Mon 24 Dec 00:06:23 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 1vl6-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vl6-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vl6-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl6-3.8-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/1vl6-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl6-3.8-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 ============================================================ Mon 24 Dec 00:06:29 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vl6-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl6-3.8-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 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-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: 170 Cell parameters: 144.124 144.124 163.018 90.000 90.000 120.000 Input sequence file: 1vl6-3.8-parrot-mrncs.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 13836 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3424 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3294 (Rfree = 0.000) for 13836 atoms. Found 76 (76 requested) and removed 71 (38 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.73 3.40 Search for helices and strands: 0 residues in 0 chains, 14113 seeds are put forward NCS extension: 0 residues added, 14113 seeds are put forward Round 1: 565 peptides, 106 chains. Longest chain 15 peptides. Score 0.311 Round 2: 733 peptides, 111 chains. Longest chain 18 peptides. Score 0.437 Round 3: 791 peptides, 105 chains. Longest chain 24 peptides. Score 0.503 Round 4: 816 peptides, 100 chains. Longest chain 33 peptides. Score 0.537 Round 5: 865 peptides, 93 chains. Longest chain 32 peptides. Score 0.592 Taking the results from Round 5 Chains 101, Residues 772, Estimated correctness of the model 0.0 % 9 chains (109 residues) have been docked in sequence ------------------------------------------------------ 18938 reflections ( 99.85 % complete ) and 24812 restraints for refining 11224 atoms. 21433 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2880 (Rfree = 0.000) for 11224 atoms. Found 59 (61 requested) and removed 95 (30 requested) atoms. Cycle 2: After refmac, R = 0.2633 (Rfree = 0.000) for 10903 atoms. Found 61 (61 requested) and removed 75 (30 requested) atoms. Cycle 3: After refmac, R = 0.2531 (Rfree = 0.000) for 10704 atoms. Found 59 (59 requested) and removed 74 (29 requested) atoms. Cycle 4: After refmac, R = 0.2439 (Rfree = 0.000) for 10582 atoms. Found 58 (58 requested) and removed 51 (29 requested) atoms. Cycle 5: After refmac, R = 0.2403 (Rfree = 0.000) for 10516 atoms. Found 58 (58 requested) and removed 54 (29 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.68 3.35 Search for helices and strands: 0 residues in 0 chains, 10944 seeds are put forward NCS extension: 19 residues added (14 deleted due to clashes), 10963 seeds are put forward Round 1: 767 peptides, 124 chains. Longest chain 24 peptides. Score 0.419 Round 2: 824 peptides, 108 chains. Longest chain 35 peptides. Score 0.517 Round 3: 842 peptides, 109 chains. Longest chain 27 peptides. Score 0.526 Round 4: 853 peptides, 107 chains. Longest chain 30 peptides. Score 0.540 Round 5: 892 peptides, 101 chains. Longest chain 40 peptides. Score 0.585 Taking the results from Round 5 Chains 109, Residues 791, Estimated correctness of the model 0.0 % 9 chains (130 residues) have been docked in sequence ------------------------------------------------------ 18938 reflections ( 99.85 % complete ) and 24043 restraints for refining 11230 atoms. 20480 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2590 (Rfree = 0.000) for 11230 atoms. Found 61 (61 requested) and removed 114 (30 requested) atoms. Cycle 7: After refmac, R = 0.2483 (Rfree = 0.000) for 11008 atoms. Found 61 (61 requested) and removed 105 (30 requested) atoms. Cycle 8: After refmac, R = 0.2387 (Rfree = 0.000) for 10873 atoms. Found 60 (60 requested) and removed 71 (30 requested) atoms. Cycle 9: After refmac, R = 0.2274 (Rfree = 0.000) for 10799 atoms. Found 49 (59 requested) and removed 66 (29 requested) atoms. Cycle 10: After refmac, R = 0.2282 (Rfree = 0.000) for 10725 atoms. Found 59 (59 requested) and removed 79 (29 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.66 3.33 Search for helices and strands: 0 residues in 0 chains, 11110 seeds are put forward NCS extension: 36 residues added (3 deleted due to clashes), 11146 seeds are put forward Round 1: 736 peptides, 118 chains. Longest chain 31 peptides. Score 0.415 Round 2: 828 peptides, 115 chains. Longest chain 28 peptides. Score 0.497 Round 3: 827 peptides, 101 chains. Longest chain 24 peptides. Score 0.541 Round 4: 833 peptides, 110 chains. Longest chain 28 peptides. Score 0.517 Round 5: 826 peptides, 96 chains. Longest chain 24 peptides. Score 0.557 Taking the results from Round 5 Chains 101, Residues 730, Estimated correctness of the model 0.0 % 6 chains (68 residues) have been docked in sequence ------------------------------------------------------ 18938 reflections ( 99.85 % complete ) and 24881 restraints for refining 11230 atoms. 21810 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2567 (Rfree = 0.000) for 11230 atoms. Found 61 (61 requested) and removed 90 (30 requested) atoms. Cycle 12: After refmac, R = 0.2452 (Rfree = 0.000) for 11065 atoms. Found 61 (61 requested) and removed 77 (30 requested) atoms. Cycle 13: After refmac, R = 0.2404 (Rfree = 0.000) for 10954 atoms. Found 60 (60 requested) and removed 61 (30 requested) atoms. Cycle 14: After refmac, R = 0.2361 (Rfree = 0.000) for 10857 atoms. Found 60 (60 requested) and removed 62 (30 requested) atoms. Cycle 15: After refmac, R = 0.1957 (Rfree = 0.000) for 10787 atoms. Found 28 (59 requested) and removed 42 (29 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.64 3.31 Search for helices and strands: 0 residues in 0 chains, 11120 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 11154 seeds are put forward Round 1: 709 peptides, 132 chains. Longest chain 16 peptides. Score 0.340 Round 2: 822 peptides, 122 chains. Longest chain 27 peptides. Score 0.469 Round 3: 824 peptides, 118 chains. Longest chain 20 peptides. Score 0.484 Round 4: 821 peptides, 118 chains. Longest chain 22 peptides. Score 0.482 Round 5: 818 peptides, 116 chains. Longest chain 20 peptides. Score 0.486 Taking the results from Round 5 Chains 118, Residues 702, Estimated correctness of the model 0.0 % 9 chains (74 residues) have been docked in sequence ------------------------------------------------------ 18938 reflections ( 99.85 % complete ) and 25094 restraints for refining 11229 atoms. 22120 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2599 (Rfree = 0.000) for 11229 atoms. Found 61 (61 requested) and removed 70 (30 requested) atoms. Cycle 17: After refmac, R = 0.2446 (Rfree = 0.000) for 11069 atoms. Found 61 (61 requested) and removed 69 (30 requested) atoms. Cycle 18: After refmac, R = 0.2060 (Rfree = 0.000) for 10976 atoms. Found 23 (60 requested) and removed 52 (30 requested) atoms. Cycle 19: After refmac, R = 0.2340 (Rfree = 0.000) for 10897 atoms. Found 60 (60 requested) and removed 56 (30 requested) atoms. Cycle 20: After refmac, R = 0.1981 (Rfree = 0.000) for 10867 atoms. Found 19 (59 requested) and removed 43 (29 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.64 3.31 Search for helices and strands: 0 residues in 0 chains, 11212 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 11231 seeds are put forward Round 1: 696 peptides, 122 chains. Longest chain 16 peptides. Score 0.366 Round 2: 761 peptides, 119 chains. Longest chain 18 peptides. Score 0.431 Round 3: 798 peptides, 113 chains. Longest chain 26 peptides. Score 0.481 Round 4: 793 peptides, 116 chains. Longest chain 22 peptides. Score 0.467 Round 5: 826 peptides, 114 chains. Longest chain 19 peptides. Score 0.499 Taking the results from Round 5 Chains 114, Residues 712, Estimated correctness of the model 0.0 % 6 chains (44 residues) have been docked in sequence ------------------------------------------------------ 18938 reflections ( 99.85 % complete ) and 25306 restraints for refining 11230 atoms. 22413 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2579 (Rfree = 0.000) for 11230 atoms. Found 61 (61 requested) and removed 72 (30 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2427 (Rfree = 0.000) for 11123 atoms. Found 61 (61 requested) and removed 68 (30 requested) atoms. Cycle 23: After refmac, R = 0.2054 (Rfree = 0.000) for 11029 atoms. Found 27 (61 requested) and removed 49 (30 requested) atoms. Cycle 24: After refmac, R = 0.1941 (Rfree = 0.000) for 10952 atoms. Found 27 (60 requested) and removed 42 (30 requested) atoms. Cycle 25: After refmac, R = 0.1902 (Rfree = 0.000) for 10905 atoms. Found 20 (60 requested) and removed 44 (30 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.65 3.32 Search for helices and strands: 0 residues in 0 chains, 11260 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 11278 seeds are put forward Round 1: 663 peptides, 119 chains. Longest chain 18 peptides. Score 0.349 Round 2: 752 peptides, 118 chains. Longest chain 17 peptides. Score 0.428 Round 3: 770 peptides, 116 chains. Longest chain 21 peptides. Score 0.449 Round 4: 779 peptides, 111 chains. Longest chain 23 peptides. Score 0.473 Round 5: 771 peptides, 116 chains. Longest chain 23 peptides. Score 0.450 Taking the results from Round 4 Chains 111, Residues 668, Estimated correctness of the model 0.0 % 5 chains (64 residues) have been docked in sequence ------------------------------------------------------ 18938 reflections ( 99.85 % complete ) and 25353 restraints for refining 11230 atoms. 22548 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2420 (Rfree = 0.000) for 11230 atoms. Found 61 (61 requested) and removed 65 (30 requested) atoms. Cycle 27: After refmac, R = 0.2353 (Rfree = 0.000) for 11139 atoms. Found 61 (61 requested) and removed 64 (30 requested) atoms. Cycle 28: After refmac, R = 0.2303 (Rfree = 0.000) for 11082 atoms. Found 61 (61 requested) and removed 60 (30 requested) atoms. Cycle 29: After refmac, R = 0.2278 (Rfree = 0.000) for 11025 atoms. Found 60 (60 requested) and removed 50 (30 requested) atoms. Cycle 30: After refmac, R = 0.2262 (Rfree = 0.000) for 10983 atoms. Found 60 (60 requested) and removed 48 (30 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.63 3.30 Search for helices and strands: 0 residues in 0 chains, 11334 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 11350 seeds are put forward Round 1: 618 peptides, 119 chains. Longest chain 16 peptides. Score 0.308 Round 2: 703 peptides, 116 chains. Longest chain 15 peptides. Score 0.395 Round 3: 706 peptides, 111 chains. Longest chain 19 peptides. Score 0.416 Round 4: 729 peptides, 112 chains. Longest chain 20 peptides. Score 0.431 Round 5: 721 peptides, 103 chains. Longest chain 15 peptides. Score 0.456 Taking the results from Round 5 Chains 103, Residues 618, Estimated correctness of the model 0.0 % 6 chains (38 residues) have been docked in sequence ------------------------------------------------------ 18938 reflections ( 99.85 % complete ) and 25694 restraints for refining 11230 atoms. 23207 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2522 (Rfree = 0.000) for 11230 atoms. Found 61 (61 requested) and removed 80 (30 requested) atoms. Cycle 32: After refmac, R = 0.2390 (Rfree = 0.000) for 11110 atoms. Found 61 (61 requested) and removed 59 (30 requested) atoms. Cycle 33: After refmac, R = 0.2383 (Rfree = 0.000) for 11033 atoms. Found 61 (61 requested) and removed 59 (30 requested) atoms. Cycle 34: After refmac, R = 0.1939 (Rfree = 0.000) for 10978 atoms. Found 24 (60 requested) and removed 36 (30 requested) atoms. Cycle 35: After refmac, R = 0.1848 (Rfree = 0.000) for 10935 atoms. Found 26 (60 requested) and removed 37 (30 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.66 3.33 Search for helices and strands: 0 residues in 0 chains, 11272 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 11295 seeds are put forward Round 1: 535 peptides, 109 chains. Longest chain 12 peptides. Score 0.270 Round 2: 668 peptides, 117 chains. Longest chain 14 peptides. Score 0.361 Round 3: 681 peptides, 107 chains. Longest chain 21 peptides. Score 0.410 Round 4: 675 peptides, 106 chains. Longest chain 20 peptides. Score 0.408 Round 5: 684 peptides, 106 chains. Longest chain 27 peptides. Score 0.416 Taking the results from Round 5 Chains 106, Residues 578, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 18938 reflections ( 99.85 % complete ) and 26138 restraints for refining 11229 atoms. 23880 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2528 (Rfree = 0.000) for 11229 atoms. Found 61 (61 requested) and removed 63 (30 requested) atoms. Cycle 37: After refmac, R = 0.2446 (Rfree = 0.000) for 11134 atoms. Found 61 (61 requested) and removed 63 (30 requested) atoms. Cycle 38: After refmac, R = 0.2493 (Rfree = 0.000) for 11052 atoms. Found 61 (61 requested) and removed 55 (30 requested) atoms. Cycle 39: After refmac, R = 0.2474 (Rfree = 0.000) for 10991 atoms. Found 60 (60 requested) and removed 51 (30 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.2463 (Rfree = 0.000) for 10952 atoms. Found 60 (60 requested) and removed 48 (30 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.61 3.29 Search for helices and strands: 0 residues in 0 chains, 11404 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 11429 seeds are put forward Round 1: 473 peptides, 97 chains. Longest chain 10 peptides. Score 0.259 Round 2: 597 peptides, 110 chains. Longest chain 12 peptides. Score 0.325 Round 3: 591 peptides, 104 chains. Longest chain 11 peptides. Score 0.343 Round 4: 580 peptides, 101 chains. Longest chain 11 peptides. Score 0.345 Round 5: 615 peptides, 108 chains. Longest chain 12 peptides. Score 0.349 Taking the results from Round 5 Chains 108, Residues 507, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 18938 reflections ( 99.85 % complete ) and 25205 restraints for refining 10880 atoms. 23222 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2610 (Rfree = 0.000) for 10880 atoms. Found 59 (59 requested) and removed 74 (29 requested) atoms. Cycle 42: After refmac, R = 0.2602 (Rfree = 0.000) for 10790 atoms. Found 59 (59 requested) and removed 56 (29 requested) atoms. Cycle 43: After refmac, R = 0.2520 (Rfree = 0.000) for 10734 atoms. Found 59 (59 requested) and removed 48 (29 requested) atoms. Cycle 44: After refmac, R = 0.2574 (Rfree = 0.000) for 10698 atoms. Found 59 (59 requested) and removed 54 (29 requested) atoms. Cycle 45: After refmac, R = 0.2551 (Rfree = 0.000) for 10664 atoms. Found 58 (58 requested) and removed 42 (29 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 3.35 Search for helices and strands: 0 residues in 0 chains, 10998 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 11010 seeds are put forward Round 1: 448 peptides, 96 chains. Longest chain 9 peptides. Score 0.237 Round 2: 532 peptides, 100 chains. Longest chain 10 peptides. Score 0.304 Round 3: 553 peptides, 98 chains. Longest chain 14 peptides. Score 0.332 Round 4: 552 peptides, 97 chains. Longest chain 14 peptides. Score 0.335 Round 5: 534 peptides, 95 chains. Longest chain 14 peptides. Score 0.327 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 97, Residues 455, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vl6-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 18938 reflections ( 99.85 % complete ) and 24160 restraints for refining 10536 atoms. 22437 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2750 (Rfree = 0.000) for 10536 atoms. Found 0 (57 requested) and removed 28 (28 requested) atoms. Cycle 47: After refmac, R = 0.2600 (Rfree = 0.000) for 10415 atoms. Found 0 (57 requested) and removed 28 (28 requested) atoms. Cycle 48: After refmac, R = 0.2189 (Rfree = 0.000) for 10336 atoms. Found 0 (57 requested) and removed 28 (28 requested) atoms. Cycle 49: After refmac, R = 0.2095 (Rfree = 0.000) for 10271 atoms. TimeTaking 143.87