Sun 23 Dec 22:23:10 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 1vl0-2.5-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vl0-2.5-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vl0-2.5-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl0-2.5-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/1vl0-2.5-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl0-2.5-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 22:23:18 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/1vl0-2.5-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl0-2.5-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 845 and 0 Target number of residues in the AU: 845 Target solvent content: 0.5652 Checking the provided sequence file Detected sequence length: 292 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 876 Adjusted target solvent content: 0.55 Input MTZ file: 1vl0-2.5-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: 20 Cell parameters: 106.471 130.661 151.225 90.000 90.000 90.000 Input sequence file: 1vl0-2.5-parrot-hancs.fasta_lf Building free atoms model in initial map for 7008 target number of atoms Had to go as low as 0.80 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: 29.987 2.500 Wilson plot Bfac: 40.08 36589 reflections ( 99.37 % complete ) and 0 restraints for refining 7833 atoms. Observations/parameters ratio is 1.17 ------------------------------------------------------ Starting model: R = 0.3978 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3931 (Rfree = 0.000) for 7833 atoms. Found 110 (141 requested) and removed 143 (70 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.11 2.91 NCS extension: 0 residues added, 7800 seeds are put forward Round 1: 295 peptides, 65 chains. Longest chain 7 peptides. Score 0.234 Round 2: 390 peptides, 79 chains. Longest chain 9 peptides. Score 0.298 Round 3: 390 peptides, 77 chains. Longest chain 9 peptides. Score 0.312 Round 4: 400 peptides, 74 chains. Longest chain 16 peptides. Score 0.350 Round 5: 404 peptides, 74 chains. Longest chain 12 peptides. Score 0.356 Taking the results from Round 5 Chains 75, Residues 330, Estimated correctness of the model 35.4 % 4 chains (22 residues) have been docked in sequence ------------------------------------------------------ 36589 reflections ( 99.37 % complete ) and 13418 restraints for refining 6567 atoms. 12107 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3604 (Rfree = 0.000) for 6567 atoms. Found 73 (119 requested) and removed 78 (59 requested) atoms. Cycle 2: After refmac, R = 0.3276 (Rfree = 0.000) for 6521 atoms. Found 51 (118 requested) and removed 66 (59 requested) atoms. Cycle 3: After refmac, R = 0.3216 (Rfree = 0.000) for 6492 atoms. Found 50 (117 requested) and removed 72 (58 requested) atoms. Cycle 4: After refmac, R = 0.3404 (Rfree = 0.000) for 6464 atoms. Found 113 (117 requested) and removed 70 (58 requested) atoms. Cycle 5: After refmac, R = 0.3293 (Rfree = 0.000) for 6491 atoms. Found 93 (117 requested) and removed 66 (58 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.76 2.58 NCS extension: 0 residues added, 6565 seeds are put forward Round 1: 381 peptides, 80 chains. Longest chain 10 peptides. Score 0.276 Round 2: 405 peptides, 72 chains. Longest chain 11 peptides. Score 0.371 Round 3: 436 peptides, 79 chains. Longest chain 12 peptides. Score 0.373 Round 4: 427 peptides, 74 chains. Longest chain 13 peptides. Score 0.392 Round 5: 418 peptides, 74 chains. Longest chain 14 peptides. Score 0.378 Taking the results from Round 4 Chains 74, Residues 353, Estimated correctness of the model 41.9 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 36589 reflections ( 99.37 % complete ) and 13322 restraints for refining 6567 atoms. 11968 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3432 (Rfree = 0.000) for 6567 atoms. Found 116 (119 requested) and removed 68 (59 requested) atoms. Cycle 7: After refmac, R = 0.3165 (Rfree = 0.000) for 6593 atoms. Found 81 (119 requested) and removed 66 (59 requested) atoms. Cycle 8: After refmac, R = 0.3148 (Rfree = 0.000) for 6597 atoms. Found 69 (119 requested) and removed 64 (59 requested) atoms. Cycle 9: After refmac, R = 0.3166 (Rfree = 0.000) for 6586 atoms. Found 83 (119 requested) and removed 65 (59 requested) atoms. Cycle 10: After refmac, R = 0.3036 (Rfree = 0.000) for 6592 atoms. Found 60 (119 requested) and removed 66 (59 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.68 2.51 NCS extension: 0 residues added, 6705 seeds are put forward Round 1: 377 peptides, 73 chains. Longest chain 11 peptides. Score 0.319 Round 2: 444 peptides, 80 chains. Longest chain 13 peptides. Score 0.379 Round 3: 427 peptides, 74 chains. Longest chain 13 peptides. Score 0.392 Round 4: 442 peptides, 76 chains. Longest chain 19 peptides. Score 0.402 Round 5: 424 peptides, 70 chains. Longest chain 12 peptides. Score 0.414 Taking the results from Round 5 Chains 70, Residues 354, Estimated correctness of the model 45.7 % 5 chains (28 residues) have been docked in sequence ------------------------------------------------------ 36589 reflections ( 99.37 % complete ) and 12945 restraints for refining 6567 atoms. 11516 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3182 (Rfree = 0.000) for 6567 atoms. Found 91 (119 requested) and removed 68 (59 requested) atoms. Cycle 12: After refmac, R = 0.3169 (Rfree = 0.000) for 6570 atoms. Found 93 (119 requested) and removed 66 (59 requested) atoms. Cycle 13: After refmac, R = 0.2885 (Rfree = 0.000) for 6579 atoms. Found 49 (119 requested) and removed 64 (59 requested) atoms. Cycle 14: After refmac, R = 0.2890 (Rfree = 0.000) for 6555 atoms. Found 59 (118 requested) and removed 64 (59 requested) atoms. Cycle 15: After refmac, R = 0.3201 (Rfree = 0.000) for 6541 atoms. Found 118 (118 requested) and removed 64 (59 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.73 2.55 NCS extension: 0 residues added, 6630 seeds are put forward Round 1: 389 peptides, 77 chains. Longest chain 9 peptides. Score 0.311 Round 2: 400 peptides, 73 chains. Longest chain 15 peptides. Score 0.357 Round 3: 398 peptides, 71 chains. Longest chain 20 peptides. Score 0.367 Round 4: 385 peptides, 67 chains. Longest chain 12 peptides. Score 0.374 Round 5: 399 peptides, 68 chains. Longest chain 16 peptides. Score 0.389 Taking the results from Round 5 Chains 68, Residues 331, Estimated correctness of the model 41.4 % 5 chains (19 residues) have been docked in sequence ------------------------------------------------------ 36589 reflections ( 99.37 % complete ) and 13097 restraints for refining 6567 atoms. 11796 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2994 (Rfree = 0.000) for 6567 atoms. Found 80 (119 requested) and removed 60 (59 requested) atoms. Cycle 17: After refmac, R = 0.2978 (Rfree = 0.000) for 6571 atoms. Found 72 (119 requested) and removed 61 (59 requested) atoms. Cycle 18: After refmac, R = 0.3086 (Rfree = 0.000) for 6567 atoms. Found 101 (119 requested) and removed 67 (59 requested) atoms. Cycle 19: After refmac, R = 0.2973 (Rfree = 0.000) for 6584 atoms. Found 91 (119 requested) and removed 62 (59 requested) atoms. Cycle 20: After refmac, R = 0.2982 (Rfree = 0.000) for 6602 atoms. Found 69 (119 requested) and removed 64 (59 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.71 2.53 NCS extension: 0 residues added, 6687 seeds are put forward Round 1: 375 peptides, 75 chains. Longest chain 11 peptides. Score 0.301 Round 2: 407 peptides, 77 chains. Longest chain 12 peptides. Score 0.340 Round 3: 414 peptides, 75 chains. Longest chain 11 peptides. Score 0.365 Round 4: 426 peptides, 78 chains. Longest chain 12 peptides. Score 0.364 Round 5: 433 peptides, 79 chains. Longest chain 12 peptides. Score 0.368 Taking the results from Round 5 Chains 79, Residues 354, Estimated correctness of the model 37.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 36589 reflections ( 99.37 % complete ) and 13223 restraints for refining 6566 atoms. 11886 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2955 (Rfree = 0.000) for 6566 atoms. Found 79 (119 requested) and removed 60 (59 requested) atoms. Cycle 22: After refmac, R = 0.2866 (Rfree = 0.000) for 6572 atoms. Found 65 (119 requested) and removed 61 (59 requested) atoms. Cycle 23: After refmac, R = 0.3173 (Rfree = 0.000) for 6566 atoms. Found 119 (119 requested) and removed 68 (59 requested) atoms. Cycle 24: After refmac, R = 0.2820 (Rfree = 0.000) for 6609 atoms. Found 77 (120 requested) and removed 64 (60 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.2689 (Rfree = 0.000) for 6610 atoms. Found 82 (120 requested) and removed 61 (60 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.67 2.50 NCS extension: 0 residues added, 6699 seeds are put forward Round 1: 374 peptides, 77 chains. Longest chain 10 peptides. Score 0.286 Round 2: 422 peptides, 77 chains. Longest chain 12 peptides. Score 0.364 Round 3: 432 peptides, 76 chains. Longest chain 12 peptides. Score 0.387 Round 4: 427 peptides, 76 chains. Longest chain 13 peptides. Score 0.379 Round 5: 429 peptides, 79 chains. Longest chain 12 peptides. Score 0.362 Taking the results from Round 3 Chains 76, Residues 356, Estimated correctness of the model 41.0 % 7 chains (34 residues) have been docked in sequence ------------------------------------------------------ 36589 reflections ( 99.37 % complete ) and 12546 restraints for refining 6567 atoms. 11122 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2775 (Rfree = 0.000) for 6567 atoms. Found 78 (119 requested) and removed 60 (59 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2741 (Rfree = 0.000) for 6577 atoms. Found 57 (119 requested) and removed 61 (59 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2634 (Rfree = 0.000) for 6568 atoms. Found 56 (119 requested) and removed 60 (59 requested) atoms. Cycle 29: After refmac, R = 0.2535 (Rfree = 0.000) for 6558 atoms. Found 48 (119 requested) and removed 60 (59 requested) atoms. Cycle 30: After refmac, R = 0.2530 (Rfree = 0.000) for 6538 atoms. Found 48 (118 requested) and removed 60 (59 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.66 2.49 NCS extension: 0 residues added, 6585 seeds are put forward Round 1: 382 peptides, 75 chains. Longest chain 11 peptides. Score 0.313 Round 2: 421 peptides, 78 chains. Longest chain 14 peptides. Score 0.356 Round 3: 427 peptides, 79 chains. Longest chain 12 peptides. Score 0.359 Round 4: 427 peptides, 77 chains. Longest chain 12 peptides. Score 0.372 Round 5: 417 peptides, 77 chains. Longest chain 12 peptides. Score 0.356 Taking the results from Round 4 Chains 77, Residues 350, Estimated correctness of the model 38.4 % 7 chains (27 residues) have been docked in sequence ------------------------------------------------------ 36589 reflections ( 99.37 % complete ) and 12621 restraints for refining 6567 atoms. 11233 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2966 (Rfree = 0.000) for 6567 atoms. Found 119 (119 requested) and removed 62 (59 requested) atoms. Cycle 32: After refmac, R = 0.2871 (Rfree = 0.000) for 6610 atoms. Found 84 (120 requested) and removed 64 (60 requested) atoms. Cycle 33: After refmac, R = 0.2717 (Rfree = 0.000) for 6621 atoms. Found 65 (120 requested) and removed 67 (60 requested) atoms. Cycle 34: After refmac, R = 0.2688 (Rfree = 0.000) for 6601 atoms. Found 70 (120 requested) and removed 60 (60 requested) atoms. Cycle 35: After refmac, R = 0.2620 (Rfree = 0.000) for 6607 atoms. Found 75 (119 requested) and removed 63 (59 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.68 2.51 NCS extension: 0 residues added, 6700 seeds are put forward Round 1: 374 peptides, 77 chains. Longest chain 10 peptides. Score 0.286 Round 2: 391 peptides, 71 chains. Longest chain 16 peptides. Score 0.356 Round 3: 372 peptides, 66 chains. Longest chain 13 peptides. Score 0.360 Round 4: 383 peptides, 68 chains. Longest chain 15 peptides. Score 0.364 Round 5: 375 peptides, 65 chains. Longest chain 15 peptides. Score 0.372 Taking the results from Round 5 Chains 67, Residues 310, Estimated correctness of the model 38.4 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 36589 reflections ( 99.37 % complete ) and 12989 restraints for refining 6567 atoms. 11762 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3255 (Rfree = 0.000) for 6567 atoms. Found 119 (119 requested) and removed 66 (59 requested) atoms. Cycle 37: After refmac, R = 0.2813 (Rfree = 0.000) for 6604 atoms. Found 99 (120 requested) and removed 63 (60 requested) atoms. Cycle 38: After refmac, R = 0.3154 (Rfree = 0.000) for 6631 atoms. Found 120 (120 requested) and removed 66 (60 requested) atoms. Cycle 39: After refmac, R = 0.2751 (Rfree = 0.000) for 6676 atoms. Found 80 (121 requested) and removed 62 (60 requested) atoms. Cycle 40: After refmac, R = 0.2711 (Rfree = 0.000) for 6691 atoms. Found 87 (121 requested) and removed 61 (60 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.68 2.51 NCS extension: 0 residues added, 6736 seeds are put forward Round 1: 350 peptides, 76 chains. Longest chain 10 peptides. Score 0.251 Round 2: 369 peptides, 67 chains. Longest chain 11 peptides. Score 0.348 Round 3: 364 peptides, 68 chains. Longest chain 10 peptides. Score 0.333 Round 4: 353 peptides, 66 chains. Longest chain 10 peptides. Score 0.329 Round 5: 352 peptides, 62 chains. Longest chain 14 peptides. Score 0.356 Taking the results from Round 5 Chains 62, Residues 290, Estimated correctness of the model 35.4 % 5 chains (16 residues) have been docked in sequence ------------------------------------------------------ 36589 reflections ( 99.37 % complete ) and 13144 restraints for refining 6566 atoms. 12011 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2855 (Rfree = 0.000) for 6566 atoms. Found 102 (119 requested) and removed 60 (59 requested) atoms. Cycle 42: After refmac, R = 0.3096 (Rfree = 0.000) for 6601 atoms. Found 119 (119 requested) and removed 63 (59 requested) atoms. Cycle 43: After refmac, R = 0.2819 (Rfree = 0.000) for 6645 atoms. Found 81 (120 requested) and removed 62 (60 requested) atoms. Cycle 44: After refmac, R = 0.2923 (Rfree = 0.000) for 6656 atoms. Found 120 (120 requested) and removed 61 (60 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.3123 (Rfree = 0.000) for 6714 atoms. Found 121 (121 requested) and removed 65 (60 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.73 2.55 NCS extension: 0 residues added, 6841 seeds are put forward Round 1: 300 peptides, 63 chains. Longest chain 11 peptides. Score 0.259 Round 2: 309 peptides, 57 chains. Longest chain 12 peptides. Score 0.320 Round 3: 305 peptides, 57 chains. Longest chain 11 peptides. Score 0.313 Round 4: 307 peptides, 53 chains. Longest chain 13 peptides. Score 0.346 Round 5: 312 peptides, 55 chains. Longest chain 12 peptides. Score 0.340 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 53, Residues 254, Estimated correctness of the model 33.6 % 1 chains (7 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 1vl0-2_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 36589 reflections ( 99.37 % complete ) and 13077 restraints for refining 6567 atoms. 12093 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2913 (Rfree = 0.000) for 6567 atoms. Found 0 (119 requested) and removed 59 (59 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.3232 (Rfree = 0.000) for 6505 atoms. Found 0 (118 requested) and removed 59 (59 requested) atoms. Cycle 48: After refmac, R = 0.2792 (Rfree = 0.000) for 6437 atoms. Found 0 (116 requested) and removed 58 (58 requested) atoms. Cycle 49: After refmac, R = 0.2788 (Rfree = 0.000) for 6375 atoms. Found 0 (115 requested) and removed 57 (57 requested) atoms. Writing output files ... TimeTaking 95.53