null Mon 24 Dec 07:30:23 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-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vky-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vky-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vky-3.6-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-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vky-3.6-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 07:30:28 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-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vky-3.6-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 702 and 0 Target number of residues in the AU: 702 Target solvent content: 0.6063 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-3.6-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-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 5552 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: 41.380 3.600 Wilson plot Bfac: 55.00 11505 reflections ( 99.71 % complete ) and 0 restraints for refining 6189 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3206 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2953 (Rfree = 0.000) for 6189 atoms. Found 39 (39 requested) and removed 80 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.21 2.77 Search for helices and strands: 0 residues in 0 chains, 6243 seeds are put forward NCS extension: 0 residues added, 6243 seeds are put forward Round 1: 312 peptides, 56 chains. Longest chain 13 peptides. Score 0.343 Round 2: 378 peptides, 56 chains. Longest chain 17 peptides. Score 0.455 Round 3: 416 peptides, 45 chains. Longest chain 29 peptides. Score 0.583 Round 4: 390 peptides, 49 chains. Longest chain 23 peptides. Score 0.521 Round 5: 391 peptides, 50 chains. Longest chain 20 peptides. Score 0.516 Taking the results from Round 3 Chains 45, Residues 371, Estimated correctness of the model 7.9 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 11505 reflections ( 99.71 % complete ) and 10942 restraints for refining 5030 atoms. 9451 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2470 (Rfree = 0.000) for 5030 atoms. Found 32 (32 requested) and removed 38 (16 requested) atoms. Cycle 2: After refmac, R = 0.2264 (Rfree = 0.000) for 4943 atoms. Found 32 (32 requested) and removed 34 (16 requested) atoms. Cycle 3: After refmac, R = 0.2180 (Rfree = 0.000) for 4913 atoms. Found 23 (31 requested) and removed 38 (15 requested) atoms. Cycle 4: After refmac, R = 0.2098 (Rfree = 0.000) for 4877 atoms. Found 25 (31 requested) and removed 39 (15 requested) atoms. Cycle 5: After refmac, R = 0.2045 (Rfree = 0.000) for 4847 atoms. Found 23 (31 requested) and removed 32 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.16 2.72 Search for helices and strands: 0 residues in 0 chains, 4973 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 4995 seeds are put forward Round 1: 366 peptides, 59 chains. Longest chain 15 peptides. Score 0.414 Round 2: 387 peptides, 46 chains. Longest chain 20 peptides. Score 0.537 Round 3: 376 peptides, 46 chains. Longest chain 24 peptides. Score 0.521 Round 4: 387 peptides, 50 chains. Longest chain 21 peptides. Score 0.510 Round 5: 386 peptides, 44 chains. Longest chain 24 peptides. Score 0.549 Taking the results from Round 5 Chains 48, Residues 342, Estimated correctness of the model 0.0 % 3 chains (47 residues) have been docked in sequence ------------------------------------------------------ 11505 reflections ( 99.71 % complete ) and 10640 restraints for refining 5032 atoms. 9135 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2486 (Rfree = 0.000) for 5032 atoms. Found 32 (32 requested) and removed 40 (16 requested) atoms. Cycle 7: After refmac, R = 0.2359 (Rfree = 0.000) for 4983 atoms. Found 30 (32 requested) and removed 33 (16 requested) atoms. Cycle 8: After refmac, R = 0.2318 (Rfree = 0.000) for 4960 atoms. Found 27 (31 requested) and removed 37 (15 requested) atoms. Cycle 9: After refmac, R = 0.2259 (Rfree = 0.000) for 4940 atoms. Found 22 (31 requested) and removed 38 (15 requested) atoms. Cycle 10: After refmac, R = 0.2170 (Rfree = 0.000) for 4913 atoms. Found 26 (31 requested) and removed 31 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.16 2.72 Search for helices and strands: 0 residues in 0 chains, 5058 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 5081 seeds are put forward Round 1: 377 peptides, 62 chains. Longest chain 17 peptides. Score 0.410 Round 2: 400 peptides, 52 chains. Longest chain 30 peptides. Score 0.516 Round 3: 401 peptides, 49 chains. Longest chain 19 peptides. Score 0.537 Round 4: 407 peptides, 50 chains. Longest chain 29 peptides. Score 0.539 Round 5: 395 peptides, 44 chains. Longest chain 32 peptides. Score 0.561 Taking the results from Round 5 Chains 44, Residues 351, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 11505 reflections ( 99.71 % complete ) and 10947 restraints for refining 5033 atoms. 9525 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2726 (Rfree = 0.000) for 5033 atoms. Found 32 (32 requested) and removed 33 (16 requested) atoms. Cycle 12: After refmac, R = 0.2574 (Rfree = 0.000) for 5004 atoms. Found 32 (32 requested) and removed 32 (16 requested) atoms. Cycle 13: After refmac, R = 0.2478 (Rfree = 0.000) for 4983 atoms. Found 32 (32 requested) and removed 36 (16 requested) atoms. Cycle 14: After refmac, R = 0.2327 (Rfree = 0.000) for 4962 atoms. Found 30 (31 requested) and removed 25 (15 requested) atoms. Cycle 15: After refmac, R = 0.2295 (Rfree = 0.000) for 4954 atoms. Found 31 (31 requested) and removed 27 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.22 2.77 Search for helices and strands: 0 residues in 0 chains, 5119 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 5147 seeds are put forward Round 1: 358 peptides, 56 chains. Longest chain 23 peptides. Score 0.423 Round 2: 385 peptides, 49 chains. Longest chain 21 peptides. Score 0.514 Round 3: 387 peptides, 51 chains. Longest chain 18 peptides. Score 0.503 Round 4: 398 peptides, 55 chains. Longest chain 23 peptides. Score 0.493 Round 5: 391 peptides, 52 chains. Longest chain 20 peptides. Score 0.503 Taking the results from Round 2 Chains 52, Residues 336, Estimated correctness of the model 0.0 % 4 chains (34 residues) have been docked in sequence ------------------------------------------------------ 11505 reflections ( 99.71 % complete ) and 10906 restraints for refining 5032 atoms. 9502 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2534 (Rfree = 0.000) for 5032 atoms. Found 32 (32 requested) and removed 35 (16 requested) atoms. Cycle 17: After refmac, R = 0.2393 (Rfree = 0.000) for 4995 atoms. Found 32 (32 requested) and removed 31 (16 requested) atoms. Cycle 18: After refmac, R = 0.2501 (Rfree = 0.000) for 4977 atoms. Found 32 (32 requested) and removed 28 (16 requested) atoms. Cycle 19: After refmac, R = 0.2277 (Rfree = 0.000) for 4962 atoms. Found 29 (31 requested) and removed 23 (15 requested) atoms. Cycle 20: After refmac, R = 0.2213 (Rfree = 0.000) for 4949 atoms. Found 19 (31 requested) and removed 25 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.18 2.74 Search for helices and strands: 0 residues in 0 chains, 5063 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 5080 seeds are put forward Round 1: 348 peptides, 57 chains. Longest chain 21 peptides. Score 0.398 Round 2: 392 peptides, 56 chains. Longest chain 24 peptides. Score 0.477 Round 3: 390 peptides, 57 chains. Longest chain 20 peptides. Score 0.467 Round 4: 391 peptides, 51 chains. Longest chain 23 peptides. Score 0.509 Round 5: 389 peptides, 49 chains. Longest chain 26 peptides. Score 0.520 Taking the results from Round 5 Chains 50, Residues 340, Estimated correctness of the model 0.0 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 11505 reflections ( 99.71 % complete ) and 10826 restraints for refining 5033 atoms. 9421 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2547 (Rfree = 0.000) for 5033 atoms. Found 32 (32 requested) and removed 26 (16 requested) atoms. Cycle 22: After refmac, R = 0.2450 (Rfree = 0.000) for 5007 atoms. Found 32 (32 requested) and removed 23 (16 requested) atoms. Cycle 23: After refmac, R = 0.2260 (Rfree = 0.000) for 4992 atoms. Found 32 (32 requested) and removed 32 (16 requested) atoms. Cycle 24: After refmac, R = 0.2173 (Rfree = 0.000) for 4986 atoms. Found 22 (32 requested) and removed 38 (16 requested) atoms. Cycle 25: After refmac, R = 0.2170 (Rfree = 0.000) for 4963 atoms. Found 25 (31 requested) and removed 28 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.19 2.75 Search for helices and strands: 0 residues in 0 chains, 5110 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 5139 seeds are put forward Round 1: 351 peptides, 56 chains. Longest chain 20 peptides. Score 0.411 Round 2: 383 peptides, 54 chains. Longest chain 36 peptides. Score 0.477 Round 3: 367 peptides, 55 chains. Longest chain 16 peptides. Score 0.444 Round 4: 376 peptides, 53 chains. Longest chain 27 peptides. Score 0.473 Round 5: 392 peptides, 56 chains. Longest chain 19 peptides. Score 0.477 Taking the results from Round 5 Chains 56, Residues 336, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 11505 reflections ( 99.71 % complete ) and 11079 restraints for refining 5032 atoms. 9732 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2503 (Rfree = 0.000) for 5032 atoms. Found 32 (32 requested) and removed 29 (16 requested) atoms. Cycle 27: After refmac, R = 0.2340 (Rfree = 0.000) for 5004 atoms. Found 26 (32 requested) and removed 30 (16 requested) atoms. Cycle 28: After refmac, R = 0.2260 (Rfree = 0.000) for 4979 atoms. Found 23 (32 requested) and removed 28 (16 requested) atoms. Cycle 29: After refmac, R = 0.2199 (Rfree = 0.000) for 4967 atoms. Found 15 (31 requested) and removed 23 (15 requested) atoms. Cycle 30: After refmac, R = 0.2168 (Rfree = 0.000) for 4953 atoms. Found 15 (31 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.23 2.78 Search for helices and strands: 0 residues in 0 chains, 5116 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 5142 seeds are put forward Round 1: 319 peptides, 53 chains. Longest chain 12 peptides. Score 0.379 Round 2: 340 peptides, 52 chains. Longest chain 20 peptides. Score 0.422 Round 3: 358 peptides, 51 chains. Longest chain 21 peptides. Score 0.459 Round 4: 347 peptides, 45 chains. Longest chain 19 peptides. Score 0.484 Round 5: 361 peptides, 46 chains. Longest chain 19 peptides. Score 0.499 Taking the results from Round 5 Chains 49, Residues 315, Estimated correctness of the model 0.0 % 6 chains (65 residues) have been docked in sequence ------------------------------------------------------ 11505 reflections ( 99.71 % complete ) and 10642 restraints for refining 5032 atoms. 9171 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2570 (Rfree = 0.000) for 5032 atoms. Found 32 (32 requested) and removed 36 (16 requested) atoms. Cycle 32: After refmac, R = 0.2363 (Rfree = 0.000) for 4995 atoms. Found 29 (32 requested) and removed 25 (16 requested) atoms. Cycle 33: After refmac, R = 0.2379 (Rfree = 0.000) for 4984 atoms. Found 27 (32 requested) and removed 25 (16 requested) atoms. Cycle 34: After refmac, R = 0.2264 (Rfree = 0.000) for 4965 atoms. Found 23 (31 requested) and removed 21 (15 requested) atoms. Cycle 35: After refmac, R = 0.2296 (Rfree = 0.000) for 4960 atoms. Found 24 (31 requested) and removed 26 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.21 2.77 Search for helices and strands: 0 residues in 0 chains, 5078 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 5105 seeds are put forward Round 1: 330 peptides, 58 chains. Longest chain 12 peptides. Score 0.360 Round 2: 380 peptides, 53 chains. Longest chain 19 peptides. Score 0.479 Round 3: 385 peptides, 52 chains. Longest chain 21 peptides. Score 0.494 Round 4: 385 peptides, 52 chains. Longest chain 22 peptides. Score 0.494 Round 5: 391 peptides, 55 chains. Longest chain 19 peptides. Score 0.482 Taking the results from Round 4 Chains 52, Residues 333, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 11505 reflections ( 99.71 % complete ) and 11192 restraints for refining 5033 atoms. 9890 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2582 (Rfree = 0.000) for 5033 atoms. Found 32 (32 requested) and removed 34 (16 requested) atoms. Cycle 37: After refmac, R = 0.2357 (Rfree = 0.000) for 5002 atoms. Found 25 (32 requested) and removed 26 (16 requested) atoms. Cycle 38: After refmac, R = 0.2235 (Rfree = 0.000) for 4985 atoms. Found 27 (32 requested) and removed 26 (16 requested) atoms. Cycle 39: After refmac, R = 0.2199 (Rfree = 0.000) for 4972 atoms. Found 22 (31 requested) and removed 32 (15 requested) atoms. Cycle 40: After refmac, R = 0.2166 (Rfree = 0.000) for 4958 atoms. Found 28 (31 requested) and removed 22 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 2.80 Search for helices and strands: 0 residues in 0 chains, 5095 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 5118 seeds are put forward Round 1: 300 peptides, 51 chains. Longest chain 16 peptides. Score 0.361 Round 2: 328 peptides, 45 chains. Longest chain 21 peptides. Score 0.454 Round 3: 340 peptides, 49 chains. Longest chain 22 peptides. Score 0.444 Round 4: 355 peptides, 47 chains. Longest chain 23 peptides. Score 0.482 Round 5: 334 peptides, 47 chains. Longest chain 20 peptides. Score 0.449 Taking the results from Round 4 Chains 48, Residues 308, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 11505 reflections ( 99.71 % complete ) and 11292 restraints for refining 5032 atoms. 10058 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2444 (Rfree = 0.000) for 5032 atoms. Found 32 (32 requested) and removed 28 (16 requested) atoms. Cycle 42: After refmac, R = 0.2279 (Rfree = 0.000) for 5015 atoms. Found 26 (32 requested) and removed 21 (16 requested) atoms. Cycle 43: After refmac, R = 0.2149 (Rfree = 0.000) for 5007 atoms. Found 24 (32 requested) and removed 25 (16 requested) atoms. Cycle 44: After refmac, R = 0.2046 (Rfree = 0.000) for 4992 atoms. Found 20 (32 requested) and removed 27 (16 requested) atoms. Cycle 45: After refmac, R = 0.2067 (Rfree = 0.000) for 4975 atoms. Found 18 (31 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.21 2.77 Search for helices and strands: 0 residues in 0 chains, 5093 seeds are put forward NCS extension: 32 residues added (2 deleted due to clashes), 5125 seeds are put forward Round 1: 295 peptides, 52 chains. Longest chain 17 peptides. Score 0.344 Round 2: 324 peptides, 51 chains. Longest chain 17 peptides. Score 0.403 Round 3: 342 peptides, 48 chains. Longest chain 18 peptides. Score 0.455 Round 4: 355 peptides, 49 chains. Longest chain 18 peptides. Score 0.468 Round 5: 345 peptides, 47 chains. Longest chain 20 peptides. Score 0.467 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 51, Residues 306, Estimated correctness of the model 0.0 % 2 chains (26 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 1vky-3_warpNtrace.pdb as input Building loops using Loopy2018 51 chains (306 residues) following loop building 2 chains (26 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11505 reflections ( 99.71 % complete ) and 10949 restraints for refining 5033 atoms. 9685 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2311 (Rfree = 0.000) for 5033 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2212 (Rfree = 0.000) for 5006 atoms. Found 0 (32 requested) and removed 14 (16 requested) atoms. Cycle 48: After refmac, R = 0.2119 (Rfree = 0.000) for 4989 atoms. Found 0 (32 requested) and removed 5 (16 requested) atoms. Cycle 49: After refmac, R = 0.2074 (Rfree = 0.000) for 4977 atoms. Found 0 (31 requested) and removed 5 (15 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:31:37 GMT 2018 Job finished. TimeTaking 61.22 Used memory is bytes: 22433192