Mon 24 Dec 00:29:09 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 1vky-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vky-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vky-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vky-3.2-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/1vky-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vky-3.2-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 00:29:13 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/1vky-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vky-3.2-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 759 and 0 Target number of residues in the AU: 759 Target solvent content: 0.5743 Checking the provided sequence file Detected sequence length: 347 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 694 Adjusted target solvent content: 0.61 Input MTZ file: 1vky-3.2-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: 23 Cell parameters: 119.363 122.591 131.880 90.000 90.000 90.000 Input sequence file: 1vky-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5552 target number of atoms Had to go as low as 0.75 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: 41.380 3.200 Wilson plot Bfac: 43.08 16292 reflections ( 99.71 % complete ) and 0 restraints for refining 6133 atoms. Observations/parameters ratio is 0.66 ------------------------------------------------------ Starting model: R = 0.3121 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2191 (Rfree = 0.000) for 6133 atoms. Found 46 (55 requested) and removed 73 (27 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.87 2.47 Search for helices and strands: 0 residues in 0 chains, 6200 seeds are put forward NCS extension: 0 residues added, 6200 seeds are put forward Round 1: 382 peptides, 56 chains. Longest chain 15 peptides. Score 0.461 Round 2: 438 peptides, 55 chains. Longest chain 22 peptides. Score 0.550 Round 3: 452 peptides, 45 chains. Longest chain 35 peptides. Score 0.628 Round 4: 457 peptides, 44 chains. Longest chain 37 peptides. Score 0.640 Round 5: 448 peptides, 45 chains. Longest chain 27 peptides. Score 0.623 Taking the results from Round 4 Chains 49, Residues 413, Estimated correctness of the model 51.4 % 8 chains (123 residues) have been docked in sequence ------------------------------------------------------ 16292 reflections ( 99.71 % complete ) and 9343 restraints for refining 5068 atoms. 7212 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2651 (Rfree = 0.000) for 5068 atoms. Found 45 (45 requested) and removed 40 (22 requested) atoms. Cycle 2: After refmac, R = 0.2501 (Rfree = 0.000) for 5000 atoms. Found 45 (45 requested) and removed 30 (22 requested) atoms. Cycle 3: After refmac, R = 0.2370 (Rfree = 0.000) for 4982 atoms. Found 32 (45 requested) and removed 25 (22 requested) atoms. Cycle 4: After refmac, R = 0.2285 (Rfree = 0.000) for 4969 atoms. Found 19 (44 requested) and removed 23 (22 requested) atoms. Cycle 5: After refmac, R = 0.2244 (Rfree = 0.000) for 4941 atoms. Found 18 (44 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.90 2.50 Search for helices and strands: 0 residues in 0 chains, 5070 seeds are put forward NCS extension: 35 residues added (21 deleted due to clashes), 5105 seeds are put forward Round 1: 420 peptides, 50 chains. Longest chain 32 peptides. Score 0.557 Round 2: 441 peptides, 43 chains. Longest chain 27 peptides. Score 0.626 Round 3: 455 peptides, 42 chains. Longest chain 41 peptides. Score 0.648 Round 4: 447 peptides, 39 chains. Longest chain 35 peptides. Score 0.656 Round 5: 453 peptides, 38 chains. Longest chain 36 peptides. Score 0.668 Taking the results from Round 5 Chains 41, Residues 415, Estimated correctness of the model 58.1 % 6 chains (113 residues) have been docked in sequence ------------------------------------------------------ 16292 reflections ( 99.71 % complete ) and 9735 restraints for refining 5066 atoms. 7617 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2775 (Rfree = 0.000) for 5066 atoms. Found 45 (45 requested) and removed 42 (22 requested) atoms. Cycle 7: After refmac, R = 0.2558 (Rfree = 0.000) for 5047 atoms. Found 37 (45 requested) and removed 28 (22 requested) atoms. Cycle 8: After refmac, R = 0.2443 (Rfree = 0.000) for 5039 atoms. Found 17 (45 requested) and removed 28 (22 requested) atoms. Cycle 9: After refmac, R = 0.2409 (Rfree = 0.000) for 5016 atoms. Found 14 (45 requested) and removed 26 (22 requested) atoms. Cycle 10: After refmac, R = 0.2346 (Rfree = 0.000) for 4993 atoms. Found 11 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.92 2.52 Search for helices and strands: 0 residues in 0 chains, 5073 seeds are put forward NCS extension: 24 residues added (29 deleted due to clashes), 5097 seeds are put forward Round 1: 413 peptides, 43 chains. Longest chain 31 peptides. Score 0.591 Round 2: 443 peptides, 39 chains. Longest chain 33 peptides. Score 0.651 Round 3: 460 peptides, 38 chains. Longest chain 33 peptides. Score 0.676 Round 4: 457 peptides, 39 chains. Longest chain 43 peptides. Score 0.667 Round 5: 432 peptides, 37 chains. Longest chain 31 peptides. Score 0.650 Taking the results from Round 3 Chains 41, Residues 422, Estimated correctness of the model 59.9 % 7 chains (159 residues) have been docked in sequence ------------------------------------------------------ 16292 reflections ( 99.71 % complete ) and 8979 restraints for refining 5068 atoms. 6597 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2678 (Rfree = 0.000) for 5068 atoms. Found 45 (45 requested) and removed 50 (22 requested) atoms. Cycle 12: After refmac, R = 0.2496 (Rfree = 0.000) for 5036 atoms. Found 37 (45 requested) and removed 31 (22 requested) atoms. Cycle 13: After refmac, R = 0.2389 (Rfree = 0.000) for 5019 atoms. Found 32 (45 requested) and removed 23 (22 requested) atoms. Cycle 14: After refmac, R = 0.2303 (Rfree = 0.000) for 5013 atoms. Found 10 (45 requested) and removed 24 (22 requested) atoms. Cycle 15: After refmac, R = 0.2279 (Rfree = 0.000) for 4995 atoms. Found 20 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.89 2.49 Search for helices and strands: 0 residues in 0 chains, 5118 seeds are put forward NCS extension: 23 residues added (8 deleted due to clashes), 5141 seeds are put forward Round 1: 416 peptides, 45 chains. Longest chain 28 peptides. Score 0.583 Round 2: 427 peptides, 43 chains. Longest chain 41 peptides. Score 0.609 Round 3: 427 peptides, 42 chains. Longest chain 22 peptides. Score 0.615 Round 4: 438 peptides, 39 chains. Longest chain 28 peptides. Score 0.645 Round 5: 434 peptides, 44 chains. Longest chain 30 peptides. Score 0.612 Taking the results from Round 4 Chains 44, Residues 399, Estimated correctness of the model 52.6 % 8 chains (118 residues) have been docked in sequence ------------------------------------------------------ 16292 reflections ( 99.71 % complete ) and 9696 restraints for refining 5067 atoms. 7620 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2625 (Rfree = 0.000) for 5067 atoms. Found 45 (45 requested) and removed 37 (22 requested) atoms. Cycle 17: After refmac, R = 0.2427 (Rfree = 0.000) for 5061 atoms. Found 31 (45 requested) and removed 26 (22 requested) atoms. Cycle 18: After refmac, R = 0.2334 (Rfree = 0.000) for 5053 atoms. Found 23 (45 requested) and removed 23 (22 requested) atoms. Cycle 19: After refmac, R = 0.2268 (Rfree = 0.000) for 5042 atoms. Found 15 (45 requested) and removed 22 (22 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2268 (Rfree = 0.000) for 5024 atoms. Found 13 (45 requested) and removed 25 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.89 2.49 Search for helices and strands: 0 residues in 0 chains, 5126 seeds are put forward NCS extension: 39 residues added (3 deleted due to clashes), 5165 seeds are put forward Round 1: 413 peptides, 49 chains. Longest chain 23 peptides. Score 0.554 Round 2: 455 peptides, 38 chains. Longest chain 43 peptides. Score 0.670 Round 3: 440 peptides, 36 chains. Longest chain 42 peptides. Score 0.664 Round 4: 441 peptides, 37 chains. Longest chain 31 peptides. Score 0.660 Round 5: 434 peptides, 41 chains. Longest chain 38 peptides. Score 0.629 Taking the results from Round 2 Chains 41, Residues 417, Estimated correctness of the model 58.5 % 9 chains (155 residues) have been docked in sequence ------------------------------------------------------ 16292 reflections ( 99.71 % complete ) and 9038 restraints for refining 5068 atoms. 6745 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2512 (Rfree = 0.000) for 5068 atoms. Found 45 (45 requested) and removed 37 (22 requested) atoms. Cycle 22: After refmac, R = 0.2338 (Rfree = 0.000) for 5056 atoms. Found 32 (45 requested) and removed 27 (22 requested) atoms. Cycle 23: After refmac, R = 0.2259 (Rfree = 0.000) for 5046 atoms. Found 27 (45 requested) and removed 27 (22 requested) atoms. Cycle 24: After refmac, R = 0.2190 (Rfree = 0.000) for 5032 atoms. Found 15 (45 requested) and removed 24 (22 requested) atoms. Cycle 25: After refmac, R = 0.2165 (Rfree = 0.000) for 5011 atoms. Found 18 (45 requested) and removed 25 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.95 2.54 Search for helices and strands: 0 residues in 0 chains, 5093 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 5111 seeds are put forward Round 1: 423 peptides, 40 chains. Longest chain 34 peptides. Score 0.622 Round 2: 451 peptides, 39 chains. Longest chain 51 peptides. Score 0.660 Round 3: 447 peptides, 40 chains. Longest chain 44 peptides. Score 0.650 Round 4: 446 peptides, 37 chains. Longest chain 37 peptides. Score 0.666 Round 5: 455 peptides, 40 chains. Longest chain 41 peptides. Score 0.659 Taking the results from Round 4 Chains 40, Residues 409, Estimated correctness of the model 57.6 % 6 chains (110 residues) have been docked in sequence ------------------------------------------------------ 16292 reflections ( 99.71 % complete ) and 9725 restraints for refining 5068 atoms. 7635 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2559 (Rfree = 0.000) for 5068 atoms. Found 45 (45 requested) and removed 37 (22 requested) atoms. Cycle 27: After refmac, R = 0.2368 (Rfree = 0.000) for 5063 atoms. Found 42 (45 requested) and removed 23 (22 requested) atoms. Cycle 28: After refmac, R = 0.2272 (Rfree = 0.000) for 5072 atoms. Found 22 (45 requested) and removed 25 (22 requested) atoms. Cycle 29: After refmac, R = 0.2205 (Rfree = 0.000) for 5059 atoms. Found 9 (45 requested) and removed 23 (22 requested) atoms. Cycle 30: After refmac, R = 0.2174 (Rfree = 0.000) for 5035 atoms. Found 18 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.90 2.50 Search for helices and strands: 0 residues in 0 chains, 5144 seeds are put forward NCS extension: 22 residues added (18 deleted due to clashes), 5166 seeds are put forward Round 1: 425 peptides, 45 chains. Longest chain 22 peptides. Score 0.595 Round 2: 447 peptides, 38 chains. Longest chain 31 peptides. Score 0.661 Round 3: 417 peptides, 42 chains. Longest chain 25 peptides. Score 0.602 Round 4: 425 peptides, 43 chains. Longest chain 24 peptides. Score 0.607 Round 5: 425 peptides, 45 chains. Longest chain 23 peptides. Score 0.595 Taking the results from Round 2 Chains 45, Residues 409, Estimated correctness of the model 56.5 % 9 chains (159 residues) have been docked in sequence ------------------------------------------------------ 16292 reflections ( 99.71 % complete ) and 8950 restraints for refining 5068 atoms. 6597 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2573 (Rfree = 0.000) for 5068 atoms. Found 45 (45 requested) and removed 49 (22 requested) atoms. Cycle 32: After refmac, R = 0.2421 (Rfree = 0.000) for 5034 atoms. Found 37 (45 requested) and removed 25 (22 requested) atoms. Cycle 33: After refmac, R = 0.2326 (Rfree = 0.000) for 5031 atoms. Found 17 (45 requested) and removed 23 (22 requested) atoms. Cycle 34: After refmac, R = 0.2278 (Rfree = 0.000) for 5009 atoms. Found 17 (45 requested) and removed 22 (22 requested) atoms. Cycle 35: After refmac, R = 0.2270 (Rfree = 0.000) for 4993 atoms. Found 19 (44 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.89 2.49 Search for helices and strands: 0 residues in 0 chains, 5089 seeds are put forward NCS extension: 20 residues added (8 deleted due to clashes), 5109 seeds are put forward Round 1: 419 peptides, 43 chains. Longest chain 26 peptides. Score 0.599 Round 2: 426 peptides, 40 chains. Longest chain 37 peptides. Score 0.625 Round 3: 420 peptides, 38 chains. Longest chain 32 peptides. Score 0.630 Round 4: 435 peptides, 43 chains. Longest chain 33 peptides. Score 0.619 Round 5: 442 peptides, 42 chains. Longest chain 30 peptides. Score 0.633 Taking the results from Round 5 Chains 51, Residues 400, Estimated correctness of the model 49.7 % 9 chains (154 residues) have been docked in sequence ------------------------------------------------------ 16292 reflections ( 99.71 % complete ) and 9126 restraints for refining 5068 atoms. 6880 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2574 (Rfree = 0.000) for 5068 atoms. Found 45 (45 requested) and removed 40 (22 requested) atoms. Cycle 37: After refmac, R = 0.2372 (Rfree = 0.000) for 5046 atoms. Found 44 (45 requested) and removed 23 (22 requested) atoms. Cycle 38: After refmac, R = 0.2286 (Rfree = 0.000) for 5044 atoms. Found 26 (45 requested) and removed 23 (22 requested) atoms. Cycle 39: After refmac, R = 0.2238 (Rfree = 0.000) for 5033 atoms. Found 23 (45 requested) and removed 22 (22 requested) atoms. Cycle 40: After refmac, R = 0.2191 (Rfree = 0.000) for 5021 atoms. Found 13 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.87 2.47 Search for helices and strands: 0 residues in 0 chains, 5123 seeds are put forward NCS extension: 29 residues added (5 deleted due to clashes), 5152 seeds are put forward Round 1: 404 peptides, 47 chains. Longest chain 40 peptides. Score 0.554 Round 2: 432 peptides, 43 chains. Longest chain 41 peptides. Score 0.615 Round 3: 425 peptides, 41 chains. Longest chain 35 peptides. Score 0.618 Round 4: 433 peptides, 37 chains. Longest chain 40 peptides. Score 0.651 Round 5: 427 peptides, 40 chains. Longest chain 49 peptides. Score 0.627 Taking the results from Round 4 Chains 40, Residues 396, Estimated correctness of the model 54.1 % 7 chains (155 residues) have been docked in sequence ------------------------------------------------------ 16292 reflections ( 99.71 % complete ) and 9128 restraints for refining 5066 atoms. 6863 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2537 (Rfree = 0.000) for 5066 atoms. Found 45 (45 requested) and removed 39 (22 requested) atoms. Cycle 42: After refmac, R = 0.2330 (Rfree = 0.000) for 5040 atoms. Found 34 (45 requested) and removed 24 (22 requested) atoms. Cycle 43: After refmac, R = 0.2244 (Rfree = 0.000) for 5030 atoms. Found 15 (45 requested) and removed 24 (22 requested) atoms. Cycle 44: After refmac, R = 0.2212 (Rfree = 0.000) for 5002 atoms. Found 24 (45 requested) and removed 22 (22 requested) atoms. Cycle 45: After refmac, R = 0.2171 (Rfree = 0.000) for 4997 atoms. Found 16 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.89 2.49 Search for helices and strands: 0 residues in 0 chains, 5082 seeds are put forward NCS extension: 31 residues added (8 deleted due to clashes), 5113 seeds are put forward Round 1: 392 peptides, 49 chains. Longest chain 29 peptides. Score 0.524 Round 2: 418 peptides, 38 chains. Longest chain 31 peptides. Score 0.627 Round 3: 422 peptides, 43 chains. Longest chain 29 peptides. Score 0.603 Round 4: 423 peptides, 35 chains. Longest chain 33 peptides. Score 0.651 Round 5: 431 peptides, 39 chains. Longest chain 37 peptides. Score 0.637 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 43, Residues 388, Estimated correctness of the model 54.1 % 7 chains (137 residues) have been docked in sequence Sequence coverage is 35 % Consider running further cycles of model building using 1vky-3_warpNtrace.pdb as input Building loops using Loopy2018 43 chains (388 residues) following loop building 7 chains (137 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16292 reflections ( 99.71 % complete ) and 9306 restraints for refining 5067 atoms. 7130 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2476 (Rfree = 0.000) for 5067 atoms. Found 0 (45 requested) and removed 14 (22 requested) atoms. Cycle 47: After refmac, R = 0.2384 (Rfree = 0.000) for 5036 atoms. Found 0 (45 requested) and removed 7 (22 requested) atoms. Cycle 48: After refmac, R = 0.2335 (Rfree = 0.000) for 5024 atoms. Found 0 (45 requested) and removed 7 (22 requested) atoms. Cycle 49: After refmac, R = 0.2303 (Rfree = 0.000) for 5012 atoms. TimeTaking 55.72