null Mon 24 Dec 07:54:40 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 1vl5-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vl5-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vl5-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.2-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/1vl5-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.2-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 07:54:45 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/1vl5-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.2-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 835 and 0 Target number of residues in the AU: 835 Target solvent content: 0.6099 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: 1vl5-3.2-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: 4 Cell parameters: 64.006 87.475 105.236 90.000 100.573 90.000 Input sequence file: 1vl5-3.2-parrot-noncs.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 3.200 Wilson plot Bfac: 56.78 19002 reflections ( 99.93 % complete ) and 0 restraints for refining 9171 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.3230 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2565 (Rfree = 0.000) for 9171 atoms. Found 48 (82 requested) and removed 76 (41 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.08 3.04 Search for helices and strands: 0 residues in 0 chains, 9316 seeds are put forward NCS extension: 0 residues added, 9316 seeds are put forward Round 1: 509 peptides, 93 chains. Longest chain 15 peptides. Score 0.378 Round 2: 586 peptides, 81 chains. Longest chain 19 peptides. Score 0.542 Round 3: 607 peptides, 80 chains. Longest chain 24 peptides. Score 0.571 Round 4: 631 peptides, 78 chains. Longest chain 24 peptides. Score 0.605 Round 5: 636 peptides, 78 chains. Longest chain 23 peptides. Score 0.610 Taking the results from Round 5 Chains 83, Residues 558, Estimated correctness of the model 43.7 % 7 chains (66 residues) have been docked in sequence ------------------------------------------------------ 19002 reflections ( 99.93 % complete ) and 16252 restraints for refining 7593 atoms. 13868 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2532 (Rfree = 0.000) for 7593 atoms. Found 68 (68 requested) and removed 54 (34 requested) atoms. Cycle 2: After refmac, R = 0.2333 (Rfree = 0.000) for 7528 atoms. Found 36 (68 requested) and removed 41 (34 requested) atoms. Cycle 3: After refmac, R = 0.2236 (Rfree = 0.000) for 7485 atoms. Found 36 (67 requested) and removed 37 (33 requested) atoms. Cycle 4: After refmac, R = 0.2136 (Rfree = 0.000) for 7458 atoms. Found 20 (67 requested) and removed 37 (33 requested) atoms. Cycle 5: After refmac, R = 0.2089 (Rfree = 0.000) for 7419 atoms. Found 15 (66 requested) and removed 33 (33 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.08 3.04 Search for helices and strands: 0 residues in 0 chains, 7638 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 7652 seeds are put forward Round 1: 560 peptides, 84 chains. Longest chain 22 peptides. Score 0.496 Round 2: 655 peptides, 87 chains. Longest chain 25 peptides. Score 0.588 Round 3: 635 peptides, 78 chains. Longest chain 27 peptides. Score 0.609 Round 4: 653 peptides, 75 chains. Longest chain 30 peptides. Score 0.640 Round 5: 630 peptides, 78 chains. Longest chain 23 peptides. Score 0.604 Taking the results from Round 4 Chains 79, Residues 578, Estimated correctness of the model 51.4 % 6 chains (83 residues) have been docked in sequence ------------------------------------------------------ 19002 reflections ( 99.93 % complete ) and 15990 restraints for refining 7595 atoms. 13376 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2407 (Rfree = 0.000) for 7595 atoms. Found 50 (68 requested) and removed 55 (34 requested) atoms. Cycle 7: After refmac, R = 0.2312 (Rfree = 0.000) for 7545 atoms. Found 25 (68 requested) and removed 45 (34 requested) atoms. Cycle 8: After refmac, R = 0.2178 (Rfree = 0.000) for 7497 atoms. Found 18 (67 requested) and removed 40 (33 requested) atoms. Cycle 9: After refmac, R = 0.2128 (Rfree = 0.000) for 7460 atoms. Found 12 (67 requested) and removed 33 (33 requested) atoms. Cycle 10: After refmac, R = 0.2059 (Rfree = 0.000) for 7418 atoms. Found 12 (66 requested) and removed 35 (33 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.05 3.01 Search for helices and strands: 0 residues in 0 chains, 7632 seeds are put forward NCS extension: 11 residues added (6 deleted due to clashes), 7643 seeds are put forward Round 1: 617 peptides, 82 chains. Longest chain 30 peptides. Score 0.572 Round 2: 657 peptides, 86 chains. Longest chain 23 peptides. Score 0.595 Round 3: 672 peptides, 75 chains. Longest chain 37 peptides. Score 0.658 Round 4: 658 peptides, 77 chains. Longest chain 45 peptides. Score 0.636 Round 5: 641 peptides, 75 chains. Longest chain 32 peptides. Score 0.629 Taking the results from Round 3 Chains 82, Residues 597, Estimated correctness of the model 55.7 % 8 chains (130 residues) have been docked in sequence ------------------------------------------------------ 19002 reflections ( 99.93 % complete ) and 15257 restraints for refining 7595 atoms. 12375 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2384 (Rfree = 0.000) for 7595 atoms. Found 56 (68 requested) and removed 66 (34 requested) atoms. Cycle 12: After refmac, R = 0.2190 (Rfree = 0.000) for 7554 atoms. Found 16 (68 requested) and removed 42 (34 requested) atoms. Cycle 13: After refmac, R = 0.2138 (Rfree = 0.000) for 7500 atoms. Found 12 (67 requested) and removed 38 (33 requested) atoms. Cycle 14: After refmac, R = 0.2111 (Rfree = 0.000) for 7459 atoms. Found 24 (67 requested) and removed 40 (33 requested) atoms. Cycle 15: After refmac, R = 0.2047 (Rfree = 0.000) for 7425 atoms. Found 17 (66 requested) and removed 37 (33 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.08 3.04 Search for helices and strands: 0 residues in 0 chains, 7631 seeds are put forward NCS extension: 9 residues added (5 deleted due to clashes), 7640 seeds are put forward Round 1: 581 peptides, 77 chains. Longest chain 22 peptides. Score 0.557 Round 2: 625 peptides, 78 chains. Longest chain 26 peptides. Score 0.599 Round 3: 632 peptides, 79 chains. Longest chain 31 peptides. Score 0.602 Round 4: 625 peptides, 75 chains. Longest chain 25 peptides. Score 0.613 Round 5: 594 peptides, 71 chains. Longest chain 38 peptides. Score 0.600 Taking the results from Round 4 Chains 79, Residues 550, Estimated correctness of the model 44.5 % 8 chains (94 residues) have been docked in sequence ------------------------------------------------------ 19002 reflections ( 99.93 % complete ) and 15917 restraints for refining 7595 atoms. 13366 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2339 (Rfree = 0.000) for 7595 atoms. Found 46 (68 requested) and removed 51 (34 requested) atoms. Cycle 17: After refmac, R = 0.2139 (Rfree = 0.000) for 7559 atoms. Found 16 (68 requested) and removed 42 (34 requested) atoms. Cycle 18: After refmac, R = 0.2084 (Rfree = 0.000) for 7517 atoms. Found 5 (67 requested) and removed 36 (33 requested) atoms. Cycle 19: After refmac, R = 0.2046 (Rfree = 0.000) for 7478 atoms. Found 16 (67 requested) and removed 33 (33 requested) atoms. Cycle 20: After refmac, R = 0.2034 (Rfree = 0.000) for 7452 atoms. Found 12 (66 requested) and removed 35 (33 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.08 3.04 Search for helices and strands: 0 residues in 0 chains, 7648 seeds are put forward NCS extension: 15 residues added (7 deleted due to clashes), 7663 seeds are put forward Round 1: 572 peptides, 80 chains. Longest chain 27 peptides. Score 0.531 Round 2: 607 peptides, 64 chains. Longest chain 27 peptides. Score 0.645 Round 3: 632 peptides, 77 chains. Longest chain 29 peptides. Score 0.611 Round 4: 607 peptides, 71 chains. Longest chain 30 peptides. Score 0.613 Round 5: 603 peptides, 75 chains. Longest chain 23 peptides. Score 0.590 Taking the results from Round 2 Chains 67, Residues 543, Estimated correctness of the model 52.6 % 10 chains (134 residues) have been docked in sequence ------------------------------------------------------ 19002 reflections ( 99.93 % complete ) and 15393 restraints for refining 7594 atoms. 12720 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2233 (Rfree = 0.000) for 7594 atoms. Found 44 (68 requested) and removed 55 (34 requested) atoms. Cycle 22: After refmac, R = 0.2127 (Rfree = 0.000) for 7561 atoms. Found 24 (68 requested) and removed 43 (34 requested) atoms. Cycle 23: After refmac, R = 0.2039 (Rfree = 0.000) for 7528 atoms. Found 10 (67 requested) and removed 34 (33 requested) atoms. Cycle 24: After refmac, R = 0.2001 (Rfree = 0.000) for 7489 atoms. Found 19 (67 requested) and removed 33 (33 requested) atoms. Cycle 25: After refmac, R = 0.1944 (Rfree = 0.000) for 7469 atoms. Found 4 (67 requested) and removed 34 (33 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.06 3.02 Search for helices and strands: 0 residues in 0 chains, 7652 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 7673 seeds are put forward Round 1: 547 peptides, 85 chains. Longest chain 25 peptides. Score 0.474 Round 2: 603 peptides, 76 chains. Longest chain 27 peptides. Score 0.586 Round 3: 611 peptides, 81 chains. Longest chain 30 peptides. Score 0.570 Round 4: 606 peptides, 72 chains. Longest chain 29 peptides. Score 0.608 Round 5: 611 peptides, 73 chains. Longest chain 26 peptides. Score 0.608 Taking the results from Round 5 Chains 77, Residues 538, Estimated correctness of the model 43.2 % 6 chains (60 residues) have been docked in sequence ------------------------------------------------------ 19002 reflections ( 99.93 % complete ) and 16523 restraints for refining 7596 atoms. 14221 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2228 (Rfree = 0.000) for 7596 atoms. Found 49 (68 requested) and removed 42 (34 requested) atoms. Cycle 27: After refmac, R = 0.2132 (Rfree = 0.000) for 7595 atoms. Found 18 (68 requested) and removed 36 (34 requested) atoms. Cycle 28: After refmac, R = 0.2042 (Rfree = 0.000) for 7567 atoms. Found 14 (68 requested) and removed 36 (34 requested) atoms. Cycle 29: After refmac, R = 0.1958 (Rfree = 0.000) for 7534 atoms. Found 11 (67 requested) and removed 35 (33 requested) atoms. Cycle 30: After refmac, R = 0.1906 (Rfree = 0.000) for 7500 atoms. Found 7 (67 requested) and removed 33 (33 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.07 3.03 Search for helices and strands: 0 residues in 0 chains, 7703 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 7721 seeds are put forward Round 1: 517 peptides, 80 chains. Longest chain 22 peptides. Score 0.464 Round 2: 571 peptides, 73 chains. Longest chain 25 peptides. Score 0.566 Round 3: 557 peptides, 74 chains. Longest chain 20 peptides. Score 0.545 Round 4: 546 peptides, 73 chains. Longest chain 20 peptides. Score 0.537 Round 5: 563 peptides, 69 chains. Longest chain 21 peptides. Score 0.577 Taking the results from Round 5 Chains 69, Residues 494, Estimated correctness of the model 34.7 % 6 chains (68 residues) have been docked in sequence ------------------------------------------------------ 19002 reflections ( 99.93 % complete ) and 16469 restraints for refining 7596 atoms. 14306 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2137 (Rfree = 0.000) for 7596 atoms. Found 32 (68 requested) and removed 48 (34 requested) atoms. Cycle 32: After refmac, R = 0.2068 (Rfree = 0.000) for 7555 atoms. Found 14 (68 requested) and removed 38 (34 requested) atoms. Cycle 33: After refmac, R = 0.1947 (Rfree = 0.000) for 7522 atoms. Found 16 (67 requested) and removed 33 (33 requested) atoms. Cycle 34: After refmac, R = 0.1892 (Rfree = 0.000) for 7494 atoms. Found 14 (67 requested) and removed 34 (33 requested) atoms. Cycle 35: After refmac, R = 0.1811 (Rfree = 0.000) for 7470 atoms. Found 6 (67 requested) and removed 33 (33 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.07 3.03 Search for helices and strands: 0 residues in 0 chains, 7664 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 7689 seeds are put forward Round 1: 488 peptides, 81 chains. Longest chain 15 peptides. Score 0.420 Round 2: 530 peptides, 75 chains. Longest chain 20 peptides. Score 0.508 Round 3: 559 peptides, 80 chains. Longest chain 20 peptides. Score 0.516 Round 4: 569 peptides, 78 chains. Longest chain 23 peptides. Score 0.538 Round 5: 567 peptides, 80 chains. Longest chain 22 peptides. Score 0.525 Taking the results from Round 4 Chains 78, Residues 491, Estimated correctness of the model 23.3 % 7 chains (75 residues) have been docked in sequence ------------------------------------------------------ 19002 reflections ( 99.93 % complete ) and 16379 restraints for refining 7596 atoms. 14150 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2087 (Rfree = 0.000) for 7596 atoms. Found 42 (68 requested) and removed 40 (34 requested) atoms. Cycle 37: After refmac, R = 0.1967 (Rfree = 0.000) for 7583 atoms. Found 16 (68 requested) and removed 39 (34 requested) atoms. Cycle 38: After refmac, R = 0.1909 (Rfree = 0.000) for 7545 atoms. Found 19 (67 requested) and removed 34 (33 requested) atoms. Cycle 39: After refmac, R = 0.1843 (Rfree = 0.000) for 7517 atoms. Found 14 (67 requested) and removed 33 (33 requested) atoms. Cycle 40: After refmac, R = 0.1779 (Rfree = 0.000) for 7491 atoms. Found 14 (67 requested) and removed 34 (33 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.06 3.02 Search for helices and strands: 0 residues in 0 chains, 7694 seeds are put forward NCS extension: 26 residues added (4 deleted due to clashes), 7720 seeds are put forward Round 1: 486 peptides, 75 chains. Longest chain 34 peptides. Score 0.452 Round 2: 514 peptides, 70 chains. Longest chain 20 peptides. Score 0.515 Round 3: 538 peptides, 73 chains. Longest chain 22 peptides. Score 0.528 Round 4: 530 peptides, 68 chains. Longest chain 21 peptides. Score 0.545 Round 5: 520 peptides, 68 chains. Longest chain 29 peptides. Score 0.533 Taking the results from Round 4 Chains 69, Residues 462, Estimated correctness of the model 25.4 % 5 chains (58 residues) have been docked in sequence ------------------------------------------------------ 19002 reflections ( 99.93 % complete ) and 16659 restraints for refining 7595 atoms. 14638 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2016 (Rfree = 0.000) for 7595 atoms. Found 40 (68 requested) and removed 40 (34 requested) atoms. Cycle 42: After refmac, R = 0.1913 (Rfree = 0.000) for 7582 atoms. Found 21 (68 requested) and removed 37 (34 requested) atoms. Cycle 43: After refmac, R = 0.1841 (Rfree = 0.000) for 7557 atoms. Found 19 (67 requested) and removed 35 (33 requested) atoms. Cycle 44: After refmac, R = 0.1786 (Rfree = 0.000) for 7537 atoms. Found 12 (67 requested) and removed 33 (33 requested) atoms. Cycle 45: After refmac, R = 0.1740 (Rfree = 0.000) for 7513 atoms. Found 6 (67 requested) and removed 33 (33 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.06 3.02 Search for helices and strands: 0 residues in 0 chains, 7708 seeds are put forward NCS extension: 18 residues added (8 deleted due to clashes), 7726 seeds are put forward Round 1: 467 peptides, 76 chains. Longest chain 20 peptides. Score 0.421 Round 2: 509 peptides, 72 chains. Longest chain 25 peptides. Score 0.498 Round 3: 513 peptides, 72 chains. Longest chain 17 peptides. Score 0.503 Round 4: 494 peptides, 70 chains. Longest chain 22 peptides. Score 0.491 Round 5: 491 peptides, 72 chains. Longest chain 16 peptides. Score 0.476 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 72, Residues 441, Estimated correctness of the model 12.3 % 1 chains (16 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vl5-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 19002 reflections ( 99.93 % complete ) and 17359 restraints for refining 7596 atoms. 15597 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1937 (Rfree = 0.000) for 7596 atoms. Found 0 (68 requested) and removed 21 (34 requested) atoms. Cycle 47: After refmac, R = 0.1925 (Rfree = 0.000) for 7568 atoms. Found 0 (67 requested) and removed 15 (33 requested) atoms. Cycle 48: After refmac, R = 0.1867 (Rfree = 0.000) for 7545 atoms. Found 0 (67 requested) and removed 16 (33 requested) atoms. Cycle 49: After refmac, R = 0.1831 (Rfree = 0.000) for 7525 atoms. Found 0 (67 requested) and removed 17 (33 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:17:18 GMT 2018 Job finished. TimeTaking 82.64 Used memory is bytes: 19054904