null Sun 23 Dec 22:23:05 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vky-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vky-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vky-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vky-3.6-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/1vky-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vky-3.6-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:23:15 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/hancs/ArpWArp/wArpResults/WorkingDir/1vky-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vky-3.6-parrot-hancs/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-hancs.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-hancs.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 6168 atoms. Observations/parameters ratio is 0.47 ------------------------------------------------------ Starting model: R = 0.3143 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2796 (Rfree = 0.000) for 6168 atoms. Found 39 (39 requested) and removed 61 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.25 2.80 Search for helices and strands: 0 residues in 0 chains, 6244 seeds are put forward NCS extension: 0 residues added, 6244 seeds are put forward Round 1: 359 peptides, 58 chains. Longest chain 17 peptides. Score 0.409 Round 2: 402 peptides, 54 chains. Longest chain 26 peptides. Score 0.505 Round 3: 404 peptides, 52 chains. Longest chain 21 peptides. Score 0.522 Round 4: 400 peptides, 49 chains. Longest chain 19 peptides. Score 0.536 Round 5: 417 peptides, 50 chains. Longest chain 27 peptides. Score 0.553 Taking the results from Round 5 Chains 50, Residues 367, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 11505 reflections ( 99.71 % complete ) and 11112 restraints for refining 5031 atoms. 9638 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2414 (Rfree = 0.000) for 5031 atoms. Found 32 (32 requested) and removed 38 (16 requested) atoms. Cycle 2: After refmac, R = 0.2300 (Rfree = 0.000) for 4922 atoms. Found 32 (32 requested) and removed 32 (16 requested) atoms. Cycle 3: After refmac, R = 0.2222 (Rfree = 0.000) for 4897 atoms. Found 31 (31 requested) and removed 36 (15 requested) atoms. Cycle 4: After refmac, R = 0.2114 (Rfree = 0.000) for 4868 atoms. Found 27 (31 requested) and removed 31 (15 requested) atoms. Cycle 5: After refmac, R = 0.2083 (Rfree = 0.000) for 4847 atoms. Found 25 (31 requested) and removed 32 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.20 2.76 Search for helices and strands: 0 residues in 0 chains, 5010 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 5040 seeds are put forward Round 1: 383 peptides, 54 chains. Longest chain 23 peptides. Score 0.477 Round 2: 404 peptides, 45 chains. Longest chain 29 peptides. Score 0.567 Round 3: 424 peptides, 48 chains. Longest chain 24 peptides. Score 0.575 Round 4: 427 peptides, 41 chains. Longest chain 28 peptides. Score 0.621 Round 5: 425 peptides, 43 chains. Longest chain 28 peptides. Score 0.607 Taking the results from Round 4 Chains 48, Residues 386, Estimated correctness of the model 22.7 % 7 chains (88 residues) have been docked in sequence ------------------------------------------------------ 11505 reflections ( 99.71 % complete ) and 10087 restraints for refining 5032 atoms. 8240 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2549 (Rfree = 0.000) for 5032 atoms. Found 32 (32 requested) and removed 49 (16 requested) atoms. Cycle 7: After refmac, R = 0.2341 (Rfree = 0.000) for 4963 atoms. Found 32 (32 requested) and removed 43 (16 requested) atoms. Cycle 8: After refmac, R = 0.2215 (Rfree = 0.000) for 4924 atoms. Found 31 (31 requested) and removed 34 (15 requested) atoms. Cycle 9: After refmac, R = 0.2124 (Rfree = 0.000) for 4906 atoms. Found 25 (31 requested) and removed 28 (15 requested) atoms. Cycle 10: After refmac, R = 0.2109 (Rfree = 0.000) for 4879 atoms. Found 31 (31 requested) and removed 25 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.23 2.78 Search for helices and strands: 0 residues in 0 chains, 5013 seeds are put forward NCS extension: 32 residues added (5 deleted due to clashes), 5045 seeds are put forward Round 1: 380 peptides, 49 chains. Longest chain 22 peptides. Score 0.506 Round 2: 420 peptides, 51 chains. Longest chain 21 peptides. Score 0.551 Round 3: 416 peptides, 47 chains. Longest chain 27 peptides. Score 0.570 Round 4: 443 peptides, 49 chains. Longest chain 37 peptides. Score 0.594 Round 5: 438 peptides, 51 chains. Longest chain 31 peptides. Score 0.575 Taking the results from Round 4 Chains 51, Residues 394, Estimated correctness of the model 12.3 % 3 chains (56 residues) have been docked in sequence ------------------------------------------------------ 11505 reflections ( 99.71 % complete ) and 10232 restraints for refining 5033 atoms. 8451 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2620 (Rfree = 0.000) for 5033 atoms. Found 32 (32 requested) and removed 40 (16 requested) atoms. Cycle 12: After refmac, R = 0.2506 (Rfree = 0.000) for 4985 atoms. Found 32 (32 requested) and removed 26 (16 requested) atoms. Cycle 13: After refmac, R = 0.2387 (Rfree = 0.000) for 4968 atoms. Found 29 (32 requested) and removed 25 (16 requested) atoms. Cycle 14: After refmac, R = 0.2321 (Rfree = 0.000) for 4960 atoms. Found 25 (31 requested) and removed 25 (15 requested) atoms. Cycle 15: After refmac, R = 0.2318 (Rfree = 0.000) for 4947 atoms. Found 18 (31 requested) and removed 28 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.21 2.77 Search for helices and strands: 0 residues in 0 chains, 5073 seeds are put forward NCS extension: 56 residues added (0 deleted due to clashes), 5129 seeds are put forward Round 1: 366 peptides, 53 chains. Longest chain 18 peptides. Score 0.457 Round 2: 396 peptides, 52 chains. Longest chain 31 peptides. Score 0.510 Round 3: 404 peptides, 45 chains. Longest chain 22 peptides. Score 0.567 Round 4: 386 peptides, 48 chains. Longest chain 19 peptides. Score 0.522 Round 5: 397 peptides, 50 chains. Longest chain 23 peptides. Score 0.525 Taking the results from Round 3 Chains 45, Residues 359, Estimated correctness of the model 1.3 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 11505 reflections ( 99.71 % complete ) and 11055 restraints for refining 5032 atoms. 9584 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2551 (Rfree = 0.000) for 5032 atoms. Found 32 (32 requested) and removed 45 (16 requested) atoms. Cycle 17: After refmac, R = 0.2484 (Rfree = 0.000) for 4991 atoms. Found 32 (32 requested) and removed 41 (16 requested) atoms. Cycle 18: After refmac, R = 0.2353 (Rfree = 0.000) for 4965 atoms. Found 31 (31 requested) and removed 27 (15 requested) atoms. Cycle 19: After refmac, R = 0.2236 (Rfree = 0.000) for 4962 atoms. Found 31 (31 requested) and removed 35 (15 requested) atoms. Cycle 20: After refmac, R = 0.2224 (Rfree = 0.000) for 4948 atoms. Found 31 (31 requested) and removed 25 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.24 2.79 Search for helices and strands: 0 residues in 0 chains, 5076 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 5097 seeds are put forward Round 1: 360 peptides, 51 chains. Longest chain 27 peptides. Score 0.462 Round 2: 397 peptides, 55 chains. Longest chain 19 peptides. Score 0.491 Round 3: 407 peptides, 52 chains. Longest chain 22 peptides. Score 0.526 Round 4: 415 peptides, 50 chains. Longest chain 22 peptides. Score 0.550 Round 5: 429 peptides, 50 chains. Longest chain 22 peptides. Score 0.569 Taking the results from Round 5 Chains 52, Residues 379, Estimated correctness of the model 2.2 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 11505 reflections ( 99.71 % complete ) and 10999 restraints for refining 5032 atoms. 9412 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2723 (Rfree = 0.000) for 5032 atoms. Found 32 (32 requested) and removed 47 (16 requested) atoms. Cycle 22: After refmac, R = 0.2686 (Rfree = 0.000) for 4987 atoms. Found 32 (32 requested) and removed 37 (16 requested) atoms. Cycle 23: After refmac, R = 0.2545 (Rfree = 0.000) for 4967 atoms. Found 31 (31 requested) and removed 36 (15 requested) atoms. Cycle 24: After refmac, R = 0.2446 (Rfree = 0.000) for 4952 atoms. Found 25 (31 requested) and removed 31 (15 requested) atoms. Cycle 25: After refmac, R = 0.2425 (Rfree = 0.000) for 4938 atoms. Found 20 (31 requested) and removed 32 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.19 2.75 Search for helices and strands: 0 residues in 0 chains, 5048 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 5072 seeds are put forward Round 1: 379 peptides, 54 chains. Longest chain 20 peptides. Score 0.470 Round 2: 411 peptides, 47 chains. Longest chain 23 peptides. Score 0.564 Round 3: 431 peptides, 52 chains. Longest chain 28 peptides. Score 0.559 Round 4: 423 peptides, 53 chains. Longest chain 22 peptides. Score 0.542 Round 5: 448 peptides, 51 chains. Longest chain 37 peptides. Score 0.588 Taking the results from Round 5 Chains 54, Residues 397, Estimated correctness of the model 9.9 % 3 chains (70 residues) have been docked in sequence ------------------------------------------------------ 11505 reflections ( 99.71 % complete ) and 10154 restraints for refining 5033 atoms. 8312 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2604 (Rfree = 0.000) for 5033 atoms. Found 32 (32 requested) and removed 46 (16 requested) atoms. Cycle 27: After refmac, R = 0.2472 (Rfree = 0.000) for 4982 atoms. Found 32 (32 requested) and removed 35 (16 requested) atoms. Cycle 28: After refmac, R = 0.2345 (Rfree = 0.000) for 4959 atoms. Found 27 (31 requested) and removed 26 (15 requested) atoms. Cycle 29: After refmac, R = 0.2248 (Rfree = 0.000) for 4948 atoms. Found 25 (31 requested) and removed 25 (15 requested) atoms. Cycle 30: After refmac, R = 0.2172 (Rfree = 0.000) for 4938 atoms. Found 18 (31 requested) and removed 29 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.18 2.74 Search for helices and strands: 0 residues in 0 chains, 5051 seeds are put forward NCS extension: 22 residues added (6 deleted due to clashes), 5073 seeds are put forward Round 1: 382 peptides, 56 chains. Longest chain 21 peptides. Score 0.461 Round 2: 401 peptides, 49 chains. Longest chain 25 peptides. Score 0.537 Round 3: 399 peptides, 54 chains. Longest chain 22 peptides. Score 0.501 Round 4: 397 peptides, 53 chains. Longest chain 21 peptides. Score 0.505 Round 5: 391 peptides, 50 chains. Longest chain 24 peptides. Score 0.516 Taking the results from Round 2 Chains 53, Residues 352, Estimated correctness of the model 0.0 % 2 chains (32 residues) have been docked in sequence ------------------------------------------------------ 11505 reflections ( 99.71 % complete ) and 10627 restraints for refining 5033 atoms. 9106 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2463 (Rfree = 0.000) for 5033 atoms. Found 32 (32 requested) and removed 45 (16 requested) atoms. Cycle 32: After refmac, R = 0.2334 (Rfree = 0.000) for 4991 atoms. Found 23 (32 requested) and removed 42 (16 requested) atoms. Cycle 33: After refmac, R = 0.2250 (Rfree = 0.000) for 4961 atoms. Found 29 (31 requested) and removed 29 (15 requested) atoms. Cycle 34: After refmac, R = 0.2174 (Rfree = 0.000) for 4947 atoms. Found 20 (31 requested) and removed 29 (15 requested) atoms. Cycle 35: After refmac, R = 0.2124 (Rfree = 0.000) for 4925 atoms. Found 31 (31 requested) and removed 30 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 2.73 Search for helices and strands: 0 residues in 0 chains, 5069 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 5099 seeds are put forward Round 1: 330 peptides, 54 chains. Longest chain 14 peptides. Score 0.390 Round 2: 364 peptides, 47 chains. Longest chain 21 peptides. Score 0.496 Round 3: 370 peptides, 46 chains. Longest chain 22 peptides. Score 0.512 Round 4: 383 peptides, 51 chains. Longest chain 21 peptides. Score 0.497 Round 5: 392 peptides, 47 chains. Longest chain 24 peptides. Score 0.537 Taking the results from Round 5 Chains 50, Residues 345, Estimated correctness of the model 0.0 % 5 chains (47 residues) have been docked in sequence ------------------------------------------------------ 11505 reflections ( 99.71 % complete ) and 10780 restraints for refining 5033 atoms. 9277 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2580 (Rfree = 0.000) for 5033 atoms. Found 32 (32 requested) and removed 49 (16 requested) atoms. Cycle 37: After refmac, R = 0.2414 (Rfree = 0.000) for 4985 atoms. Found 32 (32 requested) and removed 44 (16 requested) atoms. Cycle 38: After refmac, R = 0.2318 (Rfree = 0.000) for 4958 atoms. Found 31 (31 requested) and removed 34 (15 requested) atoms. Cycle 39: After refmac, R = 0.2184 (Rfree = 0.000) for 4943 atoms. Found 20 (31 requested) and removed 31 (15 requested) atoms. Cycle 40: After refmac, R = 0.2127 (Rfree = 0.000) for 4927 atoms. Found 24 (31 requested) and removed 30 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.15 2.71 Search for helices and strands: 0 residues in 0 chains, 5029 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 5048 seeds are put forward Round 1: 333 peptides, 47 chains. Longest chain 25 peptides. Score 0.448 Round 2: 352 peptides, 45 chains. Longest chain 21 peptides. Score 0.492 Round 3: 367 peptides, 43 chains. Longest chain 27 peptides. Score 0.528 Round 4: 381 peptides, 45 chains. Longest chain 28 peptides. Score 0.535 Round 5: 370 peptides, 45 chains. Longest chain 18 peptides. Score 0.519 Taking the results from Round 4 Chains 48, Residues 336, Estimated correctness of the model 0.0 % 5 chains (62 residues) have been docked in sequence ------------------------------------------------------ 11505 reflections ( 99.71 % complete ) and 10445 restraints for refining 5033 atoms. 8871 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2510 (Rfree = 0.000) for 5033 atoms. Found 32 (32 requested) and removed 35 (16 requested) atoms. Cycle 42: After refmac, R = 0.2314 (Rfree = 0.000) for 5003 atoms. Found 32 (32 requested) and removed 31 (16 requested) atoms. Cycle 43: After refmac, R = 0.2238 (Rfree = 0.000) for 4990 atoms. Found 32 (32 requested) and removed 29 (16 requested) atoms. Cycle 44: After refmac, R = 0.2166 (Rfree = 0.000) for 4973 atoms. Found 32 (32 requested) and removed 29 (16 requested) atoms. Cycle 45: After refmac, R = 0.2183 (Rfree = 0.000) for 4973 atoms. Found 24 (31 requested) and removed 26 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.24 2.79 Search for helices and strands: 0 residues in 0 chains, 5098 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 5131 seeds are put forward Round 1: 316 peptides, 56 chains. Longest chain 10 peptides. Score 0.350 Round 2: 348 peptides, 49 chains. Longest chain 14 peptides. Score 0.457 Round 3: 345 peptides, 49 chains. Longest chain 20 peptides. Score 0.452 Round 4: 354 peptides, 48 chains. Longest chain 16 peptides. Score 0.474 Round 5: 352 peptides, 48 chains. Longest chain 18 peptides. Score 0.471 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 48, Residues 306, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vky-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11505 reflections ( 99.71 % complete ) and 11432 restraints for refining 5033 atoms. 10256 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2521 (Rfree = 0.000) for 5033 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2370 (Rfree = 0.000) for 4989 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2336 (Rfree = 0.000) for 4957 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.2234 (Rfree = 0.000) for 4933 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:39:02 GMT 2018 Job finished. TimeTaking 75.96 Used memory is bytes: 3206064