null Sun 23 Dec 22:23:02 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 1vp4-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vp4-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vp4-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp4-3.8-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/1vp4-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp4-3.8-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 22:23:12 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/1vp4-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp4-3.8-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 684 and 0 Target number of residues in the AU: 684 Target solvent content: 0.6562 Checking the provided sequence file Detected sequence length: 425 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 850 Adjusted target solvent content: 0.57 Input MTZ file: 1vp4-3.8-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: 170 Cell parameters: 164.860 164.860 68.609 90.000 90.000 120.000 Input sequence file: 1vp4-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 6800 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: 142.773 3.800 Wilson plot Bfac: 82.24 10675 reflections ( 99.70 % complete ) and 0 restraints for refining 7579 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3566 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3331 (Rfree = 0.000) for 7579 atoms. Found 41 (41 requested) and removed 77 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.68 3.35 Search for helices and strands: 0 residues in 0 chains, 7686 seeds are put forward NCS extension: 0 residues added, 7686 seeds are put forward Round 1: 235 peptides, 49 chains. Longest chain 8 peptides. Score 0.246 Round 2: 327 peptides, 61 chains. Longest chain 12 peptides. Score 0.319 Round 3: 381 peptides, 69 chains. Longest chain 17 peptides. Score 0.350 Round 4: 401 peptides, 67 chains. Longest chain 20 peptides. Score 0.395 Round 5: 413 peptides, 68 chains. Longest chain 19 peptides. Score 0.407 Taking the results from Round 5 Chains 68, Residues 345, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 10675 reflections ( 99.70 % complete ) and 14239 restraints for refining 6149 atoms. 12881 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3050 (Rfree = 0.000) for 6149 atoms. Found 33 (33 requested) and removed 127 (16 requested) atoms. Cycle 2: After refmac, R = 0.2905 (Rfree = 0.000) for 5933 atoms. Found 27 (33 requested) and removed 203 (16 requested) atoms. Cycle 3: After refmac, R = 0.2851 (Rfree = 0.000) for 5689 atoms. Found 31 (31 requested) and removed 30 (15 requested) atoms. Cycle 4: After refmac, R = 0.2602 (Rfree = 0.000) for 5643 atoms. Found 29 (31 requested) and removed 29 (15 requested) atoms. Cycle 5: After refmac, R = 0.2868 (Rfree = 0.000) for 5618 atoms. Found 31 (31 requested) and removed 22 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.74 3.40 Search for helices and strands: 0 residues in 0 chains, 5840 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 5859 seeds are put forward Round 1: 354 peptides, 69 chains. Longest chain 13 peptides. Score 0.306 Round 2: 435 peptides, 69 chains. Longest chain 19 peptides. Score 0.433 Round 3: 458 peptides, 70 chains. Longest chain 16 peptides. Score 0.459 Round 4: 471 peptides, 69 chains. Longest chain 24 peptides. Score 0.483 Round 5: 472 peptides, 72 chains. Longest chain 23 peptides. Score 0.466 Taking the results from Round 4 Chains 72, Residues 402, Estimated correctness of the model 0.0 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 10675 reflections ( 99.70 % complete ) and 12117 restraints for refining 5640 atoms. 10487 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2853 (Rfree = 0.000) for 5640 atoms. Found 31 (31 requested) and removed 45 (15 requested) atoms. Cycle 7: After refmac, R = 0.2509 (Rfree = 0.000) for 5577 atoms. Found 15 (30 requested) and removed 43 (15 requested) atoms. Cycle 8: After refmac, R = 0.2392 (Rfree = 0.000) for 5515 atoms. Found 14 (30 requested) and removed 22 (15 requested) atoms. Cycle 9: After refmac, R = 0.2331 (Rfree = 0.000) for 5484 atoms. Found 4 (30 requested) and removed 18 (15 requested) atoms. Cycle 10: After refmac, R = 0.2443 (Rfree = 0.000) for 5457 atoms. Found 13 (30 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.71 3.38 Search for helices and strands: 0 residues in 0 chains, 5699 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 5724 seeds are put forward Round 1: 394 peptides, 74 chains. Longest chain 11 peptides. Score 0.337 Round 2: 457 peptides, 73 chains. Longest chain 17 peptides. Score 0.439 Round 3: 450 peptides, 64 chains. Longest chain 17 peptides. Score 0.485 Round 4: 456 peptides, 62 chains. Longest chain 18 peptides. Score 0.505 Round 5: 456 peptides, 61 chains. Longest chain 22 peptides. Score 0.511 Taking the results from Round 5 Chains 63, Residues 395, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 10675 reflections ( 99.70 % complete ) and 13209 restraints for refining 6022 atoms. 11612 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2602 (Rfree = 0.000) for 6022 atoms. Found 33 (33 requested) and removed 65 (16 requested) atoms. Cycle 12: After refmac, R = 0.2428 (Rfree = 0.000) for 5920 atoms. Found 32 (32 requested) and removed 45 (16 requested) atoms. Cycle 13: After refmac, R = 0.2533 (Rfree = 0.000) for 5843 atoms. Found 23 (32 requested) and removed 37 (16 requested) atoms. Cycle 14: After refmac, R = 0.2303 (Rfree = 0.000) for 5788 atoms. Found 26 (32 requested) and removed 24 (16 requested) atoms. Cycle 15: After refmac, R = 0.2458 (Rfree = 0.000) for 5747 atoms. Found 27 (31 requested) and removed 28 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.67 3.34 Search for helices and strands: 0 residues in 0 chains, 5966 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 5987 seeds are put forward Round 1: 365 peptides, 66 chains. Longest chain 14 peptides. Score 0.346 Round 2: 405 peptides, 68 chains. Longest chain 18 peptides. Score 0.395 Round 3: 453 peptides, 69 chains. Longest chain 20 peptides. Score 0.458 Round 4: 436 peptides, 64 chains. Longest chain 20 peptides. Score 0.465 Round 5: 440 peptides, 61 chains. Longest chain 25 peptides. Score 0.489 Taking the results from Round 5 Chains 61, Residues 379, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 10675 reflections ( 99.70 % complete ) and 13576 restraints for refining 6036 atoms. 12110 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2722 (Rfree = 0.000) for 6036 atoms. Found 33 (33 requested) and removed 56 (16 requested) atoms. Cycle 17: After refmac, R = 0.2421 (Rfree = 0.000) for 5963 atoms. Found 19 (33 requested) and removed 29 (16 requested) atoms. Cycle 18: After refmac, R = 0.2430 (Rfree = 0.000) for 5902 atoms. Found 24 (32 requested) and removed 35 (16 requested) atoms. Cycle 19: After refmac, R = 0.2158 (Rfree = 0.000) for 5865 atoms. Found 10 (32 requested) and removed 23 (16 requested) atoms. Cycle 20: After refmac, R = 0.2203 (Rfree = 0.000) for 5823 atoms. Found 19 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.69 3.36 Search for helices and strands: 0 residues in 0 chains, 6067 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 6093 seeds are put forward Round 1: 373 peptides, 72 chains. Longest chain 9 peptides. Score 0.317 Round 2: 424 peptides, 67 chains. Longest chain 13 peptides. Score 0.429 Round 3: 437 peptides, 67 chains. Longest chain 16 peptides. Score 0.448 Round 4: 407 peptides, 60 chains. Longest chain 19 peptides. Score 0.450 Round 5: 415 peptides, 61 chains. Longest chain 15 peptides. Score 0.455 Taking the results from Round 5 Chains 61, Residues 354, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 10675 reflections ( 99.70 % complete ) and 14174 restraints for refining 6149 atoms. 12787 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2295 (Rfree = 0.000) for 6149 atoms. Found 24 (33 requested) and removed 41 (16 requested) atoms. Cycle 22: After refmac, R = 0.2408 (Rfree = 0.000) for 6096 atoms. Found 33 (33 requested) and removed 43 (16 requested) atoms. Cycle 23: After refmac, R = 0.2233 (Rfree = 0.000) for 6066 atoms. Found 32 (33 requested) and removed 36 (16 requested) atoms. Cycle 24: After refmac, R = 0.2021 (Rfree = 0.000) for 6032 atoms. Found 10 (33 requested) and removed 26 (16 requested) atoms. Cycle 25: After refmac, R = 0.1961 (Rfree = 0.000) for 5995 atoms. Found 13 (33 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.70 3.37 Search for helices and strands: 0 residues in 0 chains, 6222 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 6235 seeds are put forward Round 1: 367 peptides, 67 chains. Longest chain 17 peptides. Score 0.342 Round 2: 430 peptides, 68 chains. Longest chain 16 peptides. Score 0.432 Round 3: 433 peptides, 66 chains. Longest chain 21 peptides. Score 0.449 Round 4: 420 peptides, 64 chains. Longest chain 20 peptides. Score 0.443 Round 5: 419 peptides, 67 chains. Longest chain 17 peptides. Score 0.422 Taking the results from Round 3 Chains 66, Residues 367, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10675 reflections ( 99.70 % complete ) and 14189 restraints for refining 6151 atoms. 12787 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2583 (Rfree = 0.000) for 6151 atoms. Found 33 (33 requested) and removed 46 (16 requested) atoms. Cycle 27: After refmac, R = 0.2400 (Rfree = 0.000) for 6094 atoms. Found 33 (33 requested) and removed 38 (16 requested) atoms. Cycle 28: After refmac, R = 0.2357 (Rfree = 0.000) for 6053 atoms. Found 33 (33 requested) and removed 29 (16 requested) atoms. Cycle 29: After refmac, R = 0.2357 (Rfree = 0.000) for 6029 atoms. Found 33 (33 requested) and removed 28 (16 requested) atoms. Cycle 30: After refmac, R = 0.1979 (Rfree = 0.000) for 6005 atoms. Found 13 (33 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.70 3.37 Search for helices and strands: 0 residues in 0 chains, 6227 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 6248 seeds are put forward Round 1: 322 peptides, 64 chains. Longest chain 12 peptides. Score 0.288 Round 2: 388 peptides, 65 chains. Longest chain 18 peptides. Score 0.389 Round 3: 416 peptides, 69 chains. Longest chain 16 peptides. Score 0.405 Round 4: 428 peptides, 67 chains. Longest chain 19 peptides. Score 0.435 Round 5: 417 peptides, 64 chains. Longest chain 16 peptides. Score 0.438 Taking the results from Round 5 Chains 64, Residues 353, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10675 reflections ( 99.70 % complete ) and 14073 restraints for refining 6151 atoms. 12725 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2187 (Rfree = 0.000) for 6151 atoms. Found 29 (33 requested) and removed 37 (16 requested) atoms. Cycle 32: After refmac, R = 0.2088 (Rfree = 0.000) for 6107 atoms. Found 25 (33 requested) and removed 34 (16 requested) atoms. Cycle 33: After refmac, R = 0.1916 (Rfree = 0.000) for 6070 atoms. Found 12 (33 requested) and removed 26 (16 requested) atoms. Cycle 34: After refmac, R = 0.1979 (Rfree = 0.000) for 6036 atoms. Found 15 (33 requested) and removed 26 (16 requested) atoms. Cycle 35: After refmac, R = 0.2141 (Rfree = 0.000) for 6006 atoms. Found 33 (33 requested) and removed 24 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.64 3.31 Search for helices and strands: 0 residues in 0 chains, 6232 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 6250 seeds are put forward Round 1: 349 peptides, 72 chains. Longest chain 18 peptides. Score 0.277 Round 2: 405 peptides, 68 chains. Longest chain 15 peptides. Score 0.395 Round 3: 412 peptides, 67 chains. Longest chain 12 peptides. Score 0.412 Round 4: 402 peptides, 66 chains. Longest chain 15 peptides. Score 0.403 Round 5: 415 peptides, 67 chains. Longest chain 13 peptides. Score 0.416 Taking the results from Round 5 Chains 67, Residues 348, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10675 reflections ( 99.70 % complete ) and 14237 restraints for refining 6151 atoms. 12912 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2351 (Rfree = 0.000) for 6151 atoms. Found 33 (33 requested) and removed 26 (16 requested) atoms. Cycle 37: After refmac, R = 0.2103 (Rfree = 0.000) for 6128 atoms. Found 9 (33 requested) and removed 32 (16 requested) atoms. Cycle 38: After refmac, R = 0.2013 (Rfree = 0.000) for 6081 atoms. Found 9 (33 requested) and removed 21 (16 requested) atoms. Cycle 39: After refmac, R = 0.1957 (Rfree = 0.000) for 6054 atoms. Found 6 (33 requested) and removed 19 (16 requested) atoms. Cycle 40: After refmac, R = 0.2164 (Rfree = 0.000) for 6024 atoms. Found 33 (33 requested) and removed 23 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.66 3.33 Search for helices and strands: 0 residues in 0 chains, 6246 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 6258 seeds are put forward Round 1: 330 peptides, 71 chains. Longest chain 11 peptides. Score 0.251 Round 2: 350 peptides, 63 chains. Longest chain 15 peptides. Score 0.342 Round 3: 358 peptides, 61 chains. Longest chain 15 peptides. Score 0.369 Round 4: 359 peptides, 63 chains. Longest chain 13 peptides. Score 0.357 Round 5: 386 peptides, 61 chains. Longest chain 16 peptides. Score 0.412 Taking the results from Round 5 Chains 62, Residues 325, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 10675 reflections ( 99.70 % complete ) and 14274 restraints for refining 6151 atoms. 12975 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2279 (Rfree = 0.000) for 6151 atoms. Found 24 (33 requested) and removed 33 (16 requested) atoms. Cycle 42: After refmac, R = 0.2218 (Rfree = 0.000) for 6105 atoms. Found 30 (33 requested) and removed 24 (16 requested) atoms. Cycle 43: After refmac, R = 0.1961 (Rfree = 0.000) for 6085 atoms. Found 9 (33 requested) and removed 21 (16 requested) atoms. Cycle 44: After refmac, R = 0.1929 (Rfree = 0.000) for 6050 atoms. Found 9 (33 requested) and removed 22 (16 requested) atoms. Cycle 45: After refmac, R = 0.2006 (Rfree = 0.000) for 6025 atoms. Found 20 (33 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 3.35 Search for helices and strands: 0 residues in 0 chains, 6207 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 6227 seeds are put forward Round 1: 308 peptides, 66 chains. Longest chain 10 peptides. Score 0.249 Round 2: 359 peptides, 67 chains. Longest chain 14 peptides. Score 0.329 Round 3: 372 peptides, 62 chains. Longest chain 18 peptides. Score 0.384 Round 4: 351 peptides, 61 chains. Longest chain 14 peptides. Score 0.358 Round 5: 345 peptides, 63 chains. Longest chain 22 peptides. Score 0.334 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 62, Residues 310, 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 1vp4-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10675 reflections ( 99.70 % complete ) and 14133 restraints for refining 6102 atoms. 12955 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2176 (Rfree = 0.000) for 6102 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2387 (Rfree = 0.000) for 6061 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2083 (Rfree = 0.000) for 6022 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.2072 (Rfree = 0.000) for 5979 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:54:13 GMT 2018 Job finished. TimeTaking 91.19 Used memory is bytes: 4047920