Mon 24 Dec 07:48:13 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 1vl6-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vl6-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vl6-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl6-3.8-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/1vl6-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl6-3.8-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 07:48:17 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/1vl6-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl6-3.8-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 1214 and 0 Target number of residues in the AU: 1214 Target solvent content: 0.6639 Checking the provided sequence file Detected sequence length: 388 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1552 Adjusted target solvent content: 0.57 Input MTZ file: 1vl6-3.8-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: 170 Cell parameters: 144.124 144.124 163.018 90.000 90.000 120.000 Input sequence file: 1vl6-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 12416 target number of atoms Had to go as low as 0.90 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: 124.815 3.800 Wilson plot Bfac: 87.74 18938 reflections ( 99.85 % complete ) and 0 restraints for refining 13831 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3390 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3404 (Rfree = 0.000) for 13831 atoms. Found 76 (76 requested) and removed 90 (38 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.72 3.39 Search for helices and strands: 0 residues in 0 chains, 14088 seeds are put forward NCS extension: 0 residues added, 14088 seeds are put forward Round 1: 511 peptides, 98 chains. Longest chain 12 peptides. Score 0.292 Round 2: 685 peptides, 105 chains. Longest chain 19 peptides. Score 0.420 Round 3: 716 peptides, 105 chains. Longest chain 19 peptides. Score 0.445 Round 4: 756 peptides, 109 chains. Longest chain 21 peptides. Score 0.463 Round 5: 756 peptides, 99 chains. Longest chain 25 peptides. Score 0.497 Taking the results from Round 5 Chains 100, Residues 657, Estimated correctness of the model 0.0 % 7 chains (49 residues) have been docked in sequence ------------------------------------------------------ 18938 reflections ( 99.85 % complete ) and 26303 restraints for refining 11226 atoms. 23630 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3034 (Rfree = 0.000) for 11226 atoms. Found 61 (61 requested) and removed 100 (30 requested) atoms. Cycle 2: After refmac, R = 0.2977 (Rfree = 0.000) for 10869 atoms. Found 61 (61 requested) and removed 68 (30 requested) atoms. Cycle 3: After refmac, R = 0.2901 (Rfree = 0.000) for 10683 atoms. Found 59 (59 requested) and removed 69 (29 requested) atoms. Cycle 4: After refmac, R = 0.2803 (Rfree = 0.000) for 10500 atoms. Found 58 (58 requested) and removed 62 (29 requested) atoms. Cycle 5: After refmac, R = 0.2816 (Rfree = 0.000) for 10374 atoms. Found 57 (57 requested) and removed 57 (28 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.65 3.32 Search for helices and strands: 0 residues in 0 chains, 10737 seeds are put forward NCS extension: 30 residues added (3 deleted due to clashes), 10767 seeds are put forward Round 1: 692 peptides, 124 chains. Longest chain 16 peptides. Score 0.355 Round 2: 819 peptides, 116 chains. Longest chain 25 peptides. Score 0.487 Round 3: 820 peptides, 114 chains. Longest chain 27 peptides. Score 0.494 Round 4: 829 peptides, 113 chains. Longest chain 27 peptides. Score 0.504 Round 5: 840 peptides, 105 chains. Longest chain 28 peptides. Score 0.538 Taking the results from Round 5 Chains 112, Residues 735, Estimated correctness of the model 0.0 % 11 chains (119 residues) have been docked in sequence ------------------------------------------------------ 18938 reflections ( 99.85 % complete ) and 22393 restraints for refining 10576 atoms. 19154 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2827 (Rfree = 0.000) for 10576 atoms. Found 58 (58 requested) and removed 99 (29 requested) atoms. Cycle 7: After refmac, R = 0.2642 (Rfree = 0.000) for 10392 atoms. Found 57 (57 requested) and removed 68 (28 requested) atoms. Cycle 8: After refmac, R = 0.2580 (Rfree = 0.000) for 10289 atoms. Found 57 (57 requested) and removed 54 (28 requested) atoms. Cycle 9: After refmac, R = 0.2501 (Rfree = 0.000) for 10210 atoms. Found 56 (56 requested) and removed 56 (28 requested) atoms. Cycle 10: After refmac, R = 0.2191 (Rfree = 0.000) for 10165 atoms. Found 25 (56 requested) and removed 42 (28 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.65 3.32 Search for helices and strands: 0 residues in 0 chains, 10506 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 10535 seeds are put forward Round 1: 711 peptides, 122 chains. Longest chain 21 peptides. Score 0.379 Round 2: 796 peptides, 110 chains. Longest chain 20 peptides. Score 0.490 Round 3: 800 peptides, 111 chains. Longest chain 29 peptides. Score 0.489 Round 4: 794 peptides, 103 chains. Longest chain 26 peptides. Score 0.512 Round 5: 804 peptides, 107 chains. Longest chain 23 peptides. Score 0.506 Taking the results from Round 4 Chains 108, Residues 691, Estimated correctness of the model 0.0 % 5 chains (49 residues) have been docked in sequence ------------------------------------------------------ 18938 reflections ( 99.85 % complete ) and 24399 restraints for refining 10983 atoms. 21582 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2728 (Rfree = 0.000) for 10983 atoms. Found 60 (60 requested) and removed 112 (30 requested) atoms. Cycle 12: After refmac, R = 0.2624 (Rfree = 0.000) for 10789 atoms. Found 60 (60 requested) and removed 71 (30 requested) atoms. Cycle 13: After refmac, R = 0.2598 (Rfree = 0.000) for 10677 atoms. Found 59 (59 requested) and removed 73 (29 requested) atoms. Cycle 14: After refmac, R = 0.2236 (Rfree = 0.000) for 10585 atoms. Found 32 (58 requested) and removed 55 (29 requested) atoms. Cycle 15: After refmac, R = 0.2145 (Rfree = 0.000) for 10507 atoms. Found 25 (58 requested) and removed 43 (29 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.67 3.34 Search for helices and strands: 0 residues in 0 chains, 10812 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 10826 seeds are put forward Round 1: 685 peptides, 123 chains. Longest chain 15 peptides. Score 0.353 Round 2: 809 peptides, 125 chains. Longest chain 15 peptides. Score 0.449 Round 3: 796 peptides, 111 chains. Longest chain 18 peptides. Score 0.486 Round 4: 791 peptides, 111 chains. Longest chain 19 peptides. Score 0.483 Round 5: 802 peptides, 111 chains. Longest chain 19 peptides. Score 0.491 Taking the results from Round 5 Chains 111, Residues 691, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 18938 reflections ( 99.85 % complete ) and 25652 restraints for refining 11202 atoms. 22961 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2747 (Rfree = 0.000) for 11202 atoms. Found 61 (61 requested) and removed 113 (30 requested) atoms. Cycle 17: After refmac, R = 0.2582 (Rfree = 0.000) for 11027 atoms. Found 61 (61 requested) and removed 87 (30 requested) atoms. Cycle 18: After refmac, R = 0.2604 (Rfree = 0.000) for 10895 atoms. Found 60 (60 requested) and removed 66 (30 requested) atoms. Cycle 19: After refmac, R = 0.2463 (Rfree = 0.000) for 10807 atoms. Found 59 (59 requested) and removed 52 (29 requested) atoms. Cycle 20: After refmac, R = 0.2187 (Rfree = 0.000) for 10739 atoms. Found 24 (59 requested) and removed 41 (29 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.65 3.32 Search for helices and strands: 0 residues in 0 chains, 11094 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 11111 seeds are put forward Round 1: 665 peptides, 123 chains. Longest chain 15 peptides. Score 0.335 Round 2: 717 peptides, 112 chains. Longest chain 23 peptides. Score 0.421 Round 3: 734 peptides, 109 chains. Longest chain 23 peptides. Score 0.445 Round 4: 733 peptides, 111 chains. Longest chain 22 peptides. Score 0.437 Round 5: 745 peptides, 108 chains. Longest chain 25 peptides. Score 0.458 Taking the results from Round 5 Chains 108, Residues 637, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 18938 reflections ( 99.85 % complete ) and 25757 restraints for refining 11229 atoms. 23269 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2677 (Rfree = 0.000) for 11229 atoms. Found 61 (61 requested) and removed 84 (30 requested) atoms. Cycle 22: After refmac, R = 0.2576 (Rfree = 0.000) for 11065 atoms. Found 61 (61 requested) and removed 58 (30 requested) atoms. Cycle 23: After refmac, R = 0.2106 (Rfree = 0.000) for 10950 atoms. Found 33 (60 requested) and removed 61 (30 requested) atoms. Cycle 24: After refmac, R = 0.2008 (Rfree = 0.000) for 10857 atoms. Found 24 (60 requested) and removed 46 (30 requested) atoms. Cycle 25: After refmac, R = 0.2071 (Rfree = 0.000) for 10813 atoms. Found 41 (59 requested) and removed 45 (29 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.65 3.32 Search for helices and strands: 0 residues in 0 chains, 11164 seeds are put forward NCS extension: 48 residues added (3 deleted due to clashes), 11212 seeds are put forward Round 1: 614 peptides, 121 chains. Longest chain 15 peptides. Score 0.297 Round 2: 698 peptides, 119 chains. Longest chain 19 peptides. Score 0.379 Round 3: 771 peptides, 124 chains. Longest chain 18 peptides. Score 0.422 Round 4: 725 peptides, 114 chains. Longest chain 20 peptides. Score 0.420 Round 5: 719 peptides, 111 chains. Longest chain 18 peptides. Score 0.426 Taking the results from Round 5 Chains 114, Residues 608, Estimated correctness of the model 0.0 % 8 chains (64 residues) have been docked in sequence ------------------------------------------------------ 18938 reflections ( 99.85 % complete ) and 25452 restraints for refining 11230 atoms. 22918 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2548 (Rfree = 0.000) for 11230 atoms. Found 61 (61 requested) and removed 95 (30 requested) atoms. Cycle 27: After refmac, R = 0.2484 (Rfree = 0.000) for 11084 atoms. Found 61 (61 requested) and removed 78 (30 requested) atoms. Cycle 28: After refmac, R = 0.2483 (Rfree = 0.000) for 11007 atoms. Found 60 (60 requested) and removed 61 (30 requested) atoms. Cycle 29: After refmac, R = 0.2007 (Rfree = 0.000) for 10956 atoms. Found 36 (60 requested) and removed 47 (30 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1918 (Rfree = 0.000) for 10908 atoms. Found 20 (60 requested) and removed 41 (30 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.64 3.31 Search for helices and strands: 0 residues in 0 chains, 11233 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 11250 seeds are put forward Round 1: 604 peptides, 121 chains. Longest chain 14 peptides. Score 0.287 Round 2: 663 peptides, 107 chains. Longest chain 20 peptides. Score 0.394 Round 3: 688 peptides, 112 chains. Longest chain 21 peptides. Score 0.397 Round 4: 714 peptides, 107 chains. Longest chain 21 peptides. Score 0.436 Round 5: 717 peptides, 110 chains. Longest chain 19 peptides. Score 0.428 Taking the results from Round 4 Chains 107, Residues 607, Estimated correctness of the model 0.0 % 4 chains (26 residues) have been docked in sequence ------------------------------------------------------ 18938 reflections ( 99.85 % complete ) and 25607 restraints for refining 11229 atoms. 23192 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2592 (Rfree = 0.000) for 11229 atoms. Found 61 (61 requested) and removed 102 (30 requested) atoms. Cycle 32: After refmac, R = 0.2477 (Rfree = 0.000) for 11091 atoms. Found 61 (61 requested) and removed 62 (30 requested) atoms. Cycle 33: After refmac, R = 0.2427 (Rfree = 0.000) for 11009 atoms. Found 60 (60 requested) and removed 65 (30 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.2432 (Rfree = 0.000) for 10928 atoms. Found 60 (60 requested) and removed 53 (30 requested) atoms. Cycle 35: After refmac, R = 0.2345 (Rfree = 0.000) for 10874 atoms. Found 60 (60 requested) and removed 49 (30 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.65 3.32 Search for helices and strands: 0 residues in 0 chains, 11218 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 11235 seeds are put forward Round 1: 550 peptides, 112 chains. Longest chain 13 peptides. Score 0.272 Round 2: 599 peptides, 105 chains. Longest chain 14 peptides. Score 0.346 Round 3: 671 peptides, 116 chains. Longest chain 15 peptides. Score 0.367 Round 4: 679 peptides, 106 chains. Longest chain 17 peptides. Score 0.412 Round 5: 664 peptides, 105 chains. Longest chain 17 peptides. Score 0.403 Taking the results from Round 4 Chains 111, Residues 573, Estimated correctness of the model 0.0 % 5 chains (41 residues) have been docked in sequence ------------------------------------------------------ 18938 reflections ( 99.85 % complete ) and 25020 restraints for refining 11067 atoms. 22705 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2554 (Rfree = 0.000) for 11067 atoms. Found 60 (60 requested) and removed 99 (30 requested) atoms. Cycle 37: After refmac, R = 0.2400 (Rfree = 0.000) for 10942 atoms. Found 60 (60 requested) and removed 80 (30 requested) atoms. Cycle 38: After refmac, R = 0.2332 (Rfree = 0.000) for 10874 atoms. Found 60 (60 requested) and removed 62 (30 requested) atoms. Cycle 39: After refmac, R = 0.2303 (Rfree = 0.000) for 10818 atoms. Found 59 (59 requested) and removed 61 (29 requested) atoms. Cycle 40: After refmac, R = 0.2342 (Rfree = 0.000) for 10770 atoms. Found 59 (59 requested) and removed 47 (29 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.62 3.30 Search for helices and strands: 0 residues in 0 chains, 11181 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 11197 seeds are put forward Round 1: 519 peptides, 107 chains. Longest chain 10 peptides. Score 0.262 Round 2: 644 peptides, 120 chains. Longest chain 13 peptides. Score 0.328 Round 3: 620 peptides, 105 chains. Longest chain 19 peptides. Score 0.365 Round 4: 619 peptides, 104 chains. Longest chain 20 peptides. Score 0.368 Round 5: 612 peptides, 99 chains. Longest chain 13 peptides. Score 0.381 Taking the results from Round 5 Chains 100, Residues 513, Estimated correctness of the model 0.0 % 4 chains (22 residues) have been docked in sequence ------------------------------------------------------ 18938 reflections ( 99.85 % complete ) and 25418 restraints for refining 11082 atoms. 23388 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2538 (Rfree = 0.000) for 11082 atoms. Found 60 (60 requested) and removed 82 (30 requested) atoms. Cycle 42: After refmac, R = 0.2616 (Rfree = 0.000) for 10980 atoms. Found 60 (60 requested) and removed 80 (30 requested) atoms. Cycle 43: After refmac, R = 0.2544 (Rfree = 0.000) for 10889 atoms. Found 60 (60 requested) and removed 65 (30 requested) atoms. Cycle 44: After refmac, R = 0.2599 (Rfree = 0.000) for 10824 atoms. Found 59 (59 requested) and removed 64 (29 requested) atoms. Cycle 45: After refmac, R = 0.2609 (Rfree = 0.000) for 10758 atoms. Found 59 (59 requested) and removed 58 (29 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.64 3.31 Search for helices and strands: 0 residues in 0 chains, 11113 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 11132 seeds are put forward Round 1: 428 peptides, 95 chains. Longest chain 8 peptides. Score 0.221 Round 2: 485 peptides, 94 chains. Longest chain 11 peptides. Score 0.284 Round 3: 500 peptides, 93 chains. Longest chain 11 peptides. Score 0.303 Round 4: 503 peptides, 93 chains. Longest chain 13 peptides. Score 0.305 Round 5: 513 peptides, 92 chains. Longest chain 13 peptides. Score 0.319 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 92, Residues 421, Estimated correctness of the model 0.0 % 7 chains (34 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 1vl6-3_warpNtrace.pdb as input Building loops using Loopy2018 92 chains (421 residues) following loop building 7 chains (34 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 18938 reflections ( 99.85 % complete ) and 23932 restraints for refining 10549 atoms. 22233 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2651 (Rfree = 0.000) for 10549 atoms. Found 0 (58 requested) and removed 29 (29 requested) atoms. Cycle 47: After refmac, R = 0.2561 (Rfree = 0.000) for 10457 atoms. Found 0 (57 requested) and removed 28 (28 requested) atoms. Cycle 48: After refmac, R = 0.2378 (Rfree = 0.000) for 10391 atoms. Found 0 (57 requested) and removed 28 (28 requested) atoms. Cycle 49: After refmac, R = 0.2055 (Rfree = 0.000) for 10334 atoms. TimeTaking 121.9