null Tue 25 Dec 19:27:57 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 1vqs-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vqs-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vqs-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqs-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/1vqs-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqs-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 ============================================================ Tue 25 Dec 19:28:07 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/1vqs-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqs-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 474 and 0 Target number of residues in the AU: 474 Target solvent content: 0.6231 Checking the provided sequence file Detected sequence length: 116 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 5 Adjusted target number of residues: 580 Adjusted target solvent content: 0.54 Input MTZ file: 1vqs-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: 97 Cell parameters: 94.778 94.778 303.043 90.000 90.000 90.000 Input sequence file: 1vqs-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 4640 target number of atoms Had to go as low as 0.85 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: 29.971 3.600 Wilson plot Bfac: 62.92 8432 reflections ( 99.56 % complete ) and 0 restraints for refining 5167 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3327 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3257 (Rfree = 0.000) for 5167 atoms. Found 33 (33 requested) and removed 32 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.38 3.20 Search for helices and strands: 0 residues in 0 chains, 5271 seeds are put forward NCS extension: 0 residues added, 5271 seeds are put forward Round 1: 261 peptides, 48 chains. Longest chain 14 peptides. Score 0.354 Round 2: 332 peptides, 47 chains. Longest chain 19 peptides. Score 0.523 Round 3: 318 peptides, 41 chains. Longest chain 21 peptides. Score 0.548 Round 4: 359 peptides, 41 chains. Longest chain 22 peptides. Score 0.623 Round 5: 365 peptides, 42 chains. Longest chain 24 peptides. Score 0.625 Taking the results from Round 5 Chains 44, Residues 323, Estimated correctness of the model 24.2 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 8432 reflections ( 99.56 % complete ) and 8860 restraints for refining 4205 atoms. 7560 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2801 (Rfree = 0.000) for 4205 atoms. Found 21 (26 requested) and removed 32 (13 requested) atoms. Cycle 2: After refmac, R = 0.2605 (Rfree = 0.000) for 4108 atoms. Found 26 (26 requested) and removed 20 (13 requested) atoms. Cycle 3: After refmac, R = 0.2377 (Rfree = 0.000) for 4078 atoms. Found 17 (26 requested) and removed 18 (13 requested) atoms. Cycle 4: After refmac, R = 0.2302 (Rfree = 0.000) for 4049 atoms. Found 14 (26 requested) and removed 22 (13 requested) atoms. Cycle 5: After refmac, R = 0.2224 (Rfree = 0.000) for 4026 atoms. Found 13 (25 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 3.19 Search for helices and strands: 0 residues in 0 chains, 4175 seeds are put forward NCS extension: 31 residues added (8 deleted due to clashes), 4206 seeds are put forward Round 1: 296 peptides, 47 chains. Longest chain 19 peptides. Score 0.447 Round 2: 325 peptides, 43 chains. Longest chain 22 peptides. Score 0.544 Round 3: 328 peptides, 48 chains. Longest chain 22 peptides. Score 0.506 Round 4: 359 peptides, 44 chains. Longest chain 21 peptides. Score 0.599 Round 5: 360 peptides, 43 chains. Longest chain 24 peptides. Score 0.609 Taking the results from Round 5 Chains 44, Residues 317, Estimated correctness of the model 18.1 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 8432 reflections ( 99.56 % complete ) and 9216 restraints for refining 4206 atoms. 7928 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2726 (Rfree = 0.000) for 4206 atoms. Found 23 (26 requested) and removed 27 (13 requested) atoms. Cycle 7: After refmac, R = 0.2583 (Rfree = 0.000) for 4165 atoms. Found 26 (26 requested) and removed 29 (13 requested) atoms. Cycle 8: After refmac, R = 0.2460 (Rfree = 0.000) for 4141 atoms. Found 23 (26 requested) and removed 24 (13 requested) atoms. Cycle 9: After refmac, R = 0.2293 (Rfree = 0.000) for 4124 atoms. Found 14 (26 requested) and removed 22 (13 requested) atoms. Cycle 10: After refmac, R = 0.2292 (Rfree = 0.000) for 4109 atoms. Found 16 (26 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.33 3.16 Search for helices and strands: 0 residues in 0 chains, 4262 seeds are put forward NCS extension: 11 residues added (4 deleted due to clashes), 4273 seeds are put forward Round 1: 304 peptides, 48 chains. Longest chain 22 peptides. Score 0.455 Round 2: 314 peptides, 42 chains. Longest chain 27 peptides. Score 0.532 Round 3: 336 peptides, 45 chains. Longest chain 18 peptides. Score 0.548 Round 4: 344 peptides, 42 chains. Longest chain 21 peptides. Score 0.589 Round 5: 353 peptides, 45 chains. Longest chain 25 peptides. Score 0.580 Taking the results from Round 4 Chains 43, Residues 302, Estimated correctness of the model 10.3 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 8432 reflections ( 99.56 % complete ) and 9159 restraints for refining 4206 atoms. 7938 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2533 (Rfree = 0.000) for 4206 atoms. Found 26 (26 requested) and removed 22 (13 requested) atoms. Cycle 12: After refmac, R = 0.2314 (Rfree = 0.000) for 4183 atoms. Found 15 (26 requested) and removed 21 (13 requested) atoms. Cycle 13: After refmac, R = 0.2273 (Rfree = 0.000) for 4156 atoms. Found 19 (26 requested) and removed 22 (13 requested) atoms. Cycle 14: After refmac, R = 0.2243 (Rfree = 0.000) for 4135 atoms. Found 16 (26 requested) and removed 19 (13 requested) atoms. Cycle 15: After refmac, R = 0.2286 (Rfree = 0.000) for 4119 atoms. Found 24 (26 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 3.18 Search for helices and strands: 0 residues in 0 chains, 4225 seeds are put forward NCS extension: 15 residues added (8 deleted due to clashes), 4240 seeds are put forward Round 1: 302 peptides, 50 chains. Longest chain 13 peptides. Score 0.431 Round 2: 315 peptides, 42 chains. Longest chain 28 peptides. Score 0.534 Round 3: 316 peptides, 44 chains. Longest chain 20 peptides. Score 0.518 Round 4: 311 peptides, 41 chains. Longest chain 24 peptides. Score 0.535 Round 5: 299 peptides, 36 chains. Longest chain 29 peptides. Score 0.556 Taking the results from Round 5 Chains 38, Residues 263, Estimated correctness of the model 0.0 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 8432 reflections ( 99.56 % complete ) and 9449 restraints for refining 4205 atoms. 8342 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2612 (Rfree = 0.000) for 4205 atoms. Found 26 (26 requested) and removed 30 (13 requested) atoms. Cycle 17: After refmac, R = 0.2479 (Rfree = 0.000) for 4162 atoms. Found 26 (26 requested) and removed 24 (13 requested) atoms. Cycle 18: After refmac, R = 0.2410 (Rfree = 0.000) for 4145 atoms. Found 26 (26 requested) and removed 24 (13 requested) atoms. Cycle 19: After refmac, R = 0.2300 (Rfree = 0.000) for 4137 atoms. Found 26 (26 requested) and removed 24 (13 requested) atoms. Cycle 20: After refmac, R = 0.2240 (Rfree = 0.000) for 4129 atoms. Found 26 (26 requested) and removed 23 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.36 3.19 Search for helices and strands: 0 residues in 0 chains, 4228 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 4246 seeds are put forward Round 1: 289 peptides, 46 chains. Longest chain 18 peptides. Score 0.441 Round 2: 319 peptides, 43 chains. Longest chain 27 peptides. Score 0.533 Round 3: 336 peptides, 44 chains. Longest chain 28 peptides. Score 0.557 Round 4: 316 peptides, 43 chains. Longest chain 24 peptides. Score 0.527 Round 5: 308 peptides, 44 chains. Longest chain 30 peptides. Score 0.501 Taking the results from Round 3 Chains 44, Residues 292, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8432 reflections ( 99.56 % complete ) and 9402 restraints for refining 4204 atoms. 8278 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2535 (Rfree = 0.000) for 4204 atoms. Found 26 (26 requested) and removed 27 (13 requested) atoms. Cycle 22: After refmac, R = 0.2357 (Rfree = 0.000) for 4180 atoms. Found 26 (26 requested) and removed 18 (13 requested) atoms. Cycle 23: After refmac, R = 0.2197 (Rfree = 0.000) for 4160 atoms. Found 20 (26 requested) and removed 20 (13 requested) atoms. Cycle 24: After refmac, R = 0.2067 (Rfree = 0.000) for 4146 atoms. Found 13 (26 requested) and removed 19 (13 requested) atoms. Cycle 25: After refmac, R = 0.2087 (Rfree = 0.000) for 4133 atoms. Found 24 (26 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.30 3.13 Search for helices and strands: 0 residues in 0 chains, 4263 seeds are put forward NCS extension: 32 residues added (0 deleted due to clashes), 4295 seeds are put forward Round 1: 278 peptides, 49 chains. Longest chain 14 peptides. Score 0.385 Round 2: 308 peptides, 44 chains. Longest chain 14 peptides. Score 0.501 Round 3: 316 peptides, 41 chains. Longest chain 19 peptides. Score 0.544 Round 4: 324 peptides, 39 chains. Longest chain 23 peptides. Score 0.577 Round 5: 334 peptides, 43 chains. Longest chain 19 peptides. Score 0.562 Taking the results from Round 4 Chains 39, Residues 285, Estimated correctness of the model 5.5 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 8432 reflections ( 99.56 % complete ) and 9335 restraints for refining 4206 atoms. 8207 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2395 (Rfree = 0.000) for 4206 atoms. Found 25 (26 requested) and removed 23 (13 requested) atoms. Cycle 27: After refmac, R = 0.2403 (Rfree = 0.000) for 4185 atoms. Found 26 (26 requested) and removed 18 (13 requested) atoms. Cycle 28: After refmac, R = 0.2324 (Rfree = 0.000) for 4184 atoms. Found 26 (26 requested) and removed 22 (13 requested) atoms. Cycle 29: After refmac, R = 0.2302 (Rfree = 0.000) for 4180 atoms. Found 26 (26 requested) and removed 20 (13 requested) atoms. Cycle 30: After refmac, R = 0.2316 (Rfree = 0.000) for 4183 atoms. Found 26 (26 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.30 3.13 Search for helices and strands: 0 residues in 0 chains, 4313 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 4332 seeds are put forward Round 1: 258 peptides, 47 chains. Longest chain 13 peptides. Score 0.357 Round 2: 292 peptides, 45 chains. Longest chain 14 peptides. Score 0.457 Round 3: 296 peptides, 43 chains. Longest chain 15 peptides. Score 0.485 Round 4: 292 peptides, 43 chains. Longest chain 14 peptides. Score 0.476 Round 5: 302 peptides, 40 chains. Longest chain 20 peptides. Score 0.526 Taking the results from Round 5 Chains 40, Residues 262, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8432 reflections ( 99.56 % complete ) and 9434 restraints for refining 4206 atoms. 8426 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2521 (Rfree = 0.000) for 4206 atoms. Found 26 (26 requested) and removed 22 (13 requested) atoms. Cycle 32: After refmac, R = 0.2325 (Rfree = 0.000) for 4191 atoms. Found 27 (27 requested) and removed 24 (13 requested) atoms. Cycle 33: After refmac, R = 0.2275 (Rfree = 0.000) for 4178 atoms. Found 26 (26 requested) and removed 22 (13 requested) atoms. Cycle 34: After refmac, R = 0.1964 (Rfree = 0.000) for 4173 atoms. Found 10 (26 requested) and removed 18 (13 requested) atoms. Cycle 35: After refmac, R = 0.2039 (Rfree = 0.000) for 4160 atoms. Found 19 (26 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.33 3.16 Search for helices and strands: 0 residues in 0 chains, 4268 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 4283 seeds are put forward Round 1: 248 peptides, 46 chains. Longest chain 14 peptides. Score 0.343 Round 2: 279 peptides, 41 chains. Longest chain 15 peptides. Score 0.467 Round 3: 295 peptides, 44 chains. Longest chain 17 peptides. Score 0.473 Round 4: 286 peptides, 42 chains. Longest chain 17 peptides. Score 0.473 Round 5: 280 peptides, 42 chains. Longest chain 14 peptides. Score 0.460 Taking the results from Round 4 Chains 42, Residues 244, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8432 reflections ( 99.56 % complete ) and 9523 restraints for refining 4206 atoms. 8589 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2455 (Rfree = 0.000) for 4206 atoms. Found 25 (26 requested) and removed 16 (13 requested) atoms. Cycle 37: After refmac, R = 0.2308 (Rfree = 0.000) for 4191 atoms. Found 26 (27 requested) and removed 22 (13 requested) atoms. Cycle 38: After refmac, R = 0.2235 (Rfree = 0.000) for 4184 atoms. Found 22 (26 requested) and removed 20 (13 requested) atoms. Cycle 39: After refmac, R = 0.2214 (Rfree = 0.000) for 4179 atoms. Found 26 (26 requested) and removed 21 (13 requested) atoms. Cycle 40: After refmac, R = 0.2158 (Rfree = 0.000) for 4179 atoms. Found 26 (26 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.30 3.13 Search for helices and strands: 0 residues in 0 chains, 4308 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 4323 seeds are put forward Round 1: 236 peptides, 47 chains. Longest chain 14 peptides. Score 0.301 Round 2: 304 peptides, 53 chains. Longest chain 14 peptides. Score 0.406 Round 3: 311 peptides, 51 chains. Longest chain 14 peptides. Score 0.441 Round 4: 310 peptides, 51 chains. Longest chain 14 peptides. Score 0.439 Round 5: 303 peptides, 49 chains. Longest chain 19 peptides. Score 0.443 Taking the results from Round 5 Chains 49, Residues 254, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8432 reflections ( 99.56 % complete ) and 9587 restraints for refining 4205 atoms. 8620 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2441 (Rfree = 0.000) for 4205 atoms. Found 26 (26 requested) and removed 16 (13 requested) atoms. Cycle 42: After refmac, R = 0.2231 (Rfree = 0.000) for 4194 atoms. Found 23 (27 requested) and removed 19 (13 requested) atoms. Cycle 43: After refmac, R = 0.2135 (Rfree = 0.000) for 4188 atoms. Found 23 (26 requested) and removed 15 (13 requested) atoms. Cycle 44: After refmac, R = 0.2060 (Rfree = 0.000) for 4187 atoms. Found 18 (26 requested) and removed 14 (13 requested) atoms. Cycle 45: After refmac, R = 0.2071 (Rfree = 0.000) for 4185 atoms. Found 20 (26 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.34 3.17 Search for helices and strands: 0 residues in 0 chains, 4301 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 4323 seeds are put forward Round 1: 216 peptides, 44 chains. Longest chain 8 peptides. Score 0.281 Round 2: 259 peptides, 46 chains. Longest chain 15 peptides. Score 0.370 Round 3: 284 peptides, 47 chains. Longest chain 16 peptides. Score 0.419 Round 4: 275 peptides, 47 chains. Longest chain 12 peptides. Score 0.398 Round 5: 282 peptides, 45 chains. Longest chain 16 peptides. Score 0.435 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 45, Residues 237, 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 1vqs-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8432 reflections ( 99.56 % complete ) and 9687 restraints for refining 4204 atoms. 8784 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2271 (Rfree = 0.000) for 4204 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2114 (Rfree = 0.000) for 4180 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2058 (Rfree = 0.000) for 4157 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.2049 (Rfree = 0.000) for 4136 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:46:21 GMT 2018 Job finished. TimeTaking 78.39 Used memory is bytes: 10938712