Mon 24 Dec 07:36:55 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 1vk8-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vk8-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vk8-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vk8-4.0-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/1vk8-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vk8-4.0-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 07:37:00 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/1vk8-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vk8-4.0-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 253 and 0 Target number of residues in the AU: 253 Target solvent content: 0.6385 Checking the provided sequence file Detected sequence length: 106 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 424 Adjusted target solvent content: 0.39 Input MTZ file: 1vk8-4.0-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: 1 Cell parameters: 47.646 47.650 49.609 73.804 62.898 73.615 Input sequence file: 1vk8-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 3392 target number of atoms Had to go as low as 0.60 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: 41.711 4.001 Wilson plot Bfac: 70.82 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2973 reflections ( 96.18 % complete ) and 0 restraints for refining 3742 atoms. Observations/parameters ratio is 0.20 ------------------------------------------------------ Starting model: R = 0.3255 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3101 (Rfree = 0.000) for 3742 atoms. Found 17 (17 requested) and removed 51 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.57 4.14 Search for helices and strands: 0 residues in 0 chains, 3778 seeds are put forward NCS extension: 0 residues added, 3778 seeds are put forward Round 1: 69 peptides, 15 chains. Longest chain 8 peptides. Score 0.222 Round 2: 105 peptides, 22 chains. Longest chain 9 peptides. Score 0.258 Round 3: 109 peptides, 21 chains. Longest chain 9 peptides. Score 0.299 Round 4: 129 peptides, 22 chains. Longest chain 11 peptides. Score 0.372 Round 5: 134 peptides, 22 chains. Longest chain 11 peptides. Score 0.394 Taking the results from Round 5 Chains 22, Residues 112, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2973 reflections ( 96.18 % complete ) and 7696 restraints for refining 3062 atoms. 7270 conditional restraints added. Observations/parameters ratio is 0.24 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2472 (Rfree = 0.000) for 3062 atoms. Found 12 (14 requested) and removed 37 (7 requested) atoms. Cycle 2: After refmac, R = 0.2287 (Rfree = 0.000) for 2970 atoms. Found 14 (14 requested) and removed 26 (7 requested) atoms. Cycle 3: After refmac, R = 0.2253 (Rfree = 0.000) for 2929 atoms. Found 13 (14 requested) and removed 14 (7 requested) atoms. Cycle 4: After refmac, R = 0.2174 (Rfree = 0.000) for 2901 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 5: After refmac, R = 0.2326 (Rfree = 0.000) for 2875 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.50 4.06 Search for helices and strands: 0 residues in 0 chains, 2948 seeds are put forward NCS extension: 0 residues added, 2948 seeds are put forward Round 1: 81 peptides, 19 chains. Longest chain 6 peptides. Score 0.196 Round 2: 98 peptides, 21 chains. Longest chain 8 peptides. Score 0.243 Round 3: 111 peptides, 22 chains. Longest chain 8 peptides. Score 0.288 Round 4: 109 peptides, 22 chains. Longest chain 7 peptides. Score 0.278 Round 5: 115 peptides, 22 chains. Longest chain 9 peptides. Score 0.307 Taking the results from Round 5 Chains 22, Residues 93, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2973 reflections ( 96.18 % complete ) and 5828 restraints for refining 2453 atoms. 5478 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1946 (Rfree = 0.000) for 2453 atoms. Found 11 (11 requested) and removed 20 (5 requested) atoms. Cycle 7: After refmac, R = 0.2074 (Rfree = 0.000) for 2425 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 8: After refmac, R = 0.1791 (Rfree = 0.000) for 2409 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 9: After refmac, R = 0.1775 (Rfree = 0.000) for 2405 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 10: After refmac, R = 0.1731 (Rfree = 0.000) for 2394 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.52 4.09 Search for helices and strands: 0 residues in 0 chains, 2477 seeds are put forward NCS extension: 0 residues added, 2477 seeds are put forward Round 1: 106 peptides, 22 chains. Longest chain 9 peptides. Score 0.263 Round 2: 150 peptides, 28 chains. Longest chain 16 peptides. Score 0.351 Round 3: 156 peptides, 26 chains. Longest chain 12 peptides. Score 0.414 Round 4: 141 peptides, 25 chains. Longest chain 11 peptides. Score 0.368 Round 5: 135 peptides, 21 chains. Longest chain 16 peptides. Score 0.418 Taking the results from Round 5 Chains 21, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2973 reflections ( 96.18 % complete ) and 5607 restraints for refining 2473 atoms. 5172 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1888 (Rfree = 0.000) for 2473 atoms. Found 11 (11 requested) and removed 29 (5 requested) atoms. Cycle 12: After refmac, R = 0.1759 (Rfree = 0.000) for 2437 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 13: After refmac, R = 0.1756 (Rfree = 0.000) for 2427 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 14: After refmac, R = 0.1546 (Rfree = 0.000) for 2428 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 15: After refmac, R = 0.1699 (Rfree = 0.000) for 2425 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.63 4.21 Search for helices and strands: 0 residues in 0 chains, 2506 seeds are put forward NCS extension: 27 residues added (4 deleted due to clashes), 2533 seeds are put forward Round 1: 117 peptides, 26 chains. Longest chain 6 peptides. Score 0.234 Round 2: 135 peptides, 25 chains. Longest chain 11 peptides. Score 0.341 Round 3: 156 peptides, 26 chains. Longest chain 15 peptides. Score 0.414 Round 4: 154 peptides, 28 chains. Longest chain 11 peptides. Score 0.368 Round 5: 155 peptides, 25 chains. Longest chain 13 peptides. Score 0.428 Taking the results from Round 5 Chains 25, Residues 130, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2973 reflections ( 96.18 % complete ) and 5656 restraints for refining 2482 atoms. 5161 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1805 (Rfree = 0.000) for 2482 atoms. Found 11 (11 requested) and removed 30 (5 requested) atoms. Cycle 17: After refmac, R = 0.1857 (Rfree = 0.000) for 2450 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 18: After refmac, R = 0.1779 (Rfree = 0.000) for 2436 atoms. Found 11 (11 requested) and removed 20 (5 requested) atoms. Cycle 19: After refmac, R = 0.1735 (Rfree = 0.000) for 2420 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 20: After refmac, R = 0.1644 (Rfree = 0.000) for 2409 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.57 4.14 Search for helices and strands: 0 residues in 0 chains, 2502 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2516 seeds are put forward Round 1: 125 peptides, 25 chains. Longest chain 10 peptides. Score 0.294 Round 2: 144 peptides, 26 chains. Longest chain 13 peptides. Score 0.362 Round 3: 142 peptides, 24 chains. Longest chain 13 peptides. Score 0.391 Round 4: 144 peptides, 23 chains. Longest chain 13 peptides. Score 0.418 Round 5: 144 peptides, 25 chains. Longest chain 12 peptides. Score 0.381 Taking the results from Round 4 Chains 23, Residues 121, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2973 reflections ( 96.18 % complete ) and 5879 restraints for refining 2555 atoms. 5418 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1815 (Rfree = 0.000) for 2555 atoms. Found 12 (12 requested) and removed 25 (6 requested) atoms. Cycle 22: After refmac, R = 0.1819 (Rfree = 0.000) for 2527 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 23: After refmac, R = 0.1598 (Rfree = 0.000) for 2510 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 24: After refmac, R = 0.1561 (Rfree = 0.000) for 2501 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 25: After refmac, R = 0.1701 (Rfree = 0.000) for 2495 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.60 4.18 Search for helices and strands: 0 residues in 0 chains, 2571 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2589 seeds are put forward Round 1: 114 peptides, 25 chains. Longest chain 7 peptides. Score 0.240 Round 2: 131 peptides, 25 chains. Longest chain 9 peptides. Score 0.322 Round 3: 132 peptides, 25 chains. Longest chain 12 peptides. Score 0.327 Round 4: 144 peptides, 26 chains. Longest chain 15 peptides. Score 0.362 Round 5: 148 peptides, 27 chains. Longest chain 12 peptides. Score 0.361 Taking the results from Round 4 Chains 26, Residues 118, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2973 reflections ( 96.18 % complete ) and 5645 restraints for refining 2501 atoms. 5182 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1725 (Rfree = 0.000) for 2501 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 27: After refmac, R = 0.1810 (Rfree = 0.000) for 2487 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 28: After refmac, R = 0.1734 (Rfree = 0.000) for 2474 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 29: After refmac, R = 0.1683 (Rfree = 0.000) for 2461 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 30: After refmac, R = 0.1782 (Rfree = 0.000) for 2458 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.65 4.24 Search for helices and strands: 0 residues in 0 chains, 2561 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 2589 seeds are put forward Round 1: 116 peptides, 26 chains. Longest chain 7 peptides. Score 0.229 Round 2: 123 peptides, 24 chains. Longest chain 8 peptides. Score 0.305 Round 3: 120 peptides, 22 chains. Longest chain 11 peptides. Score 0.331 Round 4: 129 peptides, 25 chains. Longest chain 10 peptides. Score 0.313 Round 5: 130 peptides, 21 chains. Longest chain 12 peptides. Score 0.396 Taking the results from Round 5 Chains 21, Residues 109, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2973 reflections ( 96.18 % complete ) and 5798 restraints for refining 2544 atoms. 5383 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1836 (Rfree = 0.000) for 2544 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 32: After refmac, R = 0.1784 (Rfree = 0.000) for 2526 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 33: After refmac, R = 0.1676 (Rfree = 0.000) for 2513 atoms. Found 10 (11 requested) and removed 7 (5 requested) atoms. Cycle 34: After refmac, R = 0.1323 (Rfree = 0.000) for 2511 atoms. Found 3 (11 requested) and removed 9 (5 requested) atoms. Cycle 35: After refmac, R = 0.1170 (Rfree = 0.000) for 2502 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.67 4.26 Search for helices and strands: 0 residues in 0 chains, 2597 seeds are put forward NCS extension: 0 residues added, 2597 seeds are put forward Round 1: 107 peptides, 23 chains. Longest chain 10 peptides. Score 0.247 Round 2: 123 peptides, 24 chains. Longest chain 10 peptides. Score 0.305 Round 3: 123 peptides, 23 chains. Longest chain 10 peptides. Score 0.325 Round 4: 131 peptides, 23 chains. Longest chain 10 peptides. Score 0.362 Round 5: 125 peptides, 22 chains. Longest chain 10 peptides. Score 0.354 Taking the results from Round 4 Chains 23, Residues 108, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2973 reflections ( 96.18 % complete ) and 5941 restraints for refining 2536 atoms. 5532 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1854 (Rfree = 0.000) for 2536 atoms. Found 10 (12 requested) and removed 14 (6 requested) atoms. Cycle 37: After refmac, R = 0.1670 (Rfree = 0.000) for 2524 atoms. Found 11 (12 requested) and removed 14 (6 requested) atoms. Cycle 38: After refmac, R = 0.1781 (Rfree = 0.000) for 2515 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 39: After refmac, R = 0.1560 (Rfree = 0.000) for 2509 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 40: After refmac, R = 0.1731 (Rfree = 0.000) for 2506 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.60 4.18 Search for helices and strands: 0 residues in 0 chains, 2580 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 2586 seeds are put forward Round 1: 89 peptides, 20 chains. Longest chain 7 peptides. Score 0.218 Round 2: 114 peptides, 23 chains. Longest chain 9 peptides. Score 0.282 Round 3: 119 peptides, 23 chains. Longest chain 14 peptides. Score 0.306 Round 4: 118 peptides, 21 chains. Longest chain 9 peptides. Score 0.342 Round 5: 115 peptides, 22 chains. Longest chain 9 peptides. Score 0.307 Taking the results from Round 4 Chains 21, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2973 reflections ( 96.18 % complete ) and 5597 restraints for refining 2442 atoms. 5230 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1832 (Rfree = 0.000) for 2442 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 42: After refmac, R = 0.1964 (Rfree = 0.000) for 2421 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 43: After refmac, R = 0.1712 (Rfree = 0.000) for 2415 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 44: After refmac, R = 0.1845 (Rfree = 0.000) for 2412 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 45: After refmac, R = 0.1141 (Rfree = 0.000) for 2405 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.66 4.25 Search for helices and strands: 0 residues in 0 chains, 2493 seeds are put forward NCS extension: 0 residues added, 2493 seeds are put forward Round 1: 79 peptides, 18 chains. Longest chain 7 peptides. Score 0.208 Round 2: 97 peptides, 18 chains. Longest chain 9 peptides. Score 0.304 Round 3: 91 peptides, 16 chains. Longest chain 9 peptides. Score 0.318 Round 4: 96 peptides, 17 chains. Longest chain 10 peptides. Score 0.320 Round 5: 99 peptides, 19 chains. Longest chain 10 peptides. Score 0.292 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 79, 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 1vk8-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2973 reflections ( 96.18 % complete ) and 5430 restraints for refining 2373 atoms. 5131 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1697 (Rfree = 0.000) for 2373 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1780 (Rfree = 0.000) for 2361 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1631 (Rfree = 0.000) for 2351 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1657 (Rfree = 0.000) for 2342 atoms. TimeTaking 35.17