845 reflections ( 99.92 % complete ) and 15828 restraints for refining 7565 atoms. 13280 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2247 (Rfree = 0.000) for 7565 atoms. Found 37 (57 requested) and removed 49 (28 requested) atoms. Cycle 22: After refmac, R = 0.2146 (Rfree = 0.000) for 7517 atoms. Found 23 (57 requested) and removed 34 (28 requested) atoms. Cycle 23: After refmac, R = 0.2103 (Rfree = 0.000) for 7471 atoms. Found 27 (56 requested) and removed 36 (28 requested) atoms. Cycle 24: After refmac, R = 0.2057 (Rfree = 0.000) for 7437 atoms. Found 25 (56 requested) and removed 33 (28 requested) atoms. Cycle 25: After refmac, R = 0.2041 (Rfree = 0.000) for 7410 atoms. Found 27 (56 requested) and removed 32 (28 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.21 3.17 Search for helices and strands: 0 residues in 0 chains, 7646 seeds are put forward NCS extension: 24 residues added (5 deleted due to clashes), 7670 seeds are put forward Round 1: 530 peptides, 84 chains. Longest chain 17 peptides. Score 0.458 Round 2: 597 peptides, 79 chains. Longest chain 24 peptides. Score 0.565 Round 3: 590 peptides, 75 chains. Longest chain 30 peptides. Score 0.577 Round 4: 591 peptides, 76 chains. Longest chain 30 peptides. Score 0.573 Round 5: 585 peptides, 70 chains. Longest chain 18 peptides. Score 0.595 Taking the results from Round 5 Chains 76, Residues 515, Estimated correctness of the model 27.0 % 7 chains (64 residues) have been docked in sequence ------------------------------------------------------ 15845 reflections ( 99.92 % complete ) and 16490 restraints for refining 7565 atoms. 14278 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2280 (Rfree = 0.000) for 7565 atoms. Found 40 (57 requested) and removed 43 (28 requested) atoms. Cycle 27: After refmac, R = 0.2180 (Rfree = 0.000) for 7534 atoms. Found 28 (57 requested) and removed 42 (28 requested) atoms. Cycle 28: After refmac, R = 0.2089 (Rfree = 0.000) for 7510 atoms. Found 23 (56 requested) and removed 35 (28 requested) atoms. Cycle 29: After refmac, R = 0.2008 (Rfree = 0.000) for 7487 atoms. Found 15 (56 requested) and removed 38 (28 requested) atoms. Cycle 30: After refmac, R = 0.1940 (Rfree = 0.000) for 7461 atoms. Found 21 (56 requested) and removed 35 (28 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.19 3.15 Search for helices and strands: 0 residues in 0 chains, 7683 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 7699 seeds are put forward Round 1: 491 peptides, 83 chains. Longest chain 19 peptides. Score 0.412 Round 2: 589 peptides, 81 chains. Longest chain 25 peptides. Score 0.546 Round 3: 574 peptides, 81 chains. Longest chain 21 peptides. Score 0.528 Round 4: 578 peptides, 76 chains. Longest chain 31 peptides. Score 0.558 Round 5: 559 peptides, 80 chains. Longest chain 32 peptides. Score 0.516 Taking the results from Round 4 Chains 82, Residues 502, Estimated correctness of the model 14.4 % 8 chains (70 residues) have been docked in sequence ------------------------------------------------------ 15845 reflections ( 99.92 % complete ) and 16339 restraints for refining 7564 atoms. 14143 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2193 (Rfree = 0.000) for 7564 atoms. Found 29 (57 requested) and removed 45 (28 requested) atoms. Cycle 32: After refmac, R = 0.1989 (Rfree = 0.000) for 7510 atoms. Found 16 (56 requested) and removed 37 (28 requested) atoms. Cycle 33: After refmac, R = 0.1895 (Rfree = 0.000) for 7474 atoms. Found 9 (56 requested) and removed 33 (28 requested) atoms. Cycle 34: After refmac, R = 0.1823 (Rfree = 0.000) for 7435 atoms. Found 12 (56 requested) and removed 30 (28 requested) atoms. Cycle 35: After refmac, R = 0.1779 (Rfree = 0.000) for 7415 atoms. Found 5 (56 requested) and removed 30 (28 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.20 3.16 Search for helices and strands: 0 residues in 0 chains, 7657 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 7676 seeds are put forward Round 1: 459 peptides, 77 chains. Longest chain 20 peptides. Score 0.404 Round 2: 508 peptides, 72 chains. Longest chain 21 peptides. Score 0.497 Round 3: 536 peptides, 77 chains. Longest chain 18 peptides. Score 0.504 Round 4: 551 peptides, 74 chains. Longest chain 20 peptides. Score 0.538 Round 5: 562 peptides, 77 chains. Longest chain 26 peptides. Score 0.535 Taking the results from Round 4 Chains 78, Residues 477, Estimated correctness of the model 7.2 % 5 chains (56 residues) have been docked in sequence ------------------------------------------------------ 15845 reflections ( 99.92 % complete ) and 16475 restraints for refining 7563 atoms. 14404 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2052 (Rfree = 0.000) for 7563 atoms. Found 21 (57 requested) and removed 38 (28 requested) atoms. Cycle 37: After refmac, R = 0.1918 (Rfree = 0.000) for 7506 atoms. Found 21 (56 requested) and removed 35 (28 requested) atoms. Cycle 38: After refmac, R = 0.1840 (Rfree = 0.000) for 7475 atoms. Found 9 (56 requested) and removed 33 (28 requested) atoms. Cycle 39: After refmac, R = 0.1814 (Rfree = 0.000) for 7439 atoms. Found 15 (56 requested) and removed 34 (28 requested) atoms. Cycle 40: After refmac, R = 0.1751 (Rfree = 0.000) for 7416 atoms. Found 11 (56 requested) and removed 32 (28 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.22 3.18 Search for helices and strands: 0 residues in 0 chains, 7630 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 7656 seeds are put forward Round 1: 456 peptides, 79 chains. Longest chain 14 peptides. Score 0.387 Round 2: 503 peptides, 80 chains. Longest chain 16 peptides. Score 0.446 Round 3: 497 peptides, 77 chains. Longest chain 16 peptides. Score 0.455 Round 4: 519 peptides, 73 chains. Longest chain 22 peptides. Score 0.505 Round 5: 520 peptides, 74 chains. Longest chain 20 peptides. Score 0.501 Taking the results from Round 4 Chains 73, Residues 446, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 15845 reflections ( 99.92 % complete ) and 17299 restraints for refining 7564 atoms. 15533 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1998 (Rfree = 0.000) for 7564 atoms. Found 29 (57 requested) and removed 36 (28 requested) atoms. Cycle 42: After refmac, R = 0.1863 (Rfree = 0.000) for 7543 atoms. Found 16 (57 requested) and removed 34 (28 requested) atoms. Cycle 43: After refmac, R = 0.1822 (Rfree = 0.000) for 7520 atoms. Found 21 (56 requested) and removed 29 (28 requested) atoms. Cycle 44: After refmac, R = 0.1804 (Rfree = 0.000) for 7506 atoms. Found 14 (56 requested) and removed 34 (28 requested) atoms. Cycle 45: After refmac, R = 0.1762 (Rfree = 0.000) for 7477 atoms. Found 11 (56 requested) and removed 29 (28 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.21 3.17 Search for helices and strands: 0 residues in 0 chains, 7664 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 7689 seeds are put forward Round 1: 426 peptides, 76 chains. Longest chain 18 peptides. Score 0.363 Round 2: 463 peptides, 69 chains. Longest chain 25 peptides. Score 0.457 Round 3: 488 peptides, 71 chains. Longest chain 20 peptides. Score 0.477 Round 4: 479 peptides, 69 chains. Longest chain 23 peptides. Score 0.477 Round 5: 493 peptides, 72 chains. Longest chain 14 peptides. Score 0.478 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 73, Residues 421, Estimated correctness of the model 0.0 % 4 chains (19 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 1vl5-3_warpNtrace.pdb as input Building loops using Loopy2018 73 chains (421 residues) following loop building 4 chains (19 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 15845 reflections ( 99.92 % complete ) and 17385 restraints for refining 7565 atoms. 15732 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1957 (Rfree = 0.000) for 7565 atoms. Found 0 (57 requested) and removed 28 (28 requested) atoms. Cycle 47: After refmac, R = 0.1861 (Rfree = 0.000) for 7519 atoms. Found 0 (56 requested) and removed 28 (28 requested) atoms. Cycle 48: After refmac, R = 0.1814 (Rfree = 0.000) for 7486 atoms. Found 0 (56 requested) and removed 28 (28 requested) atoms. Cycle 49: After refmac, R = 0.1781 (Rfree = 0.000) for 7451 atoms. TimeTaking 94.05