null Sun 23 Dec 22:22:43 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vkm-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkm-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkm-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkm-4.0-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/1vkm-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkm-4.0-parrot-hancs ############### 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 22:22:53 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/hancs/ArpWArp/wArpResults/WorkingDir/1vkm-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkm-4.0-parrot-hancs/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 1100 and 0 Target number of residues in the AU: 1100 Target solvent content: 0.6460 Checking the provided sequence file Detected sequence length: 297 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1782 Adjusted target solvent content: 0.43 Input MTZ file: 1vkm-4.0-parrot-hancs.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: 19 Cell parameters: 91.732 131.100 139.844 90.000 90.000 90.000 Input sequence file: 1vkm-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 14256 target number of atoms Had to go as low as 0.65 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: 75.160 4.000 Wilson plot Bfac: 75.51 14774 reflections ( 99.96 % complete ) and 0 restraints for refining 15740 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3212 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3180 (Rfree = 0.000) for 15740 atoms. Found 73 (74 requested) and removed 109 (37 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.74 4.11 Search for helices and strands: 0 residues in 0 chains, 16022 seeds are put forward NCS extension: 0 residues added, 16022 seeds are put forward Round 1: 578 peptides, 119 chains. Longest chain 8 peptides. Score 0.283 Round 2: 743 peptides, 132 chains. Longest chain 15 peptides. Score 0.394 Round 3: 848 peptides, 131 chains. Longest chain 22 peptides. Score 0.492 Round 4: 856 peptides, 127 chains. Longest chain 17 peptides. Score 0.513 Round 5: 884 peptides, 126 chains. Longest chain 27 peptides. Score 0.539 Taking the results from Round 5 Chains 128, Residues 758, Estimated correctness of the model 0.0 % 4 chains (29 residues) have been docked in sequence ------------------------------------------------------ 14774 reflections ( 99.96 % complete ) and 30750 restraints for refining 12872 atoms. 27769 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2722 (Rfree = 0.000) for 12872 atoms. Found 40 (61 requested) and removed 84 (30 requested) atoms. Cycle 2: After refmac, R = 0.2409 (Rfree = 0.000) for 12584 atoms. Found 36 (60 requested) and removed 72 (30 requested) atoms. Cycle 3: After refmac, R = 0.2326 (Rfree = 0.000) for 12419 atoms. Found 37 (59 requested) and removed 77 (29 requested) atoms. Cycle 4: After refmac, R = 0.2381 (Rfree = 0.000) for 12284 atoms. Found 37 (58 requested) and removed 86 (29 requested) atoms. Cycle 5: After refmac, R = 0.2266 (Rfree = 0.000) for 12163 atoms. Found 32 (58 requested) and removed 54 (29 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.62 3.98 Search for helices and strands: 0 residues in 0 chains, 12634 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 12647 seeds are put forward Round 1: 649 peptides, 128 chains. Longest chain 14 peptides. Score 0.317 Round 2: 800 peptides, 134 chains. Longest chain 14 peptides. Score 0.439 Round 3: 822 peptides, 131 chains. Longest chain 16 peptides. Score 0.470 Round 4: 838 peptides, 128 chains. Longest chain 17 peptides. Score 0.494 Round 5: 883 peptides, 129 chains. Longest chain 20 peptides. Score 0.528 Taking the results from Round 5 Chains 134, Residues 754, Estimated correctness of the model 0.0 % 9 chains (82 residues) have been docked in sequence ------------------------------------------------------ 14774 reflections ( 99.96 % complete ) and 28467 restraints for refining 12352 atoms. 25359 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2325 (Rfree = 0.000) for 12352 atoms. Found 31 (58 requested) and removed 123 (29 requested) atoms. Cycle 7: After refmac, R = 0.2250 (Rfree = 0.000) for 12131 atoms. Found 25 (58 requested) and removed 97 (29 requested) atoms. Cycle 8: After refmac, R = 0.1848 (Rfree = 0.000) for 11987 atoms. Found 16 (57 requested) and removed 67 (28 requested) atoms. Cycle 9: After refmac, R = 0.1746 (Rfree = 0.000) for 11896 atoms. Found 7 (56 requested) and removed 50 (28 requested) atoms. Cycle 10: After refmac, R = 0.1788 (Rfree = 0.000) for 11833 atoms. Found 8 (56 requested) and removed 48 (28 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.68 4.04 Search for helices and strands: 0 residues in 0 chains, 12233 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 12252 seeds are put forward Round 1: 720 peptides, 138 chains. Longest chain 15 peptides. Score 0.347 Round 2: 834 peptides, 132 chains. Longest chain 23 peptides. Score 0.476 Round 3: 821 peptides, 127 chains. Longest chain 19 peptides. Score 0.484 Round 4: 839 peptides, 119 chains. Longest chain 20 peptides. Score 0.528 Round 5: 843 peptides, 121 chains. Longest chain 19 peptides. Score 0.524 Taking the results from Round 4 Chains 122, Residues 720, Estimated correctness of the model 0.0 % 7 chains (59 residues) have been docked in sequence ------------------------------------------------------ 14774 reflections ( 99.96 % complete ) and 28356 restraints for refining 12405 atoms. 25434 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2326 (Rfree = 0.000) for 12405 atoms. Found 51 (58 requested) and removed 124 (29 requested) atoms. Cycle 12: After refmac, R = 0.2160 (Rfree = 0.000) for 12240 atoms. Found 34 (58 requested) and removed 83 (29 requested) atoms. Cycle 13: After refmac, R = 0.2079 (Rfree = 0.000) for 12134 atoms. Found 37 (57 requested) and removed 82 (28 requested) atoms. Cycle 14: After refmac, R = 0.2031 (Rfree = 0.000) for 12045 atoms. Found 38 (57 requested) and removed 77 (28 requested) atoms. Cycle 15: After refmac, R = 0.2070 (Rfree = 0.000) for 11961 atoms. Found 40 (57 requested) and removed 55 (28 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.61 3.97 Search for helices and strands: 0 residues in 0 chains, 12348 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 12368 seeds are put forward Round 1: 630 peptides, 126 chains. Longest chain 14 peptides. Score 0.306 Round 2: 787 peptides, 138 chains. Longest chain 18 peptides. Score 0.411 Round 3: 784 peptides, 132 chains. Longest chain 17 peptides. Score 0.432 Round 4: 815 peptides, 133 chains. Longest chain 18 peptides. Score 0.456 Round 5: 802 peptides, 127 chains. Longest chain 28 peptides. Score 0.467 Taking the results from Round 5 Chains 128, Residues 675, Estimated correctness of the model 0.0 % 8 chains (60 residues) have been docked in sequence ------------------------------------------------------ 14774 reflections ( 99.96 % complete ) and 28981 restraints for refining 12538 atoms. 26218 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2092 (Rfree = 0.000) for 12538 atoms. Found 31 (59 requested) and removed 126 (29 requested) atoms. Cycle 17: After refmac, R = 0.2010 (Rfree = 0.000) for 12360 atoms. Found 40 (59 requested) and removed 84 (29 requested) atoms. Cycle 18: After refmac, R = 0.1898 (Rfree = 0.000) for 12271 atoms. Found 33 (58 requested) and removed 71 (29 requested) atoms. Cycle 19: After refmac, R = 0.1898 (Rfree = 0.000) for 12182 atoms. Found 43 (58 requested) and removed 66 (29 requested) atoms. Cycle 20: After refmac, R = 0.1882 (Rfree = 0.000) for 12130 atoms. Found 50 (57 requested) and removed 56 (28 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.60 3.95 Search for helices and strands: 0 residues in 0 chains, 12536 seeds are put forward NCS extension: 27 residues added (4 deleted due to clashes), 12563 seeds are put forward Round 1: 628 peptides, 127 chains. Longest chain 12 peptides. Score 0.300 Round 2: 705 peptides, 129 chains. Longest chain 13 peptides. Score 0.369 Round 3: 730 peptides, 129 chains. Longest chain 15 peptides. Score 0.394 Round 4: 749 peptides, 124 chains. Longest chain 17 peptides. Score 0.431 Round 5: 783 peptides, 125 chains. Longest chain 17 peptides. Score 0.458 Taking the results from Round 5 Chains 127, Residues 658, Estimated correctness of the model 0.0 % 8 chains (43 residues) have been docked in sequence ------------------------------------------------------ 14774 reflections ( 99.96 % complete ) and 29783 restraints for refining 12833 atoms. 27177 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2058 (Rfree = 0.000) for 12833 atoms. Found 44 (60 requested) and removed 167 (30 requested) atoms. Cycle 22: After refmac, R = 0.1986 (Rfree = 0.000) for 12627 atoms. Found 49 (60 requested) and removed 93 (30 requested) atoms. Cycle 23: After refmac, R = 0.1518 (Rfree = 0.000) for 12516 atoms. Found 19 (59 requested) and removed 61 (29 requested) atoms. Cycle 24: After refmac, R = 0.1391 (Rfree = 0.000) for 12434 atoms. Found 13 (59 requested) and removed 46 (29 requested) atoms. Cycle 25: After refmac, R = 0.1380 (Rfree = 0.000) for 12384 atoms. Found 10 (58 requested) and removed 47 (29 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.59 3.94 Search for helices and strands: 0 residues in 0 chains, 12753 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 12772 seeds are put forward Round 1: 594 peptides, 127 chains. Longest chain 10 peptides. Score 0.264 Round 2: 700 peptides, 130 chains. Longest chain 13 peptides. Score 0.360 Round 3: 693 peptides, 120 chains. Longest chain 15 peptides. Score 0.395 Round 4: 707 peptides, 119 chains. Longest chain 13 peptides. Score 0.413 Round 5: 682 peptides, 117 chains. Longest chain 14 peptides. Score 0.397 Taking the results from Round 4 Chains 119, Residues 588, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 14774 reflections ( 99.96 % complete ) and 29916 restraints for refining 12733 atoms. 27654 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2020 (Rfree = 0.000) for 12733 atoms. Found 51 (60 requested) and removed 105 (30 requested) atoms. Cycle 27: After refmac, R = 0.2117 (Rfree = 0.000) for 12622 atoms. Found 60 (60 requested) and removed 93 (30 requested) atoms. Cycle 28: After refmac, R = 0.2070 (Rfree = 0.000) for 12551 atoms. Found 59 (59 requested) and removed 85 (29 requested) atoms. Cycle 29: After refmac, R = 0.1590 (Rfree = 0.000) for 12480 atoms. Found 14 (59 requested) and removed 52 (29 requested) atoms. Cycle 30: After refmac, R = 0.1525 (Rfree = 0.000) for 12414 atoms. Found 9 (59 requested) and removed 41 (29 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.62 3.98 Search for helices and strands: 0 residues in 0 chains, 12784 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 12796 seeds are put forward Round 1: 585 peptides, 127 chains. Longest chain 10 peptides. Score 0.254 Round 2: 695 peptides, 126 chains. Longest chain 14 peptides. Score 0.372 Round 3: 679 peptides, 120 chains. Longest chain 20 peptides. Score 0.382 Round 4: 664 peptides, 117 chains. Longest chain 12 peptides. Score 0.380 Round 5: 686 peptides, 116 chains. Longest chain 13 peptides. Score 0.405 Taking the results from Round 5 Chains 117, Residues 570, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 14774 reflections ( 99.96 % complete ) and 29559 restraints for refining 12638 atoms. 27358 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2072 (Rfree = 0.000) for 12638 atoms. Found 55 (60 requested) and removed 121 (30 requested) atoms. Cycle 32: After refmac, R = 0.2209 (Rfree = 0.000) for 12507 atoms. Found 59 (59 requested) and removed 72 (29 requested) atoms. Cycle 33: After refmac, R = 0.2101 (Rfree = 0.000) for 12430 atoms. Found 56 (59 requested) and removed 70 (29 requested) atoms. Cycle 34: After refmac, R = 0.1699 (Rfree = 0.000) for 12356 atoms. Found 11 (58 requested) and removed 62 (29 requested) atoms. Cycle 35: After refmac, R = 0.1584 (Rfree = 0.000) for 12265 atoms. Found 5 (58 requested) and removed 44 (29 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.60 3.95 Search for helices and strands: 0 residues in 0 chains, 12587 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 12598 seeds are put forward Round 1: 485 peptides, 105 chains. Longest chain 8 peptides. Score 0.244 Round 2: 622 peptides, 122 chains. Longest chain 12 peptides. Score 0.316 Round 3: 632 peptides, 111 chains. Longest chain 12 peptides. Score 0.373 Round 4: 613 peptides, 111 chains. Longest chain 16 peptides. Score 0.354 Round 5: 606 peptides, 110 chains. Longest chain 13 peptides. Score 0.352 Taking the results from Round 3 Chains 111, Residues 521, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14774 reflections ( 99.96 % complete ) and 28587 restraints for refining 12229 atoms. 26614 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2135 (Rfree = 0.000) for 12229 atoms. Found 58 (58 requested) and removed 104 (29 requested) atoms. Cycle 37: After refmac, R = 0.2192 (Rfree = 0.000) for 12130 atoms. Found 57 (57 requested) and removed 70 (28 requested) atoms. Cycle 38: After refmac, R = 0.2160 (Rfree = 0.000) for 12087 atoms. Found 57 (57 requested) and removed 69 (28 requested) atoms. Cycle 39: After refmac, R = 0.2093 (Rfree = 0.000) for 12039 atoms. Found 57 (57 requested) and removed 59 (28 requested) atoms. Cycle 40: After refmac, R = 0.2134 (Rfree = 0.000) for 12019 atoms. Found 57 (57 requested) and removed 62 (28 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.59 3.94 Search for helices and strands: 0 residues in 0 chains, 12377 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 12391 seeds are put forward Round 1: 404 peptides, 89 chains. Longest chain 11 peptides. Score 0.227 Round 2: 479 peptides, 96 chains. Longest chain 9 peptides. Score 0.280 Round 3: 502 peptides, 91 chains. Longest chain 11 peptides. Score 0.329 Round 4: 508 peptides, 94 chains. Longest chain 17 peptides. Score 0.321 Round 5: 513 peptides, 91 chains. Longest chain 11 peptides. Score 0.341 Taking the results from Round 5 Chains 91, Residues 422, Estimated correctness of the model 0.0 % 5 chains (23 residues) have been docked in sequence ------------------------------------------------------ 14774 reflections ( 99.96 % complete ) and 27816 restraints for refining 11961 atoms. 26172 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2138 (Rfree = 0.000) for 11961 atoms. Found 56 (56 requested) and removed 79 (28 requested) atoms. Cycle 42: After refmac, R = 0.2080 (Rfree = 0.000) for 11904 atoms. Found 56 (56 requested) and removed 79 (28 requested) atoms. Cycle 43: After refmac, R = 0.2026 (Rfree = 0.000) for 11854 atoms. Found 56 (56 requested) and removed 72 (28 requested) atoms. Cycle 44: After refmac, R = 0.2043 (Rfree = 0.000) for 11816 atoms. Found 56 (56 requested) and removed 67 (28 requested) atoms. Cycle 45: After refmac, R = 0.2099 (Rfree = 0.000) for 11792 atoms. Found 56 (56 requested) and removed 45 (28 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.55 3.90 Search for helices and strands: 0 residues in 0 chains, 12152 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 12164 seeds are put forward Round 1: 390 peptides, 86 chains. Longest chain 9 peptides. Score 0.226 Round 2: 448 peptides, 86 chains. Longest chain 10 peptides. Score 0.294 Round 3: 441 peptides, 88 chains. Longest chain 10 peptides. Score 0.276 Round 4: 431 peptides, 80 chains. Longest chain 13 peptides. Score 0.304 Round 5: 438 peptides, 82 chains. Longest chain 12 peptides. Score 0.302 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 80, Residues 351, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vkm-4_warpNtrace.pdb as input Building loops using Loopy2018 80 chains (351 residues) following loop building 2 chains (12 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14774 reflections ( 99.96 % complete ) and 26311 restraints for refining 11452 atoms. 24956 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2037 (Rfree = 0.000) for 11452 atoms. Found 0 (54 requested) and removed 27 (27 requested) atoms. Cycle 47: After refmac, R = 0.2018 (Rfree = 0.000) for 11397 atoms. Found 0 (54 requested) and removed 27 (27 requested) atoms. Cycle 48: After refmac, R = 0.1588 (Rfree = 0.000) for 11344 atoms. Found 0 (54 requested) and removed 27 (27 requested) atoms. Cycle 49: After refmac, R = 0.1422 (Rfree = 0.000) for 11301 atoms. Found 0 (53 requested) and removed 26 (26 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:36:12 GMT 2018 Job finished. TimeTaking 133.48 Used memory is bytes: 20681184