null Mon 24 Dec 07:35:24 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 1vky-3.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vky-3.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vky-3.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vky-3.0-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/1vky-3.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vky-3.0-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 07:35:29 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/1vky-3.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vky-3.0-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 806 and 0 Target number of residues in the AU: 806 Target solvent content: 0.5479 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-3.0-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: 23 Cell parameters: 119.363 122.591 131.880 90.000 90.000 90.000 Input sequence file: 1vky-3.0-parrot-noncs.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 3.000 Wilson plot Bfac: 34.93 19666 reflections ( 99.68 % complete ) and 0 restraints for refining 6178 atoms. Observations/parameters ratio is 0.80 ------------------------------------------------------ Starting model: R = 0.3243 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2251 (Rfree = 0.000) for 6178 atoms. Found 52 (66 requested) and removed 115 (33 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.64 2.27 Search for helices and strands: 0 residues in 0 chains, 6226 seeds are put forward NCS extension: 0 residues added, 6226 seeds are put forward Round 1: 360 peptides, 58 chains. Longest chain 20 peptides. Score 0.411 Round 2: 394 peptides, 57 chains. Longest chain 29 peptides. Score 0.473 Round 3: 390 peptides, 52 chains. Longest chain 26 peptides. Score 0.501 Round 4: 402 peptides, 52 chains. Longest chain 30 peptides. Score 0.519 Round 5: 412 peptides, 48 chains. Longest chain 25 peptides. Score 0.559 Taking the results from Round 5 Chains 51, Residues 364, Estimated correctness of the model 42.5 % 5 chains (70 residues) have been docked in sequence ------------------------------------------------------ 19666 reflections ( 99.68 % complete ) and 9990 restraints for refining 5094 atoms. 8292 conditional restraints added. Observations/parameters ratio is 0.97 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2733 (Rfree = 0.000) for 5094 atoms. Found 54 (54 requested) and removed 33 (27 requested) atoms. Cycle 2: After refmac, R = 0.2564 (Rfree = 0.000) for 5073 atoms. Found 55 (55 requested) and removed 32 (27 requested) atoms. Cycle 3: After refmac, R = 0.2462 (Rfree = 0.000) for 5083 atoms. Found 40 (54 requested) and removed 30 (27 requested) atoms. Cycle 4: After refmac, R = 0.2458 (Rfree = 0.000) for 5081 atoms. Found 31 (54 requested) and removed 30 (27 requested) atoms. Cycle 5: After refmac, R = 0.2383 (Rfree = 0.000) for 5075 atoms. Found 20 (54 requested) and removed 31 (27 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.65 2.28 Search for helices and strands: 0 residues in 0 chains, 5177 seeds are put forward NCS extension: 23 residues added (4 deleted due to clashes), 5200 seeds are put forward Round 1: 380 peptides, 48 chains. Longest chain 26 peptides. Score 0.513 Round 2: 388 peptides, 45 chains. Longest chain 33 peptides. Score 0.545 Round 3: 402 peptides, 44 chains. Longest chain 37 peptides. Score 0.571 Round 4: 428 peptides, 52 chains. Longest chain 28 peptides. Score 0.555 Round 5: 414 peptides, 43 chains. Longest chain 34 peptides. Score 0.593 Taking the results from Round 5 Chains 44, Residues 371, Estimated correctness of the model 50.4 % 5 chains (94 residues) have been docked in sequence ------------------------------------------------------ 19666 reflections ( 99.68 % complete ) and 9665 restraints for refining 5094 atoms. 7781 conditional restraints added. Observations/parameters ratio is 0.97 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2719 (Rfree = 0.000) for 5094 atoms. Found 54 (54 requested) and removed 48 (27 requested) atoms. Cycle 7: After refmac, R = 0.2534 (Rfree = 0.000) for 5067 atoms. Found 47 (55 requested) and removed 29 (27 requested) atoms. Cycle 8: After refmac, R = 0.2440 (Rfree = 0.000) for 5070 atoms. Found 36 (54 requested) and removed 28 (27 requested) atoms. Cycle 9: After refmac, R = 0.2374 (Rfree = 0.000) for 5064 atoms. Found 22 (54 requested) and removed 27 (27 requested) atoms. Cycle 10: After refmac, R = 0.2338 (Rfree = 0.000) for 5048 atoms. Found 10 (54 requested) and removed 29 (27 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.67 2.30 Search for helices and strands: 0 residues in 0 chains, 5143 seeds are put forward NCS extension: 17 residues added (11 deleted due to clashes), 5160 seeds are put forward Round 1: 404 peptides, 52 chains. Longest chain 32 peptides. Score 0.522 Round 2: 439 peptides, 46 chains. Longest chain 30 peptides. Score 0.606 Round 3: 443 peptides, 46 chains. Longest chain 34 peptides. Score 0.611 Round 4: 444 peptides, 44 chains. Longest chain 40 peptides. Score 0.624 Round 5: 433 peptides, 45 chains. Longest chain 31 peptides. Score 0.605 Taking the results from Round 4 Chains 46, Residues 400, Estimated correctness of the model 57.1 % 6 chains (119 residues) have been docked in sequence ------------------------------------------------------ 19666 reflections ( 99.68 % complete ) and 9430 restraints for refining 5095 atoms. 7373 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2714 (Rfree = 0.000) for 5095 atoms. Found 54 (54 requested) and removed 42 (27 requested) atoms. Cycle 12: After refmac, R = 0.2516 (Rfree = 0.000) for 5084 atoms. Found 37 (55 requested) and removed 31 (27 requested) atoms. Cycle 13: After refmac, R = 0.2449 (Rfree = 0.000) for 5074 atoms. Found 34 (54 requested) and removed 34 (27 requested) atoms. Cycle 14: After refmac, R = 0.2470 (Rfree = 0.000) for 5066 atoms. Found 25 (54 requested) and removed 34 (27 requested) atoms. Cycle 15: After refmac, R = 0.2349 (Rfree = 0.000) for 5050 atoms. Found 21 (54 requested) and removed 32 (27 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.69 2.32 Search for helices and strands: 0 residues in 0 chains, 5164 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 5175 seeds are put forward Round 1: 397 peptides, 46 chains. Longest chain 25 peptides. Score 0.551 Round 2: 425 peptides, 44 chains. Longest chain 32 peptides. Score 0.601 Round 3: 423 peptides, 46 chains. Longest chain 24 peptides. Score 0.586 Round 4: 419 peptides, 42 chains. Longest chain 56 peptides. Score 0.605 Round 5: 436 peptides, 46 chains. Longest chain 32 peptides. Score 0.603 Taking the results from Round 4 Chains 44, Residues 377, Estimated correctness of the model 53.0 % 4 chains (97 residues) have been docked in sequence ------------------------------------------------------ 19666 reflections ( 99.68 % complete ) and 9677 restraints for refining 5095 atoms. 7776 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2856 (Rfree = 0.000) for 5095 atoms. Found 54 (54 requested) and removed 50 (27 requested) atoms. Cycle 17: After refmac, R = 0.2513 (Rfree = 0.000) for 5073 atoms. Found 46 (55 requested) and removed 35 (27 requested) atoms. Cycle 18: After refmac, R = 0.2395 (Rfree = 0.000) for 5072 atoms. Found 27 (54 requested) and removed 31 (27 requested) atoms. Cycle 19: After refmac, R = 0.2342 (Rfree = 0.000) for 5058 atoms. Found 18 (54 requested) and removed 28 (27 requested) atoms. Cycle 20: After refmac, R = 0.2306 (Rfree = 0.000) for 5041 atoms. Found 17 (54 requested) and removed 29 (27 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.67 2.30 Search for helices and strands: 0 residues in 0 chains, 5150 seeds are put forward NCS extension: 45 residues added (1 deleted due to clashes), 5195 seeds are put forward Round 1: 412 peptides, 47 chains. Longest chain 28 peptides. Score 0.565 Round 2: 431 peptides, 42 chains. Longest chain 38 peptides. Score 0.620 Round 3: 433 peptides, 43 chains. Longest chain 32 peptides. Score 0.617 Round 4: 435 peptides, 40 chains. Longest chain 51 peptides. Score 0.636 Round 5: 432 peptides, 40 chains. Longest chain 42 peptides. Score 0.633 Taking the results from Round 4 Chains 40, Residues 395, Estimated correctness of the model 59.5 % 4 chains (115 residues) have been docked in sequence ------------------------------------------------------ 19666 reflections ( 99.68 % complete ) and 9301 restraints for refining 5094 atoms. 7225 conditional restraints added. Observations/parameters ratio is 0.97 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2633 (Rfree = 0.000) for 5094 atoms. Found 54 (54 requested) and removed 39 (27 requested) atoms. Cycle 22: After refmac, R = 0.2437 (Rfree = 0.000) for 5089 atoms. Found 26 (55 requested) and removed 29 (27 requested) atoms. Cycle 23: After refmac, R = 0.2388 (Rfree = 0.000) for 5075 atoms. Found 22 (54 requested) and removed 28 (27 requested) atoms. Cycle 24: After refmac, R = 0.2329 (Rfree = 0.000) for 5061 atoms. Found 19 (54 requested) and removed 30 (27 requested) atoms. Cycle 25: After refmac, R = 0.2296 (Rfree = 0.000) for 5045 atoms. Found 23 (54 requested) and removed 27 (27 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.68 2.31 Search for helices and strands: 0 residues in 0 chains, 5150 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 5170 seeds are put forward Round 1: 409 peptides, 41 chains. Longest chain 54 peptides. Score 0.598 Round 2: 435 peptides, 39 chains. Longest chain 54 peptides. Score 0.642 Round 3: 440 peptides, 40 chains. Longest chain 54 peptides. Score 0.642 Round 4: 430 peptides, 39 chains. Longest chain 41 peptides. Score 0.636 Round 5: 435 peptides, 41 chains. Longest chain 51 peptides. Score 0.631 Taking the results from Round 3 Chains 44, Residues 400, Estimated correctness of the model 60.7 % 9 chains (189 residues) have been docked in sequence ------------------------------------------------------ 19666 reflections ( 99.68 % complete ) and 8561 restraints for refining 5093 atoms. 6178 conditional restraints added. Observations/parameters ratio is 0.97 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2539 (Rfree = 0.000) for 5093 atoms. Found 54 (54 requested) and removed 51 (27 requested) atoms. Cycle 27: After refmac, R = 0.2380 (Rfree = 0.000) for 5079 atoms. Found 40 (54 requested) and removed 30 (27 requested) atoms. Cycle 28: After refmac, R = 0.2266 (Rfree = 0.000) for 5074 atoms. Found 23 (54 requested) and removed 29 (27 requested) atoms. Cycle 29: After refmac, R = 0.2197 (Rfree = 0.000) for 5056 atoms. Found 26 (54 requested) and removed 28 (27 requested) atoms. Cycle 30: After refmac, R = 0.2160 (Rfree = 0.000) for 5043 atoms. Found 29 (54 requested) and removed 28 (27 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.66 2.29 Search for helices and strands: 0 residues in 0 chains, 5139 seeds are put forward NCS extension: 23 residues added (12 deleted due to clashes), 5162 seeds are put forward Round 1: 397 peptides, 39 chains. Longest chain 31 peptides. Score 0.595 Round 2: 421 peptides, 37 chains. Longest chain 33 peptides. Score 0.637 Round 3: 416 peptides, 37 chains. Longest chain 33 peptides. Score 0.631 Round 4: 421 peptides, 38 chains. Longest chain 30 peptides. Score 0.631 Round 5: 429 peptides, 41 chains. Longest chain 37 peptides. Score 0.623 Taking the results from Round 2 Chains 37, Residues 384, Estimated correctness of the model 59.7 % 9 chains (188 residues) have been docked in sequence ------------------------------------------------------ 19666 reflections ( 99.68 % complete ) and 8673 restraints for refining 5094 atoms. 6370 conditional restraints added. Observations/parameters ratio is 0.97 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2375 (Rfree = 0.000) for 5094 atoms. Found 54 (54 requested) and removed 41 (27 requested) atoms. Cycle 32: After refmac, R = 0.2204 (Rfree = 0.000) for 5098 atoms. Found 24 (55 requested) and removed 32 (27 requested) atoms. Cycle 33: After refmac, R = 0.2157 (Rfree = 0.000) for 5082 atoms. Found 25 (54 requested) and removed 27 (27 requested) atoms. Cycle 34: After refmac, R = 0.2113 (Rfree = 0.000) for 5074 atoms. Found 26 (54 requested) and removed 33 (27 requested) atoms. Cycle 35: After refmac, R = 0.2104 (Rfree = 0.000) for 5065 atoms. Found 24 (54 requested) and removed 30 (27 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.66 2.29 Search for helices and strands: 0 residues in 0 chains, 5185 seeds are put forward NCS extension: 23 residues added (27 deleted due to clashes), 5208 seeds are put forward Round 1: 397 peptides, 36 chains. Longest chain 38 peptides. Score 0.614 Round 2: 419 peptides, 37 chains. Longest chain 46 peptides. Score 0.635 Round 3: 423 peptides, 38 chains. Longest chain 32 peptides. Score 0.634 Round 4: 444 peptides, 38 chains. Longest chain 51 peptides. Score 0.658 Round 5: 433 peptides, 42 chains. Longest chain 31 peptides. Score 0.622 Taking the results from Round 4 Chains 41, Residues 406, Estimated correctness of the model 63.9 % 9 chains (194 residues) have been docked in sequence ------------------------------------------------------ 19666 reflections ( 99.68 % complete ) and 8366 restraints for refining 5095 atoms. 5921 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2476 (Rfree = 0.000) for 5095 atoms. Found 54 (54 requested) and removed 56 (27 requested) atoms. Cycle 37: After refmac, R = 0.2298 (Rfree = 0.000) for 5082 atoms. Found 52 (54 requested) and removed 29 (27 requested) atoms. Cycle 38: After refmac, R = 0.2182 (Rfree = 0.000) for 5096 atoms. Found 24 (55 requested) and removed 34 (27 requested) atoms. Cycle 39: After refmac, R = 0.2129 (Rfree = 0.000) for 5080 atoms. Found 25 (54 requested) and removed 28 (27 requested) atoms. Cycle 40: After refmac, R = 0.2095 (Rfree = 0.000) for 5073 atoms. Found 30 (54 requested) and removed 31 (27 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.64 2.27 Search for helices and strands: 0 residues in 0 chains, 5205 seeds are put forward NCS extension: 67 residues added (15 deleted due to clashes), 5272 seeds are put forward Round 1: 391 peptides, 38 chains. Longest chain 33 peptides. Score 0.594 Round 2: 421 peptides, 33 chains. Longest chain 51 peptides. Score 0.660 Round 3: 401 peptides, 36 chains. Longest chain 47 peptides. Score 0.619 Round 4: 426 peptides, 38 chains. Longest chain 46 peptides. Score 0.637 Round 5: 432 peptides, 42 chains. Longest chain 51 peptides. Score 0.621 Taking the results from Round 2 Chains 38, Residues 388, Estimated correctness of the model 64.3 % 10 chains (250 residues) have been docked in sequence ------------------------------------------------------ 19666 reflections ( 99.68 % complete ) and 7758 restraints for refining 5095 atoms. 5095 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2430 (Rfree = 0.000) for 5095 atoms. Found 54 (54 requested) and removed 47 (27 requested) atoms. Cycle 42: After refmac, R = 0.2259 (Rfree = 0.000) for 5080 atoms. Found 39 (55 requested) and removed 33 (27 requested) atoms. Cycle 43: After refmac, R = 0.2205 (Rfree = 0.000) for 5075 atoms. Found 20 (54 requested) and removed 30 (27 requested) atoms. Cycle 44: After refmac, R = 0.2146 (Rfree = 0.000) for 5061 atoms. Found 16 (54 requested) and removed 28 (27 requested) atoms. Cycle 45: After refmac, R = 0.2110 (Rfree = 0.000) for 5046 atoms. Found 22 (54 requested) and removed 30 (27 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.65 2.28 Search for helices and strands: 0 residues in 0 chains, 5141 seeds are put forward NCS extension: 43 residues added (27 deleted due to clashes), 5184 seeds are put forward Round 1: 409 peptides, 34 chains. Longest chain 51 peptides. Score 0.640 Round 2: 412 peptides, 31 chains. Longest chain 41 peptides. Score 0.661 Round 3: 405 peptides, 32 chains. Longest chain 35 peptides. Score 0.647 Round 4: 405 peptides, 33 chains. Longest chain 51 peptides. Score 0.641 Round 5: 413 peptides, 35 chains. Longest chain 45 peptides. Score 0.639 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 37, Residues 381, Estimated correctness of the model 64.5 % 12 chains (251 residues) have been docked in sequence Sequence coverage is 65 % Consider running further cycles of model building using 1vky-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 256 A and 263 A Built loop between residues 54 B and 58 B 33 chains (384 residues) following loop building 10 chains (260 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 19666 reflections ( 99.68 % complete ) and 7794 restraints for refining 5095 atoms. 5188 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2445 (Rfree = 0.000) for 5095 atoms. Found 0 (54 requested) and removed 6 (27 requested) atoms. Cycle 47: After refmac, R = 0.2309 (Rfree = 0.000) for 5080 atoms. Found 0 (54 requested) and removed 3 (27 requested) atoms. Cycle 48: After refmac, R = 0.2248 (Rfree = 0.000) for 5067 atoms. Found 0 (54 requested) and removed 1 (27 requested) atoms. Cycle 49: After refmac, R = 0.2213 (Rfree = 0.000) for 5060 atoms. Found 0 (54 requested) and removed 3 (27 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:45:47 GMT 2018 Job finished. TimeTaking 70.37 Used memory is bytes: 10134960