Mon 24 Dec 08:05:44 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 1vrb-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vrb-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vrb-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vrb-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/1vrb-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vrb-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 08:05:48 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/1vrb-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vrb-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 874 and 0 Target number of residues in the AU: 874 Target solvent content: 0.6664 Checking the provided sequence file Detected sequence length: 342 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1368 Adjusted target solvent content: 0.48 Input MTZ file: 1vrb-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: 19 Cell parameters: 47.576 104.273 285.843 90.000 90.000 90.000 Input sequence file: 1vrb-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 10944 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: 48.979 3.800 Wilson plot Bfac: 89.57 14699 reflections ( 99.13 % complete ) and 0 restraints for refining 12072 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3656 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3330 (Rfree = 0.000) for 12072 atoms. Found 66 (66 requested) and removed 184 (33 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.70 3.80 Search for helices and strands: 0 residues in 0 chains, 12162 seeds are put forward NCS extension: 0 residues added, 12162 seeds are put forward Round 1: 370 peptides, 79 chains. Longest chain 8 peptides. Score 0.245 Round 2: 508 peptides, 91 chains. Longest chain 14 peptides. Score 0.357 Round 3: 534 peptides, 94 chains. Longest chain 13 peptides. Score 0.373 Round 4: 580 peptides, 96 chains. Longest chain 15 peptides. Score 0.415 Round 5: 595 peptides, 95 chains. Longest chain 15 peptides. Score 0.437 Taking the results from Round 5 Chains 95, Residues 500, Estimated correctness of the model 0.0 % 7 chains (30 residues) have been docked in sequence ------------------------------------------------------ 14699 reflections ( 99.13 % complete ) and 23710 restraints for refining 9891 atoms. 21731 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2840 (Rfree = 0.000) for 9891 atoms. Found 50 (54 requested) and removed 101 (27 requested) atoms. Cycle 2: After refmac, R = 0.2664 (Rfree = 0.000) for 9678 atoms. Found 41 (54 requested) and removed 91 (27 requested) atoms. Cycle 3: After refmac, R = 0.2177 (Rfree = 0.000) for 9538 atoms. Found 26 (52 requested) and removed 65 (26 requested) atoms. Cycle 4: After refmac, R = 0.2069 (Rfree = 0.000) for 9437 atoms. Found 11 (52 requested) and removed 50 (26 requested) atoms. Cycle 5: After refmac, R = 0.2018 (Rfree = 0.000) for 9367 atoms. Found 12 (51 requested) and removed 48 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.64 3.74 Search for helices and strands: 0 residues in 0 chains, 9645 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 9657 seeds are put forward Round 1: 490 peptides, 99 chains. Longest chain 9 peptides. Score 0.293 Round 2: 560 peptides, 92 chains. Longest chain 14 peptides. Score 0.413 Round 3: 572 peptides, 100 chains. Longest chain 15 peptides. Score 0.387 Round 4: 576 peptides, 97 chains. Longest chain 17 peptides. Score 0.406 Round 5: 597 peptides, 98 chains. Longest chain 15 peptides. Score 0.425 Taking the results from Round 5 Chains 98, Residues 499, Estimated correctness of the model 0.0 % 6 chains (30 residues) have been docked in sequence ------------------------------------------------------ 14699 reflections ( 99.13 % complete ) and 22051 restraints for refining 9522 atoms. 20078 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2477 (Rfree = 0.000) for 9522 atoms. Found 47 (52 requested) and removed 119 (26 requested) atoms. Cycle 7: After refmac, R = 0.2360 (Rfree = 0.000) for 9372 atoms. Found 51 (51 requested) and removed 74 (25 requested) atoms. Cycle 8: After refmac, R = 0.2335 (Rfree = 0.000) for 9296 atoms. Found 50 (51 requested) and removed 74 (25 requested) atoms. Cycle 9: After refmac, R = 0.2343 (Rfree = 0.000) for 9213 atoms. Found 50 (50 requested) and removed 59 (25 requested) atoms. Cycle 10: After refmac, R = 0.2023 (Rfree = 0.000) for 9148 atoms. Found 19 (50 requested) and removed 48 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.60 3.70 Search for helices and strands: 0 residues in 0 chains, 9465 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 9479 seeds are put forward Round 1: 478 peptides, 94 chains. Longest chain 9 peptides. Score 0.304 Round 2: 555 peptides, 96 chains. Longest chain 12 peptides. Score 0.387 Round 3: 552 peptides, 89 chains. Longest chain 15 peptides. Score 0.418 Round 4: 568 peptides, 89 chains. Longest chain 15 peptides. Score 0.436 Round 5: 590 peptides, 93 chains. Longest chain 20 peptides. Score 0.441 Taking the results from Round 5 Chains 93, Residues 497, Estimated correctness of the model 0.0 % 6 chains (25 residues) have been docked in sequence ------------------------------------------------------ 14699 reflections ( 99.13 % complete ) and 22158 restraints for refining 9603 atoms. 20199 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2454 (Rfree = 0.000) for 9603 atoms. Found 52 (52 requested) and removed 108 (26 requested) atoms. Cycle 12: After refmac, R = 0.2453 (Rfree = 0.000) for 9483 atoms. Found 52 (52 requested) and removed 73 (26 requested) atoms. Cycle 13: After refmac, R = 0.2265 (Rfree = 0.000) for 9392 atoms. Found 52 (52 requested) and removed 63 (26 requested) atoms. Cycle 14: After refmac, R = 0.2266 (Rfree = 0.000) for 9330 atoms. Found 51 (51 requested) and removed 55 (25 requested) atoms. Cycle 15: After refmac, R = 0.2241 (Rfree = 0.000) for 9276 atoms. Found 51 (51 requested) and removed 55 (25 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.59 3.69 Search for helices and strands: 0 residues in 0 chains, 9607 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 9622 seeds are put forward Round 1: 450 peptides, 92 chains. Longest chain 10 peptides. Score 0.280 Round 2: 533 peptides, 95 chains. Longest chain 13 peptides. Score 0.366 Round 3: 545 peptides, 91 chains. Longest chain 13 peptides. Score 0.401 Round 4: 531 peptides, 91 chains. Longest chain 13 peptides. Score 0.384 Round 5: 546 peptides, 90 chains. Longest chain 15 peptides. Score 0.407 Taking the results from Round 5 Chains 91, Residues 456, Estimated correctness of the model 0.0 % 5 chains (27 residues) have been docked in sequence ------------------------------------------------------ 14699 reflections ( 99.13 % complete ) and 21549 restraints for refining 9447 atoms. 19742 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2563 (Rfree = 0.000) for 9447 atoms. Found 51 (51 requested) and removed 110 (25 requested) atoms. Cycle 17: After refmac, R = 0.2350 (Rfree = 0.000) for 9310 atoms. Found 51 (51 requested) and removed 59 (25 requested) atoms. Cycle 18: After refmac, R = 0.2375 (Rfree = 0.000) for 9259 atoms. Found 51 (51 requested) and removed 63 (25 requested) atoms. Cycle 19: After refmac, R = 0.2279 (Rfree = 0.000) for 9189 atoms. Found 50 (50 requested) and removed 48 (25 requested) atoms. Cycle 20: After refmac, R = 0.2418 (Rfree = 0.000) for 9146 atoms. Found 50 (50 requested) and removed 48 (25 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.61 3.71 Search for helices and strands: 0 residues in 0 chains, 9467 seeds are put forward NCS extension: 11 residues added (5 deleted due to clashes), 9478 seeds are put forward Round 1: 384 peptides, 84 chains. Longest chain 10 peptides. Score 0.236 Round 2: 446 peptides, 87 chains. Longest chain 10 peptides. Score 0.302 Round 3: 485 peptides, 88 chains. Longest chain 15 peptides. Score 0.345 Round 4: 467 peptides, 83 chains. Longest chain 12 peptides. Score 0.349 Round 5: 442 peptides, 75 chains. Longest chain 13 peptides. Score 0.362 Taking the results from Round 5 Chains 75, Residues 367, Estimated correctness of the model 0.0 % 4 chains (21 residues) have been docked in sequence ------------------------------------------------------ 14699 reflections ( 99.13 % complete ) and 21637 restraints for refining 9318 atoms. 20194 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2457 (Rfree = 0.000) for 9318 atoms. Found 51 (51 requested) and removed 103 (25 requested) atoms. Cycle 22: After refmac, R = 0.2479 (Rfree = 0.000) for 9228 atoms. Found 50 (50 requested) and removed 70 (25 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2400 (Rfree = 0.000) for 9168 atoms. Found 50 (50 requested) and removed 51 (25 requested) atoms. Cycle 24: After refmac, R = 0.2026 (Rfree = 0.000) for 9128 atoms. Found 15 (50 requested) and removed 36 (25 requested) atoms. Cycle 25: After refmac, R = 0.1896 (Rfree = 0.000) for 9082 atoms. Found 19 (50 requested) and removed 35 (25 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.64 3.74 Search for helices and strands: 0 residues in 0 chains, 9313 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 9326 seeds are put forward Round 1: 381 peptides, 81 chains. Longest chain 11 peptides. Score 0.249 Round 2: 485 peptides, 88 chains. Longest chain 11 peptides. Score 0.345 Round 3: 472 peptides, 84 chains. Longest chain 13 peptides. Score 0.350 Round 4: 465 peptides, 76 chains. Longest chain 14 peptides. Score 0.384 Round 5: 452 peptides, 77 chains. Longest chain 13 peptides. Score 0.363 Taking the results from Round 4 Chains 76, Residues 389, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 14699 reflections ( 99.13 % complete ) and 21462 restraints for refining 9287 atoms. 19961 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2470 (Rfree = 0.000) for 9287 atoms. Found 51 (51 requested) and removed 136 (25 requested) atoms. Cycle 27: After refmac, R = 0.2417 (Rfree = 0.000) for 9167 atoms. Found 50 (50 requested) and removed 92 (25 requested) atoms. Cycle 28: After refmac, R = 0.2319 (Rfree = 0.000) for 9085 atoms. Found 50 (50 requested) and removed 41 (25 requested) atoms. Cycle 29: After refmac, R = 0.2023 (Rfree = 0.000) for 9061 atoms. Found 16 (50 requested) and removed 47 (25 requested) atoms. Cycle 30: After refmac, R = 0.1942 (Rfree = 0.000) for 9015 atoms. Found 16 (49 requested) and removed 33 (24 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.67 3.77 Search for helices and strands: 0 residues in 0 chains, 9234 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 9252 seeds are put forward Round 1: 383 peptides, 83 chains. Longest chain 10 peptides. Score 0.240 Round 2: 441 peptides, 80 chains. Longest chain 16 peptides. Score 0.333 Round 3: 434 peptides, 79 chains. Longest chain 12 peptides. Score 0.330 Round 4: 464 peptides, 82 chains. Longest chain 12 peptides. Score 0.351 Round 5: 477 peptides, 81 chains. Longest chain 15 peptides. Score 0.372 Taking the results from Round 5 Chains 81, Residues 396, Estimated correctness of the model 0.0 % 9 chains (40 residues) have been docked in sequence ------------------------------------------------------ 14699 reflections ( 99.13 % complete ) and 21027 restraints for refining 9275 atoms. 19442 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2493 (Rfree = 0.000) for 9275 atoms. Found 51 (51 requested) and removed 67 (25 requested) atoms. Cycle 32: After refmac, R = 0.2447 (Rfree = 0.000) for 9210 atoms. Found 50 (50 requested) and removed 62 (25 requested) atoms. Cycle 33: After refmac, R = 0.2319 (Rfree = 0.000) for 9154 atoms. Found 50 (50 requested) and removed 49 (25 requested) atoms. Cycle 34: After refmac, R = 0.1982 (Rfree = 0.000) for 9129 atoms. Found 19 (50 requested) and removed 40 (25 requested) atoms. Cycle 35: After refmac, R = 0.1964 (Rfree = 0.000) for 9095 atoms. Found 15 (50 requested) and removed 31 (25 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.67 3.77 Search for helices and strands: 0 residues in 0 chains, 9346 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 9364 seeds are put forward Round 1: 357 peptides, 79 chains. Longest chain 9 peptides. Score 0.227 Round 2: 418 peptides, 78 chains. Longest chain 14 peptides. Score 0.315 Round 3: 432 peptides, 79 chains. Longest chain 12 peptides. Score 0.327 Round 4: 454 peptides, 80 chains. Longest chain 14 peptides. Score 0.349 Round 5: 441 peptides, 79 chains. Longest chain 14 peptides. Score 0.339 Taking the results from Round 4 Chains 80, Residues 374, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 14699 reflections ( 99.13 % complete ) and 21489 restraints for refining 9292 atoms. 20041 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2347 (Rfree = 0.000) for 9292 atoms. Found 51 (51 requested) and removed 72 (25 requested) atoms. Cycle 37: After refmac, R = 0.2331 (Rfree = 0.000) for 9234 atoms. Found 50 (50 requested) and removed 54 (25 requested) atoms. Cycle 38: After refmac, R = 0.2287 (Rfree = 0.000) for 9199 atoms. Found 50 (50 requested) and removed 45 (25 requested) atoms. Cycle 39: After refmac, R = 0.2212 (Rfree = 0.000) for 9181 atoms. Found 50 (50 requested) and removed 39 (25 requested) atoms. Cycle 40: After refmac, R = 0.2193 (Rfree = 0.000) for 9177 atoms. Found 50 (50 requested) and removed 46 (25 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.66 3.76 Search for helices and strands: 0 residues in 0 chains, 9467 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 9492 seeds are put forward Round 1: 370 peptides, 80 chains. Longest chain 9 peptides. Score 0.240 Round 2: 410 peptides, 81 chains. Longest chain 15 peptides. Score 0.288 Round 3: 410 peptides, 79 chains. Longest chain 14 peptides. Score 0.299 Round 4: 430 peptides, 74 chains. Longest chain 17 peptides. Score 0.352 Round 5: 428 peptides, 82 chains. Longest chain 11 peptides. Score 0.306 Taking the results from Round 4 Chains 75, Residues 356, Estimated correctness of the model 0.0 % 5 chains (27 residues) have been docked in sequence ------------------------------------------------------ 14699 reflections ( 99.13 % complete ) and 21625 restraints for refining 9336 atoms. 20197 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2193 (Rfree = 0.000) for 9336 atoms. Found 51 (51 requested) and removed 63 (25 requested) atoms. Cycle 42: After refmac, R = 0.2140 (Rfree = 0.000) for 9264 atoms. Found 51 (51 requested) and removed 43 (25 requested) atoms. Cycle 43: After refmac, R = 0.2158 (Rfree = 0.000) for 9246 atoms. Found 50 (50 requested) and removed 47 (25 requested) atoms. Cycle 44: After refmac, R = 0.2124 (Rfree = 0.000) for 9223 atoms. Found 50 (50 requested) and removed 54 (25 requested) atoms. Cycle 45: After refmac, R = 0.2110 (Rfree = 0.000) for 9203 atoms. Found 50 (50 requested) and removed 45 (25 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.61 3.71 Search for helices and strands: 0 residues in 0 chains, 9442 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 9457 seeds are put forward Round 1: 286 peptides, 63 chains. Longest chain 8 peptides. Score 0.221 Round 2: 365 peptides, 72 chains. Longest chain 9 peptides. Score 0.279 Round 3: 361 peptides, 69 chains. Longest chain 10 peptides. Score 0.291 Round 4: 390 peptides, 71 chains. Longest chain 10 peptides. Score 0.318 Round 5: 391 peptides, 65 chains. Longest chain 16 peptides. Score 0.353 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 66, Residues 326, Estimated correctness of the model 0.0 % 5 chains (37 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 1vrb-3_warpNtrace.pdb as input Building loops using Loopy2018 66 chains (326 residues) following loop building 5 chains (37 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14699 reflections ( 99.13 % complete ) and 21727 restraints for refining 9397 atoms. 20344 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2192 (Rfree = 0.000) for 9397 atoms. Found 0 (51 requested) and removed 25 (25 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2186 (Rfree = 0.000) for 9326 atoms. Found 0 (51 requested) and removed 25 (25 requested) atoms. Cycle 48: After refmac, R = 0.2115 (Rfree = 0.000) for 9270 atoms. Found 0 (51 requested) and removed 25 (25 requested) atoms. Cycle 49: After refmac, R = 0.2058 (Rfree = 0.000) for 9227 atoms. TimeTaking 93.67