Mon 24 Dec 07:33:25 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 1vm8-2.5-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vm8-2.5-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vm8-2.5-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vm8-2.5-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/1vm8-2.5-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vm8-2.5-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 07:33:29 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/1vm8-2.5-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vm8-2.5-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 1004 and 0 Target number of residues in the AU: 1004 Target solvent content: 0.5622 Checking the provided sequence file Detected sequence length: 534 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 1068 Adjusted target solvent content: 0.53 Input MTZ file: 1vm8-2.5-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: 80.094 73.402 107.132 90.000 99.827 90.000 Input sequence file: 1vm8-2.5-parrot-noncs.fasta_lf Building free atoms model in initial map for 8544 target number of atoms Had to go as low as 0.50 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: 105.560 2.500 Wilson plot Bfac: 39.13 42288 reflections ( 99.19 % complete ) and 0 restraints for refining 9517 atoms. Observations/parameters ratio is 1.11 ------------------------------------------------------ Starting model: R = 0.3437 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2526 (Rfree = 0.000) for 9517 atoms. Found 121 (172 requested) and removed 190 (86 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.56 2.46 NCS extension: 0 residues added, 9448 seeds are put forward Round 1: 460 peptides, 91 chains. Longest chain 13 peptides. Score 0.311 Round 2: 525 peptides, 92 chains. Longest chain 15 peptides. Score 0.394 Round 3: 578 peptides, 96 chains. Longest chain 19 peptides. Score 0.439 Round 4: 576 peptides, 91 chains. Longest chain 36 peptides. Score 0.462 Round 5: 597 peptides, 83 chains. Longest chain 42 peptides. Score 0.527 Taking the results from Round 5 Chains 86, Residues 514, Estimated correctness of the model 63.3 % 10 chains (101 residues) have been docked in sequence ------------------------------------------------------ 42288 reflections ( 99.19 % complete ) and 16688 restraints for refining 8004 atoms. 14362 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2989 (Rfree = 0.000) for 8004 atoms. Found 108 (145 requested) and removed 94 (72 requested) atoms. Cycle 2: After refmac, R = 0.2888 (Rfree = 0.000) for 7970 atoms. Found 106 (145 requested) and removed 82 (72 requested) atoms. Cycle 3: After refmac, R = 0.2803 (Rfree = 0.000) for 7960 atoms. Found 112 (144 requested) and removed 89 (72 requested) atoms. Cycle 4: After refmac, R = 0.2673 (Rfree = 0.000) for 7963 atoms. Found 72 (144 requested) and removed 78 (72 requested) atoms. Cycle 5: After refmac, R = 0.2616 (Rfree = 0.000) for 7944 atoms. Found 90 (144 requested) and removed 76 (72 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.56 2.46 NCS extension: 35 residues added (3 deleted due to clashes), 8071 seeds are put forward Round 1: 534 peptides, 88 chains. Longest chain 15 peptides. Score 0.427 Round 2: 577 peptides, 80 chains. Longest chain 20 peptides. Score 0.520 Round 3: 587 peptides, 77 chains. Longest chain 41 peptides. Score 0.545 Round 4: 590 peptides, 74 chains. Longest chain 28 peptides. Score 0.563 Round 5: 602 peptides, 78 chains. Longest chain 41 peptides. Score 0.556 Taking the results from Round 4 Chains 76, Residues 516, Estimated correctness of the model 68.3 % 7 chains (86 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 42288 reflections ( 99.19 % complete ) and 16709 restraints for refining 8006 atoms. 14399 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2738 (Rfree = 0.000) for 8006 atoms. Found 111 (145 requested) and removed 86 (72 requested) atoms. Cycle 7: After refmac, R = 0.2591 (Rfree = 0.000) for 8014 atoms. Found 103 (145 requested) and removed 79 (72 requested) atoms. Cycle 8: After refmac, R = 0.2522 (Rfree = 0.000) for 8030 atoms. Found 74 (145 requested) and removed 75 (72 requested) atoms. Cycle 9: After refmac, R = 0.2412 (Rfree = 0.000) for 8016 atoms. Found 76 (145 requested) and removed 74 (72 requested) atoms. Cycle 10: After refmac, R = 0.2351 (Rfree = 0.000) for 8010 atoms. Found 80 (145 requested) and removed 74 (72 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.55 2.45 NCS extension: 9 residues added (4 deleted due to clashes), 8068 seeds are put forward Round 1: 542 peptides, 75 chains. Longest chain 28 peptides. Score 0.505 Round 2: 599 peptides, 71 chains. Longest chain 31 peptides. Score 0.586 Round 3: 585 peptides, 65 chains. Longest chain 39 peptides. Score 0.600 Round 4: 593 peptides, 67 chains. Longest chain 29 peptides. Score 0.598 Round 5: 601 peptides, 69 chains. Longest chain 29 peptides. Score 0.597 Taking the results from Round 3 Chains 73, Residues 520, Estimated correctness of the model 73.0 % 11 chains (127 residues) have been docked in sequence ------------------------------------------------------ 42288 reflections ( 99.19 % complete ) and 15830 restraints for refining 8006 atoms. 13361 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2665 (Rfree = 0.000) for 8006 atoms. Found 137 (145 requested) and removed 92 (72 requested) atoms. Cycle 12: After refmac, R = 0.2525 (Rfree = 0.000) for 8035 atoms. Found 108 (146 requested) and removed 78 (73 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2507 (Rfree = 0.000) for 8052 atoms. Found 110 (146 requested) and removed 78 (73 requested) atoms. Cycle 14: After refmac, R = 0.2492 (Rfree = 0.000) for 8071 atoms. Found 88 (146 requested) and removed 75 (73 requested) atoms. Cycle 15: After refmac, R = 0.2489 (Rfree = 0.000) for 8075 atoms. Found 99 (146 requested) and removed 77 (73 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.56 2.46 NCS extension: 0 residues added, 8168 seeds are put forward Round 1: 542 peptides, 74 chains. Longest chain 28 peptides. Score 0.510 Round 2: 571 peptides, 61 chains. Longest chain 41 peptides. Score 0.604 Round 3: 563 peptides, 62 chains. Longest chain 42 peptides. Score 0.592 Round 4: 591 peptides, 72 chains. Longest chain 38 peptides. Score 0.573 Round 5: 559 peptides, 69 chains. Longest chain 38 peptides. Score 0.554 Taking the results from Round 2 Chains 62, Residues 510, Estimated correctness of the model 73.5 % 10 chains (166 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 42288 reflections ( 99.19 % complete ) and 15310 restraints for refining 8005 atoms. 12674 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2592 (Rfree = 0.000) for 8005 atoms. Found 127 (145 requested) and removed 77 (72 requested) atoms. Cycle 17: After refmac, R = 0.2581 (Rfree = 0.000) for 8039 atoms. Found 124 (146 requested) and removed 79 (73 requested) atoms. Cycle 18: After refmac, R = 0.2469 (Rfree = 0.000) for 8070 atoms. Found 102 (146 requested) and removed 75 (73 requested) atoms. Cycle 19: After refmac, R = 0.2496 (Rfree = 0.000) for 8083 atoms. Found 100 (146 requested) and removed 77 (73 requested) atoms. Cycle 20: After refmac, R = 0.2441 (Rfree = 0.000) for 8096 atoms. Found 91 (147 requested) and removed 74 (73 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.57 2.47 NCS extension: 17 residues added (6 deleted due to clashes), 8166 seeds are put forward Round 1: 547 peptides, 75 chains. Longest chain 37 peptides. Score 0.511 Round 2: 581 peptides, 67 chains. Longest chain 38 peptides. Score 0.586 Round 3: 594 peptides, 69 chains. Longest chain 39 peptides. Score 0.590 Round 4: 575 peptides, 65 chains. Longest chain 40 peptides. Score 0.590 Round 5: 581 peptides, 64 chains. Longest chain 37 peptides. Score 0.600 Taking the results from Round 5 Chains 70, Residues 517, Estimated correctness of the model 73.0 % 13 chains (183 residues) have been docked in sequence ------------------------------------------------------ 42288 reflections ( 99.19 % complete ) and 15165 restraints for refining 8006 atoms. 12471 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2588 (Rfree = 0.000) for 8006 atoms. Found 131 (145 requested) and removed 83 (72 requested) atoms. Cycle 22: After refmac, R = 0.2466 (Rfree = 0.000) for 8043 atoms. Found 96 (146 requested) and removed 76 (73 requested) atoms. Cycle 23: After refmac, R = 0.2386 (Rfree = 0.000) for 8050 atoms. Found 84 (146 requested) and removed 75 (73 requested) atoms. Cycle 24: After refmac, R = 0.2331 (Rfree = 0.000) for 8046 atoms. Found 84 (146 requested) and removed 73 (73 requested) atoms. Cycle 25: After refmac, R = 0.2309 (Rfree = 0.000) for 8052 atoms. Found 74 (146 requested) and removed 76 (73 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.54 2.44 NCS extension: 16 residues added (10 deleted due to clashes), 8076 seeds are put forward Round 1: 524 peptides, 65 chains. Longest chain 39 peptides. Score 0.536 Round 2: 562 peptides, 53 chains. Longest chain 39 peptides. Score 0.632 Round 3: 574 peptides, 57 chains. Longest chain 32 peptides. Score 0.625 Round 4: 579 peptides, 54 chains. Longest chain 32 peptides. Score 0.643 Round 5: 574 peptides, 58 chains. Longest chain 27 peptides. Score 0.621 Taking the results from Round 4 Chains 62, Residues 525, Estimated correctness of the model 78.1 % 13 chains (188 residues) have been docked in sequence ------------------------------------------------------ 42288 reflections ( 99.19 % complete ) and 14649 restraints for refining 8004 atoms. 11856 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2498 (Rfree = 0.000) for 8004 atoms. Found 124 (145 requested) and removed 75 (72 requested) atoms. Cycle 27: After refmac, R = 0.2422 (Rfree = 0.000) for 8038 atoms. Found 104 (146 requested) and removed 74 (73 requested) atoms. Cycle 28: After refmac, R = 0.2452 (Rfree = 0.000) for 8064 atoms. Found 93 (146 requested) and removed 79 (73 requested) atoms. Cycle 29: After refmac, R = 0.2417 (Rfree = 0.000) for 8076 atoms. Found 86 (146 requested) and removed 79 (73 requested) atoms. Cycle 30: After refmac, R = 0.2399 (Rfree = 0.000) for 8079 atoms. Found 87 (146 requested) and removed 76 (73 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.55 2.45 NCS extension: 11 residues added (2 deleted due to clashes), 8125 seeds are put forward Round 1: 556 peptides, 72 chains. Longest chain 29 peptides. Score 0.536 Round 2: 584 peptides, 60 chains. Longest chain 39 peptides. Score 0.621 Round 3: 588 peptides, 62 chains. Longest chain 39 peptides. Score 0.616 Round 4: 572 peptides, 56 chains. Longest chain 39 peptides. Score 0.628 Round 5: 571 peptides, 54 chains. Longest chain 39 peptides. Score 0.635 Taking the results from Round 5 Chains 55, Residues 517, Estimated correctness of the model 77.2 % 10 chains (157 residues) have been docked in sequence ------------------------------------------------------ 42288 reflections ( 99.19 % complete ) and 15138 restraints for refining 8006 atoms. 12504 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2525 (Rfree = 0.000) for 8006 atoms. Found 132 (145 requested) and removed 79 (72 requested) atoms. Cycle 32: After refmac, R = 0.2535 (Rfree = 0.000) for 8053 atoms. Found 124 (146 requested) and removed 76 (73 requested) atoms. Cycle 33: After refmac, R = 0.2485 (Rfree = 0.000) for 8098 atoms. Found 105 (146 requested) and removed 76 (73 requested) atoms. Cycle 34: After refmac, R = 0.2522 (Rfree = 0.000) for 8121 atoms. Found 120 (147 requested) and removed 77 (73 requested) atoms. Cycle 35: After refmac, R = 0.2488 (Rfree = 0.000) for 8159 atoms. Found 102 (148 requested) and removed 76 (74 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.54 2.44 NCS extension: 29 residues added (5 deleted due to clashes), 8234 seeds are put forward Round 1: 541 peptides, 66 chains. Longest chain 31 peptides. Score 0.550 Round 2: 552 peptides, 58 chains. Longest chain 39 peptides. Score 0.599 Round 3: 568 peptides, 59 chains. Longest chain 40 peptides. Score 0.610 Round 4: 557 peptides, 58 chains. Longest chain 40 peptides. Score 0.604 Round 5: 565 peptides, 61 chains. Longest chain 39 peptides. Score 0.598 Taking the results from Round 3 Chains 65, Residues 509, Estimated correctness of the model 74.2 % 13 chains (177 residues) have been docked in sequence ------------------------------------------------------ 42288 reflections ( 99.19 % complete ) and 14787 restraints for refining 8006 atoms. 12108 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2604 (Rfree = 0.000) for 8006 atoms. Found 145 (145 requested) and removed 81 (72 requested) atoms. Cycle 37: After refmac, R = 0.2552 (Rfree = 0.000) for 8058 atoms. Found 117 (146 requested) and removed 76 (73 requested) atoms. Cycle 38: After refmac, R = 0.2518 (Rfree = 0.000) for 8085 atoms. Found 123 (146 requested) and removed 77 (73 requested) atoms. Cycle 39: After refmac, R = 0.2485 (Rfree = 0.000) for 8119 atoms. Found 137 (147 requested) and removed 74 (73 requested) atoms. Cycle 40: After refmac, R = 0.2536 (Rfree = 0.000) for 8172 atoms. Found 124 (148 requested) and removed 79 (74 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.58 2.48 NCS extension: 9 residues added (5 deleted due to clashes), 8258 seeds are put forward Round 1: 524 peptides, 69 chains. Longest chain 25 peptides. Score 0.516 Round 2: 549 peptides, 60 chains. Longest chain 27 peptides. Score 0.587 Round 3: 573 peptides, 62 chains. Longest chain 33 peptides. Score 0.601 Round 4: 556 peptides, 58 chains. Longest chain 45 peptides. Score 0.603 Round 5: 560 peptides, 65 chains. Longest chain 31 peptides. Score 0.574 Taking the results from Round 4 Chains 61, Residues 498, Estimated correctness of the model 73.4 % 8 chains (136 residues) have been docked in sequence ------------------------------------------------------ 42288 reflections ( 99.19 % complete ) and 15351 restraints for refining 8006 atoms. 12875 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2556 (Rfree = 0.000) for 8006 atoms. Found 121 (145 requested) and removed 78 (72 requested) atoms. Cycle 42: After refmac, R = 0.2504 (Rfree = 0.000) for 8044 atoms. Found 113 (145 requested) and removed 77 (72 requested) atoms. Cycle 43: After refmac, R = 0.2457 (Rfree = 0.000) for 8070 atoms. Found 100 (146 requested) and removed 75 (73 requested) atoms. Cycle 44: After refmac, R = 0.2443 (Rfree = 0.000) for 8084 atoms. Found 103 (146 requested) and removed 75 (73 requested) atoms. Cycle 45: After refmac, R = 0.2467 (Rfree = 0.000) for 8099 atoms. Found 116 (147 requested) and removed 77 (73 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.56 2.46 NCS extension: 37 residues added (14 deleted due to clashes), 8197 seeds are put forward Round 1: 504 peptides, 66 chains. Longest chain 25 peptides. Score 0.508 Round 2: 540 peptides, 54 chains. Longest chain 26 peptides. Score 0.606 Round 3: 549 peptides, 58 chains. Longest chain 26 peptides. Score 0.596 Round 4: 569 peptides, 56 chains. Longest chain 33 peptides. Score 0.625 Round 5: 538 peptides, 57 chains. Longest chain 31 peptides. Score 0.590 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 61, Residues 513, Estimated correctness of the model 76.0 % 9 chains (159 residues) have been docked in sequence Sequence coverage is 30 % Consider running further cycles of model building using 1vm8-2_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 168 A and 182 A Built loop between residues 272 A and 275 A 57 chains (517 residues) following loop building 7 chains (174 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 42288 reflections ( 99.19 % complete ) and 14625 restraints for refining 8005 atoms. 11944 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2603 (Rfree = 0.000) for 8005 atoms. Found 0 (145 requested) and removed 46 (72 requested) atoms. Cycle 47: After refmac, R = 0.2518 (Rfree = 0.000) for 7944 atoms. Found 0 (144 requested) and removed 38 (72 requested) atoms. Cycle 48: After refmac, R = 0.2487 (Rfree = 0.000) for 7895 atoms. Found 0 (143 requested) and removed 53 (71 requested) atoms. Cycle 49: After refmac, R = 0.2447 (Rfree = 0.000) for 7833 atoms. TimeTaking 90.02