Sun 23 Dec 23:57:36 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vl5-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vl5-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vl5-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.4-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.4-parrot-mrncs ############### 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 23:57:40 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.4-parrot-mrncs/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-mrncs.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-mrncs.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 9174 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3040 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2544 (Rfree = 0.000) for 9174 atoms. Found 60 (69 requested) and removed 63 (34 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.20 3.16 Search for helices and strands: 0 residues in 0 chains, 9347 seeds are put forward NCS extension: 0 residues added, 9347 seeds are put forward Round 1: 523 peptides, 91 chains. Longest chain 14 peptides. Score 0.409 Round 2: 597 peptides, 80 chains. Longest chain 24 peptides. Score 0.560 Round 3: 655 peptides, 80 chains. Longest chain 34 peptides. Score 0.620 Round 4: 655 peptides, 73 chains. Longest chain 31 peptides. Score 0.651 Round 5: 657 peptides, 76 chains. Longest chain 27 peptides. Score 0.640 Taking the results from Round 4 Chains 76, Residues 582, Estimated correctness of the model 44.4 % 6 chains (120 residues) have been docked in sequence ------------------------------------------------------ 15845 reflections ( 99.92 % complete ) and 15086 restraints for refining 7561 atoms. 12266 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2338 (Rfree = 0.000) for 7561 atoms. Found 43 (57 requested) and removed 57 (28 requested) atoms. Cycle 2: After refmac, R = 0.2249 (Rfree = 0.000) for 7393 atoms. Found 26 (56 requested) and removed 38 (28 requested) atoms. Cycle 3: After refmac, R = 0.2195 (Rfree = 0.000) for 7321 atoms. Found 16 (55 requested) and removed 36 (27 requested) atoms. Cycle 4: After refmac, R = 0.2141 (Rfree = 0.000) for 7253 atoms. Found 30 (55 requested) and removed 37 (27 requested) atoms. Cycle 5: After refmac, R = 0.2070 (Rfree = 0.000) for 7204 atoms. Found 29 (54 requested) and removed 33 (27 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.19 3.15 Search for helices and strands: 0 residues in 0 chains, 7477 seeds are put forward NCS extension: 9 residues added (14 deleted due to clashes), 7486 seeds are put forward Round 1: 575 peptides, 81 chains. Longest chain 29 peptides. Score 0.529 Round 2: 650 peptides, 74 chains. Longest chain 26 peptides. Score 0.642 Round 3: 674 peptides, 72 chains. Longest chain 47 peptides. Score 0.672 Round 4: 676 peptides, 66 chains. Longest chain 40 peptides. Score 0.698 Round 5: 686 peptides, 65 chains. Longest chain 43 peptides. Score 0.709 Taking the results from Round 5 Chains 72, Residues 621, Estimated correctness of the model 60.2 % 9 chains (181 residues) have been docked in sequence Building loops using Loopy2018 72 chains (621 residues) following loop building 9 chains (181 residues) in sequence following loop building ------------------------------------------------------ 15845 reflections ( 99.92 % complete ) and 14780 restraints for refining 7565 atoms. 11565 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2329 (Rfree = 0.000) for 7565 atoms. Found 51 (57 requested) and removed 55 (28 requested) atoms. Cycle 7: After refmac, R = 0.2120 (Rfree = 0.000) for 7497 atoms. Found 25 (56 requested) and removed 41 (28 requested) atoms. Cycle 8: After refmac, R = 0.2160 (Rfree = 0.000) for 7448 atoms. Found 13 (54 requested) and removed 38 (28 requested) atoms. Cycle 9: After refmac, R = 0.2076 (Rfree = 0.000) for 7399 atoms. Found 24 (53 requested) and removed 37 (28 requested) atoms. Cycle 10: After refmac, R = 0.2007 (Rfree = 0.000) for 7368 atoms. Found 13 (51 requested) and removed 28 (27 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.21 3.17 Search for helices and strands: 0 residues in 0 chains, 7618 seeds are put forward NCS extension: 17 residues added (8 deleted due to clashes), 7635 seeds are put forward Round 1: 603 peptides, 83 chains. Longest chain 30 peptides. Score 0.551 Round 2: 632 peptides, 75 chains. Longest chain 27 peptides. Score 0.620 Round 3: 610 peptides, 69 chains. Longest chain 25 peptides. Score 0.625 Round 4: 626 peptides, 75 chains. Longest chain 27 peptides. Score 0.614 Round 5: 624 peptides, 68 chains. Longest chain 23 peptides. Score 0.643 Taking the results from Round 5 Chains 74, Residues 556, Estimated correctness of the model 42.1 % 9 chains (134 residues) have been docked in sequence ------------------------------------------------------ 15845 reflections ( 99.92 % complete ) and 15534 restraints for refining 7565 atoms. 12798 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2285 (Rfree = 0.000) for 7565 atoms. Found 37 (51 requested) and removed 46 (28 requested) atoms. Cycle 12: After refmac, R = 0.2116 (Rfree = 0.000) for 7495 atoms. Found 33 (51 requested) and removed 37 (28 requested) atoms. Cycle 13: After refmac, R = 0.2012 (Rfree = 0.000) for 7467 atoms. Found 21 (50 requested) and removed 31 (28 requested) atoms. Cycle 14: After refmac, R = 0.1932 (Rfree = 0.000) for 7446 atoms. Found 18 (50 requested) and removed 36 (28 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1882 (Rfree = 0.000) for 7417 atoms. Found 11 (50 requested) and removed 39 (28 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.20 3.16 Search for helices and strands: 0 residues in 0 chains, 7646 seeds are put forward NCS extension: 21 residues added (6 deleted due to clashes), 7667 seeds are put forward Round 1: 549 peptides, 76 chains. Longest chain 17 peptides. Score 0.525 Round 2: 604 peptides, 66 chains. Longest chain 26 peptides. Score 0.633 Round 3: 606 peptides, 66 chains. Longest chain 35 peptides. Score 0.635 Round 4: 610 peptides, 70 chains. Longest chain 29 peptides. Score 0.621 Round 5: 611 peptides, 69 chains. Longest chain 28 peptides. Score 0.626 Taking the results from Round 3 Chains 70, Residues 540, Estimated correctness of the model 39.7 % 6 chains (106 residues) have been docked in sequence ------------------------------------------------------ 15845 reflections ( 99.92 % complete ) and 15938 restraints for refining 7565 atoms. 13363 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2219 (Rfree = 0.000) for 7565 atoms. Found 28 (51 requested) and removed 53 (28 requested) atoms. Cycle 17: After refmac, R = 0.2043 (Rfree = 0.000) for 7511 atoms. Found 33 (50 requested) and removed 35 (28 requested) atoms. Cycle 18: After refmac, R = 0.1855 (Rfree = 0.000) for 7493 atoms. Found 14 (50 requested) and removed 32 (28 requested) atoms. Cycle 19: After refmac, R = 0.1814 (Rfree = 0.000) for 7459 atoms. Found 16 (50 requested) and removed 37 (28 requested) atoms. Cycle 20: After refmac, R = 0.1748 (Rfree = 0.000) for 7432 atoms. Found 8 (50 requested) and removed 35 (28 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.21 3.17 Search for helices and strands: 0 residues in 0 chains, 7640 seeds are put forward NCS extension: 19 residues added (17 deleted due to clashes), 7659 seeds are put forward Round 1: 572 peptides, 85 chains. Longest chain 22 peptides. Score 0.505 Round 2: 618 peptides, 80 chains. Longest chain 24 peptides. Score 0.582 Round 3: 626 peptides, 82 chains. Longest chain 20 peptides. Score 0.581 Round 4: 616 peptides, 73 chains. Longest chain 23 peptides. Score 0.613 Round 5: 586 peptides, 70 chains. Longest chain 20 peptides. Score 0.596 Taking the results from Round 4 Chains 78, Residues 543, Estimated correctness of the model 32.9 % 13 chains (151 residues) have been docked in sequence ------------------------------------------------------ 15845 reflections ( 99.92 % complete ) and 15322 restraints for refining 7564 atoms. 12630 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2115 (Rfree = 0.000) for 7564 atoms. Found 35 (51 requested) and removed 50 (28 requested) atoms. Cycle 22: After refmac, R = 0.1910 (Rfree = 0.000) for 7509 atoms. Found 23 (50 requested) and removed 39 (28 requested) atoms. Cycle 23: After refmac, R = 0.1863 (Rfree = 0.000) for 7471 atoms. Found 19 (50 requested) and removed 35 (28 requested) atoms. Cycle 24: After refmac, R = 0.1829 (Rfree = 0.000) for 7442 atoms. Found 11 (50 requested) and removed 30 (28 requested) atoms. Cycle 25: After refmac, R = 0.1807 (Rfree = 0.000) for 7408 atoms. Found 17 (50 requested) and removed 29 (28 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.22 3.18 Search for helices and strands: 0 residues in 0 chains, 7627 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 7654 seeds are put forward Round 1: 532 peptides, 80 chains. Longest chain 20 peptides. Score 0.483 Round 2: 555 peptides, 71 chains. Longest chain 20 peptides. Score 0.558 Round 3: 567 peptides, 68 chains. Longest chain 30 peptides. Score 0.586 Round 4: 570 peptides, 67 chains. Longest chain 20 peptides. Score 0.594 Round 5: 580 peptides, 74 chains. Longest chain 23 peptides. Score 0.571 Taking the results from Round 4 Chains 75, Residues 503, Estimated correctness of the model 26.7 % 11 chains (120 residues) have been docked in sequence ------------------------------------------------------ 15845 reflections ( 99.92 % complete ) and 15651 restraints for refining 7565 atoms. 13181 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2149 (Rfree = 0.000) for 7565 atoms. Found 35 (51 requested) and removed 54 (28 requested) atoms. Cycle 27: After refmac, R = 0.2020 (Rfree = 0.000) for 7514 atoms. Found 17 (50 requested) and removed 33 (28 requested) atoms. Cycle 28: After refmac, R = 0.1946 (Rfree = 0.000) for 7471 atoms. Found 9 (50 requested) and removed 35 (28 requested) atoms. Cycle 29: After refmac, R = 0.1911 (Rfree = 0.000) for 7435 atoms. Found 14 (50 requested) and removed 35 (28 requested) atoms. Cycle 30: After refmac, R = 0.1863 (Rfree = 0.000) for 7405 atoms. Found 13 (49 requested) and removed 32 (27 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.22 3.18 Search for helices and strands: 0 residues in 0 chains, 7589 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 7603 seeds are put forward Round 1: 505 peptides, 84 chains. Longest chain 22 peptides. Score 0.425 Round 2: 552 peptides, 77 chains. Longest chain 21 peptides. Score 0.523 Round 3: 560 peptides, 69 chains. Longest chain 22 peptides. Score 0.573 Round 4: 568 peptides, 76 chains. Longest chain 24 peptides. Score 0.547 Round 5: 587 peptides, 82 chains. Longest chain 22 peptides. Score 0.538 Taking the results from Round 3 Chains 72, Residues 491, Estimated correctness of the model 19.6 % 5 chains (49 residues) have been docked in sequence ------------------------------------------------------ 15845 reflections ( 99.92 % complete ) and 16733 restraints for refining 7564 atoms. 14664 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2107 (Rfree = 0.000) for 7564 atoms. Found 44 (51 requested) and removed 36 (28 requested) atoms. Cycle 32: After refmac, R = 0.2015 (Rfree = 0.000) for 7542 atoms. Found 23 (51 requested) and removed 34 (28 requested) atoms. Cycle 33: After refmac, R = 0.1920 (Rfree = 0.000) for 7522 atoms. Found 14 (50 requested) and removed 30 (28 requested) atoms. Cycle 34: After refmac, R = 0.1882 (Rfree = 0.000) for 7497 atoms. Found 33 (50 requested) and removed 33 (28 requested) atoms. Cycle 35: After refmac, R = 0.1795 (Rfree = 0.000) for 7489 atoms. Found 21 (50 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, 7724 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 7745 seeds are put forward Round 1: 474 peptides, 78 chains. Longest chain 15 peptides. Score 0.418 Round 2: 538 peptides, 71 chains. Longest chain 20 peptides. Score 0.538 Round 3: 523 peptides, 69 chains. Longest chain 21 peptides. Score 0.531 Round 4: 546 peptides, 76 chains. Longest chain 27 peptides. Score 0.521 Round 5: 558 peptides, 73 chains. Longest chain 22 peptides. Score 0.551 Taking the results from Round 5 Chains 76, Residues 485, Estimated correctness of the model 11.9 % 5 chains (37 residues) have been docked in sequence ------------------------------------------------------ 15845 reflections ( 99.92 % complete ) and 16729 restraints for refining 7564 atoms. 14730 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2150 (Rfree = 0.000) for 7564 atoms. Found 26 (51 requested) and removed 38 (28 requested) atoms. Cycle 37: After refmac, R = 0.2001 (Rfree = 0.000) for 7532 atoms. Found 13 (51 requested) and removed 38 (28 requested) atoms. Cycle 38: After refmac, R = 0.1949 (Rfree = 0.000) for 7498 atoms. Found 15 (50 requested) and removed 32 (28 requested) atoms. Cycle 39: After refmac, R = 0.1873 (Rfree = 0.000) for 7467 atoms. Found 10 (50 requested) and removed 36 (28 requested) atoms. Cycle 40: After refmac, R = 0.1853 (Rfree = 0.000) for 7434 atoms. Found 19 (50 requested) and removed 35 (28 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.20 3.16 Search for helices and strands: 0 residues in 0 chains, 7628 seeds are put forward NCS extension: 23 residues added (4 deleted due to clashes), 7651 seeds are put forward Round 1: 450 peptides, 80 chains. Longest chain 15 peptides. Score 0.373 Round 2: 471 peptides, 72 chains. Longest chain 21 peptides. Score 0.450 Round 3: 484 peptides, 72 chains. Longest chain 22 peptides. Score 0.467 Round 4: 488 peptides, 73 chains. Longest chain 18 peptides. Score 0.466 Round 5: 512 peptides, 73 chains. Longest chain 23 peptides. Score 0.496 Taking the results from Round 5 Chains 75, Residues 439, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 15845 reflections ( 99.92 % complete ) and 17274 restraints for refining 7565 atoms. 15553 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2015 (Rfree = 0.000) for 7565 atoms. Found 27 (51 requested) and removed 36 (28 requested) atoms. Cycle 42: After refmac, R = 0.1917 (Rfree = 0.000) for 7537 atoms. Found 19 (51 requested) and removed 32 (28 requested) atoms. Cycle 43: After refmac, R = 0.1835 (Rfree = 0.000) for 7510 atoms. Found 15 (50 requested) and removed 31 (28 requested) atoms. Cycle 44: After refmac, R = 0.1791 (Rfree = 0.000) for 7483 atoms. Found 12 (50 requested) and removed 32 (28 requested) atoms. Cycle 45: After refmac, R = 0.1729 (Rfree = 0.000) for 7462 atoms. Found 8 (50 requested) and removed 33 (28 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.19 3.15 Search for helices and strands: 0 residues in 0 chains, 7664 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 7694 seeds are put forward Round 1: 401 peptides, 74 chains. Longest chain 14 peptides. Score 0.339 Round 2: 472 peptides, 75 chains. Longest chain 20 peptides. Score 0.433 Round 3: 475 peptides, 73 chains. Longest chain 16 peptides. Score 0.449 Round 4: 451 peptides, 66 chains. Longest chain 16 peptides. Score 0.458 Round 5: 462 peptides, 67 chains. Longest chain 20 peptides. Score 0.467 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 68, Residues 395, Estimated correctness of the model 0.0 % 2 chains (18 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 68 chains (395 residues) following loop building 2 chains (18 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 15845 reflections ( 99.92 % complete ) and 17347 restraints for refining 7565 atoms. 15765 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1936 (Rfree = 0.000) for 7565 atoms. Found 0 (51 requested) and removed 28 (28 requested) atoms. Cycle 47: After refmac, R = 0.1881 (Rfree = 0.000) for 7519 atoms. Found 0 (50 requested) and removed 28 (28 requested) atoms. Cycle 48: After refmac, R = 0.1860 (Rfree = 0.000) for 7480 atoms. Found 0 (50 requested) and removed 28 (28 requested) atoms. Cycle 49: After refmac, R = 0.1811 (Rfree = 0.000) for 7441 atoms. TimeTaking 73.15