Mon 24 Dec 00:42:09 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 1vl0-2.5-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vl0-2.5-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vl0-2.5-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl0-2.5-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/1vl0-2.5-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl0-2.5-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 00:42:19 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/1vl0-2.5-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl0-2.5-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 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-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: 20 Cell parameters: 106.471 130.661 151.225 90.000 90.000 90.000 Input sequence file: 1vl0-2.5-parrot-mrncs.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 7805 atoms. Observations/parameters ratio is 1.17 ------------------------------------------------------ Starting model: R = 0.3979 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3973 (Rfree = 0.000) for 7805 atoms. Found 119 (141 requested) and removed 143 (70 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.85 2.67 NCS extension: 0 residues added, 7781 seeds are put forward Round 1: 259 peptides, 59 chains. Longest chain 7 peptides. Score 0.213 Round 2: 332 peptides, 67 chains. Longest chain 10 peptides. Score 0.286 Round 3: 355 peptides, 73 chains. Longest chain 11 peptides. Score 0.282 Round 4: 370 peptides, 73 chains. Longest chain 14 peptides. Score 0.307 Round 5: 416 peptides, 80 chains. Longest chain 12 peptides. Score 0.334 Taking the results from Round 5 Chains 81, Residues 336, Estimated correctness of the model 31.4 % 9 chains (46 residues) have been docked in sequence ------------------------------------------------------ 36589 reflections ( 99.37 % complete ) and 13145 restraints for refining 6563 atoms. 11753 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3568 (Rfree = 0.000) for 6563 atoms. Found 86 (119 requested) and removed 83 (59 requested) atoms. Cycle 2: After refmac, R = 0.3362 (Rfree = 0.000) for 6534 atoms. Found 76 (119 requested) and removed 76 (59 requested) atoms. Cycle 3: After refmac, R = 0.3387 (Rfree = 0.000) for 6519 atoms. Found 108 (118 requested) and removed 87 (59 requested) atoms. Cycle 4: After refmac, R = 0.3341 (Rfree = 0.000) for 6517 atoms. Found 93 (118 requested) and removed 68 (59 requested) atoms. Cycle 5: After refmac, R = 0.3146 (Rfree = 0.000) for 6527 atoms. Found 73 (118 requested) and removed 70 (59 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.76 2.58 NCS extension: 0 residues added, 6609 seeds are put forward Round 1: 369 peptides, 78 chains. Longest chain 8 peptides. Score 0.270 Round 2: 414 peptides, 77 chains. Longest chain 12 peptides. Score 0.352 Round 3: 406 peptides, 72 chains. Longest chain 15 peptides. Score 0.373 Round 4: 405 peptides, 71 chains. Longest chain 12 peptides. Score 0.378 Round 5: 423 peptides, 77 chains. Longest chain 13 peptides. Score 0.366 Taking the results from Round 4 Chains 71, Residues 334, Estimated correctness of the model 39.4 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 36589 reflections ( 99.37 % complete ) and 13250 restraints for refining 6565 atoms. 11914 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3553 (Rfree = 0.000) for 6565 atoms. Found 119 (119 requested) and removed 75 (59 requested) atoms. Cycle 7: After refmac, R = 0.3189 (Rfree = 0.000) for 6582 atoms. Found 85 (119 requested) and removed 70 (59 requested) atoms. Cycle 8: After refmac, R = 0.3470 (Rfree = 0.000) for 6571 atoms. Found 119 (119 requested) and removed 68 (59 requested) atoms. Cycle 9: After refmac, R = 0.3308 (Rfree = 0.000) for 6608 atoms. Found 76 (120 requested) and removed 72 (60 requested) atoms. Cycle 10: After refmac, R = 0.3217 (Rfree = 0.000) for 6593 atoms. Found 98 (119 requested) and removed 63 (59 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.85 2.67 NCS extension: 0 residues added, 6659 seeds are put forward Round 1: 356 peptides, 74 chains. Longest chain 14 peptides. Score 0.276 Round 2: 414 peptides, 76 chains. Longest chain 15 peptides. Score 0.358 Round 3: 418 peptides, 76 chains. Longest chain 15 peptides. Score 0.365 Round 4: 423 peptides, 77 chains. Longest chain 13 peptides. Score 0.366 Round 5: 412 peptides, 72 chains. Longest chain 20 peptides. Score 0.382 Taking the results from Round 5 Chains 72, Residues 340, Estimated correctness of the model 40.1 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 36589 reflections ( 99.37 % complete ) and 13273 restraints for refining 6567 atoms. 11975 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3230 (Rfree = 0.000) for 6567 atoms. Found 82 (119 requested) and removed 69 (59 requested) atoms. Cycle 12: After refmac, R = 0.3256 (Rfree = 0.000) for 6558 atoms. Found 91 (119 requested) and removed 62 (59 requested) atoms. Cycle 13: After refmac, R = 0.3035 (Rfree = 0.000) for 6568 atoms. Found 53 (119 requested) and removed 63 (59 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.3407 (Rfree = 0.000) for 6545 atoms. Found 118 (118 requested) and removed 71 (59 requested) atoms. Cycle 15: After refmac, R = 0.2999 (Rfree = 0.000) for 6580 atoms. Found 69 (119 requested) and removed 64 (59 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.76 2.58 NCS extension: 0 residues added, 6677 seeds are put forward Round 1: 390 peptides, 82 chains. Longest chain 8 peptides. Score 0.277 Round 2: 426 peptides, 81 chains. Longest chain 13 peptides. Score 0.344 Round 3: 415 peptides, 78 chains. Longest chain 13 peptides. Score 0.346 Round 4: 439 peptides, 80 chains. Longest chain 15 peptides. Score 0.371 Round 5: 426 peptides, 74 chains. Longest chain 14 peptides. Score 0.391 Taking the results from Round 5 Chains 74, Residues 352, Estimated correctness of the model 41.7 % 5 chains (19 residues) have been docked in sequence ------------------------------------------------------ 36589 reflections ( 99.37 % complete ) and 13107 restraints for refining 6567 atoms. 11718 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3215 (Rfree = 0.000) for 6567 atoms. Found 107 (119 requested) and removed 66 (59 requested) atoms. Cycle 17: After refmac, R = 0.2981 (Rfree = 0.000) for 6592 atoms. Found 72 (119 requested) and removed 66 (59 requested) atoms. Cycle 18: After refmac, R = 0.3377 (Rfree = 0.000) for 6580 atoms. Found 119 (119 requested) and removed 68 (59 requested) atoms. Cycle 19: After refmac, R = 0.3231 (Rfree = 0.000) for 6619 atoms. Found 120 (120 requested) and removed 67 (60 requested) atoms. Cycle 20: After refmac, R = 0.2874 (Rfree = 0.000) for 6654 atoms. Found 54 (121 requested) and removed 63 (60 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.71 2.53 NCS extension: 0 residues added, 6738 seeds are put forward Round 1: 364 peptides, 77 chains. Longest chain 12 peptides. Score 0.268 Round 2: 408 peptides, 78 chains. Longest chain 12 peptides. Score 0.335 Round 3: 422 peptides, 76 chains. Longest chain 13 peptides. Score 0.371 Round 4: 426 peptides, 77 chains. Longest chain 14 peptides. Score 0.371 Round 5: 430 peptides, 74 chains. Longest chain 14 peptides. Score 0.397 Taking the results from Round 5 Chains 74, Residues 356, Estimated correctness of the model 42.8 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 36589 reflections ( 99.37 % complete ) and 13015 restraints for refining 6567 atoms. 11607 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3235 (Rfree = 0.000) for 6567 atoms. Found 119 (119 requested) and removed 59 (59 requested) atoms. Cycle 22: After refmac, R = 0.3005 (Rfree = 0.000) for 6617 atoms. Found 90 (120 requested) and removed 65 (60 requested) atoms. Cycle 23: After refmac, R = 0.2994 (Rfree = 0.000) for 6631 atoms. Found 79 (120 requested) and removed 65 (60 requested) atoms. Cycle 24: After refmac, R = 0.3082 (Rfree = 0.000) for 6638 atoms. Found 120 (120 requested) and removed 63 (60 requested) atoms. Cycle 25: After refmac, R = 0.2968 (Rfree = 0.000) for 6689 atoms. Found 94 (121 requested) and removed 61 (60 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.68 2.51 NCS extension: 0 residues added, 6816 seeds are put forward Round 1: 366 peptides, 73 chains. Longest chain 10 peptides. Score 0.300 Round 2: 383 peptides, 71 chains. Longest chain 14 peptides. Score 0.343 Round 3: 381 peptides, 67 chains. Longest chain 12 peptides. Score 0.367 Round 4: 401 peptides, 68 chains. Longest chain 16 peptides. Score 0.392 Round 5: 405 peptides, 71 chains. Longest chain 13 peptides. Score 0.378 Taking the results from Round 4 Chains 68, Residues 333, Estimated correctness of the model 41.9 % 4 chains (18 residues) have been docked in sequence ------------------------------------------------------ 36589 reflections ( 99.37 % complete ) and 12979 restraints for refining 6566 atoms. 11661 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3388 (Rfree = 0.000) for 6566 atoms. Found 119 (119 requested) and removed 63 (59 requested) atoms. Cycle 27: After refmac, R = 0.2941 (Rfree = 0.000) for 6613 atoms. Found 73 (120 requested) and removed 63 (60 requested) atoms. Cycle 28: After refmac, R = 0.2910 (Rfree = 0.000) for 6616 atoms. Found 81 (120 requested) and removed 63 (60 requested) atoms. Cycle 29: After refmac, R = 0.2742 (Rfree = 0.000) for 6629 atoms. Found 53 (120 requested) and removed 63 (60 requested) atoms. Cycle 30: After refmac, R = 0.2797 (Rfree = 0.000) for 6610 atoms. Found 56 (120 requested) and removed 60 (60 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.72 2.54 NCS extension: 0 residues added, 6632 seeds are put forward Round 1: 367 peptides, 75 chains. Longest chain 12 peptides. Score 0.288 Round 2: 398 peptides, 66 chains. Longest chain 16 peptides. Score 0.401 Round 3: 391 peptides, 67 chains. Longest chain 15 peptides. Score 0.383 Round 4: 395 peptides, 65 chains. Longest chain 15 peptides. Score 0.403 Round 5: 386 peptides, 66 chains. Longest chain 15 peptides. Score 0.382 Taking the results from Round 4 Chains 65, Residues 330, Estimated correctness of the model 43.8 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 36589 reflections ( 99.37 % complete ) and 13090 restraints for refining 6567 atoms. 11819 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2906 (Rfree = 0.000) for 6567 atoms. Found 93 (119 requested) and removed 59 (59 requested) atoms. Cycle 32: After refmac, R = 0.3093 (Rfree = 0.000) for 6594 atoms. Found 119 (119 requested) and removed 60 (59 requested) atoms. Cycle 33: After refmac, R = 0.3165 (Rfree = 0.000) for 6647 atoms. Found 120 (120 requested) and removed 66 (60 requested) atoms. Cycle 34: After refmac, R = 0.3080 (Rfree = 0.000) for 6693 atoms. Found 121 (121 requested) and removed 66 (60 requested) atoms. Cycle 35: After refmac, R = 0.3186 (Rfree = 0.000) for 6740 atoms. Found 122 (122 requested) and removed 69 (61 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.71 2.53 NCS extension: 0 residues added, 6868 seeds are put forward Round 1: 354 peptides, 73 chains. Longest chain 9 peptides. Score 0.280 Round 2: 380 peptides, 67 chains. Longest chain 16 peptides. Score 0.366 Round 3: 391 peptides, 68 chains. Longest chain 14 peptides. Score 0.377 Round 4: 390 peptides, 69 chains. Longest chain 15 peptides. Score 0.368 Round 5: 366 peptides, 66 chains. Longest chain 12 peptides. Score 0.350 Taking the results from Round 3 Chains 68, Residues 323, Estimated correctness of the model 39.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 36589 reflections ( 99.37 % complete ) and 13007 restraints for refining 6567 atoms. 11783 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2843 (Rfree = 0.000) for 6567 atoms. Found 105 (119 requested) and removed 59 (59 requested) atoms. Cycle 37: After refmac, R = 0.2751 (Rfree = 0.000) for 6606 atoms. Found 68 (119 requested) and removed 60 (59 requested) atoms. Cycle 38: After refmac, R = 0.2971 (Rfree = 0.000) for 6603 atoms. Found 119 (119 requested) and removed 62 (59 requested) atoms. Cycle 39: After refmac, R = 0.2760 (Rfree = 0.000) for 6659 atoms. Found 69 (120 requested) and removed 61 (60 requested) atoms. Cycle 40: After refmac, R = 0.2790 (Rfree = 0.000) for 6657 atoms. Found 89 (120 requested) and removed 61 (60 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.66 2.49 NCS extension: 0 residues added, 6750 seeds are put forward Round 1: 335 peptides, 70 chains. Longest chain 10 peptides. Score 0.269 Round 2: 376 peptides, 71 chains. Longest chain 13 peptides. Score 0.331 Round 3: 379 peptides, 66 chains. Longest chain 13 peptides. Score 0.371 Round 4: 394 peptides, 68 chains. Longest chain 13 peptides. Score 0.381 Round 5: 399 peptides, 72 chains. Longest chain 11 peptides. Score 0.362 Taking the results from Round 4 Chains 71, Residues 326, Estimated correctness of the model 40.0 % 5 chains (30 residues) have been docked in sequence ------------------------------------------------------ 36589 reflections ( 99.37 % complete ) and 12754 restraints for refining 6567 atoms. 11425 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2907 (Rfree = 0.000) for 6567 atoms. Found 114 (119 requested) and removed 62 (59 requested) atoms. Cycle 42: After refmac, R = 0.2890 (Rfree = 0.000) for 6609 atoms. Found 93 (120 requested) and removed 63 (60 requested) atoms. Cycle 43: After refmac, R = 0.2838 (Rfree = 0.000) for 6620 atoms. Found 95 (120 requested) and removed 62 (60 requested) atoms. Cycle 44: After refmac, R = 0.2851 (Rfree = 0.000) for 6644 atoms. Found 94 (120 requested) and removed 63 (60 requested) atoms. Cycle 45: After refmac, R = 0.2816 (Rfree = 0.000) for 6669 atoms. Found 72 (121 requested) and removed 63 (60 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.66 2.49 NCS extension: 0 residues added, 6700 seeds are put forward Round 1: 347 peptides, 73 chains. Longest chain 9 peptides. Score 0.268 Round 2: 362 peptides, 63 chains. Longest chain 17 peptides. Score 0.365 Round 3: 359 peptides, 64 chains. Longest chain 13 peptides. Score 0.353 Round 4: 360 peptides, 61 chains. Longest chain 17 peptides. Score 0.376 Round 5: 364 peptides, 63 chains. Longest chain 16 peptides. Score 0.368 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 61, Residues 299, Estimated correctness of the model 39.1 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 3 % 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 13009 restraints for refining 6567 atoms. 11855 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2793 (Rfree = 0.000) for 6567 atoms. Found 0 (119 requested) and removed 37 (59 requested) atoms. Cycle 47: After refmac, R = 0.2705 (Rfree = 0.000) for 6525 atoms. Found 0 (118 requested) and removed 23 (59 requested) atoms. Cycle 48: After refmac, R = 0.3012 (Rfree = 0.000) for 6500 atoms. Found 0 (117 requested) and removed 28 (58 requested) atoms. Cycle 49: After refmac, R = 0.2903 (Rfree = 0.000) for 6464 atoms. Found 0 (117 requested) and removed 32 (58 requested) atoms. Writing output files ... TimeTaking 97.2