Mon 24 Dec 07:58:45 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 1vqs-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vqs-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vqs-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqs-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/1vqs-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqs-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 07:58:49 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/1vqs-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqs-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 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-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: 97 Cell parameters: 94.778 94.778 303.043 90.000 90.000 90.000 Input sequence file: 1vqs-3.6-parrot-noncs.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 5115 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3364 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3320 (Rfree = 0.000) for 5115 atoms. Found 32 (32 requested) and removed 32 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.36 3.19 Search for helices and strands: 0 residues in 0 chains, 5210 seeds are put forward NCS extension: 0 residues added, 5210 seeds are put forward Round 1: 252 peptides, 44 chains. Longest chain 12 peptides. Score 0.374 Round 2: 328 peptides, 50 chains. Longest chain 16 peptides. Score 0.487 Round 3: 340 peptides, 49 chains. Longest chain 15 peptides. Score 0.521 Round 4: 374 peptides, 48 chains. Longest chain 20 peptides. Score 0.594 Round 5: 377 peptides, 44 chains. Longest chain 19 peptides. Score 0.630 Taking the results from Round 5 Chains 45, Residues 333, Estimated correctness of the model 26.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 8432 reflections ( 99.56 % complete ) and 9095 restraints for refining 4206 atoms. 7771 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2784 (Rfree = 0.000) for 4206 atoms. Found 26 (26 requested) and removed 25 (13 requested) atoms. Cycle 2: After refmac, R = 0.2563 (Rfree = 0.000) for 4139 atoms. Found 21 (26 requested) and removed 21 (13 requested) atoms. Cycle 3: After refmac, R = 0.2460 (Rfree = 0.000) for 4117 atoms. Found 12 (26 requested) and removed 22 (13 requested) atoms. Cycle 4: After refmac, R = 0.2373 (Rfree = 0.000) for 4084 atoms. Found 18 (26 requested) and removed 20 (13 requested) atoms. Cycle 5: After refmac, R = 0.2340 (Rfree = 0.000) for 4073 atoms. Found 21 (26 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 3.17 Search for helices and strands: 0 residues in 0 chains, 4177 seeds are put forward NCS extension: 14 residues added (4 deleted due to clashes), 4191 seeds are put forward Round 1: 296 peptides, 44 chains. Longest chain 15 peptides. Score 0.476 Round 2: 342 peptides, 47 chains. Longest chain 20 peptides. Score 0.543 Round 3: 357 peptides, 44 chains. Longest chain 23 peptides. Score 0.596 Round 4: 356 peptides, 44 chains. Longest chain 23 peptides. Score 0.594 Round 5: 345 peptides, 43 chains. Longest chain 22 peptides. Score 0.582 Taking the results from Round 3 Chains 46, Residues 313, Estimated correctness of the model 13.1 % 2 chains (34 residues) have been docked in sequence ------------------------------------------------------ 8432 reflections ( 99.56 % complete ) and 8874 restraints for refining 4206 atoms. 7516 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2669 (Rfree = 0.000) for 4206 atoms. Found 26 (26 requested) and removed 25 (13 requested) atoms. Cycle 7: After refmac, R = 0.2526 (Rfree = 0.000) for 4183 atoms. Found 25 (26 requested) and removed 22 (13 requested) atoms. Cycle 8: After refmac, R = 0.2563 (Rfree = 0.000) for 4169 atoms. Found 26 (26 requested) and removed 32 (13 requested) atoms. Cycle 9: After refmac, R = 0.2558 (Rfree = 0.000) for 4152 atoms. Found 26 (26 requested) and removed 32 (13 requested) atoms. Cycle 10: After refmac, R = 0.2570 (Rfree = 0.000) for 4127 atoms. Found 26 (26 requested) and removed 30 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.32 3.15 Search for helices and strands: 0 residues in 0 chains, 4239 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 4260 seeds are put forward Round 1: 302 peptides, 46 chains. Longest chain 20 peptides. Score 0.469 Round 2: 326 peptides, 41 chains. Longest chain 16 peptides. Score 0.564 Round 3: 338 peptides, 43 chains. Longest chain 21 peptides. Score 0.569 Round 4: 326 peptides, 40 chains. Longest chain 20 peptides. Score 0.572 Round 5: 327 peptides, 42 chains. Longest chain 20 peptides. Score 0.557 Taking the results from Round 4 Chains 41, Residues 286, Estimated correctness of the model 3.4 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 8432 reflections ( 99.56 % complete ) and 9182 restraints for refining 4205 atoms. 8009 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2712 (Rfree = 0.000) for 4205 atoms. Found 25 (26 requested) and removed 26 (13 requested) atoms. Cycle 12: After refmac, R = 0.2507 (Rfree = 0.000) for 4167 atoms. Found 26 (26 requested) and removed 20 (13 requested) atoms. Cycle 13: After refmac, R = 0.2489 (Rfree = 0.000) for 4149 atoms. Found 26 (26 requested) and removed 21 (13 requested) atoms. Cycle 14: After refmac, R = 0.2497 (Rfree = 0.000) for 4139 atoms. Found 26 (26 requested) and removed 24 (13 requested) atoms. Cycle 15: After refmac, R = 0.2372 (Rfree = 0.000) for 4128 atoms. Found 22 (26 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.36 3.19 Search for helices and strands: 0 residues in 0 chains, 4261 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 4277 seeds are put forward Round 1: 301 peptides, 49 chains. Longest chain 14 peptides. Score 0.438 Round 2: 339 peptides, 49 chains. Longest chain 17 peptides. Score 0.519 Round 3: 339 peptides, 47 chains. Longest chain 19 peptides. Score 0.537 Round 4: 342 peptides, 49 chains. Longest chain 18 peptides. Score 0.525 Round 5: 359 peptides, 44 chains. Longest chain 35 peptides. Score 0.599 Taking the results from Round 5 Chains 46, Residues 315, Estimated correctness of the model 14.3 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 8432 reflections ( 99.56 % complete ) and 9235 restraints for refining 4206 atoms. 7978 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2671 (Rfree = 0.000) for 4206 atoms. Found 20 (26 requested) and removed 25 (13 requested) atoms. Cycle 17: After refmac, R = 0.2496 (Rfree = 0.000) for 4176 atoms. Found 17 (26 requested) and removed 23 (13 requested) atoms. Cycle 18: After refmac, R = 0.2462 (Rfree = 0.000) for 4157 atoms. Found 21 (26 requested) and removed 22 (13 requested) atoms. Cycle 19: After refmac, R = 0.2348 (Rfree = 0.000) for 4144 atoms. Found 17 (26 requested) and removed 23 (13 requested) atoms. Cycle 20: After refmac, R = 0.2235 (Rfree = 0.000) for 4125 atoms. Found 17 (26 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.35 3.18 Search for helices and strands: 0 residues in 0 chains, 4265 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 4276 seeds are put forward Round 1: 286 peptides, 49 chains. Longest chain 17 peptides. Score 0.404 Round 2: 315 peptides, 46 chains. Longest chain 15 peptides. Score 0.497 Round 3: 311 peptides, 44 chains. Longest chain 15 peptides. Score 0.507 Round 4: 307 peptides, 45 chains. Longest chain 14 peptides. Score 0.490 Round 5: 347 peptides, 48 chains. Longest chain 17 peptides. Score 0.544 Taking the results from Round 5 Chains 50, Residues 299, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 8432 reflections ( 99.56 % complete ) and 9290 restraints for refining 4205 atoms. 8104 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2566 (Rfree = 0.000) for 4205 atoms. Found 23 (26 requested) and removed 27 (13 requested) atoms. Cycle 22: After refmac, R = 0.2430 (Rfree = 0.000) for 4168 atoms. Found 22 (26 requested) and removed 20 (13 requested) atoms. Cycle 23: After refmac, R = 0.2221 (Rfree = 0.000) for 4152 atoms. Found 11 (26 requested) and removed 16 (13 requested) atoms. Cycle 24: After refmac, R = 0.2302 (Rfree = 0.000) for 4139 atoms. Found 16 (26 requested) and removed 14 (13 requested) atoms. Cycle 25: After refmac, R = 0.2283 (Rfree = 0.000) for 4133 atoms. Found 19 (26 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.36 3.19 Search for helices and strands: 0 residues in 0 chains, 4268 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 4289 seeds are put forward Round 1: 278 peptides, 51 chains. Longest chain 13 peptides. Score 0.364 Round 2: 305 peptides, 43 chains. Longest chain 16 peptides. Score 0.504 Round 3: 306 peptides, 39 chains. Longest chain 19 peptides. Score 0.543 Round 4: 316 peptides, 38 chains. Longest chain 28 peptides. Score 0.571 Round 5: 311 peptides, 39 chains. Longest chain 22 peptides. Score 0.552 Taking the results from Round 4 Chains 38, Residues 278, Estimated correctness of the model 3.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8432 reflections ( 99.56 % complete ) and 9413 restraints for refining 4206 atoms. 8339 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2496 (Rfree = 0.000) for 4206 atoms. Found 22 (26 requested) and removed 20 (13 requested) atoms. Cycle 27: After refmac, R = 0.2368 (Rfree = 0.000) for 4190 atoms. Found 22 (26 requested) and removed 20 (13 requested) atoms. Cycle 28: After refmac, R = 0.2340 (Rfree = 0.000) for 4182 atoms. Found 19 (26 requested) and removed 16 (13 requested) atoms. Cycle 29: After refmac, R = 0.2285 (Rfree = 0.000) for 4178 atoms. Found 23 (26 requested) and removed 16 (13 requested) atoms. Cycle 30: After refmac, R = 0.2035 (Rfree = 0.000) for 4173 atoms. Found 10 (26 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.35 3.18 Search for helices and strands: 0 residues in 0 chains, 4302 seeds are put forward NCS extension: 38 residues added (4 deleted due to clashes), 4340 seeds are put forward Round 1: 282 peptides, 49 chains. Longest chain 13 peptides. Score 0.394 Round 2: 316 peptides, 42 chains. Longest chain 23 peptides. Score 0.536 Round 3: 326 peptides, 48 chains. Longest chain 25 peptides. Score 0.502 Round 4: 327 peptides, 46 chains. Longest chain 18 peptides. Score 0.522 Round 5: 319 peptides, 41 chains. Longest chain 23 peptides. Score 0.550 Taking the results from Round 5 Chains 42, Residues 278, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 8432 reflections ( 99.56 % complete ) and 9502 restraints for refining 4206 atoms. 8400 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2622 (Rfree = 0.000) for 4206 atoms. Found 26 (26 requested) and removed 23 (13 requested) atoms. Cycle 32: After refmac, R = 0.2425 (Rfree = 0.000) for 4184 atoms. Found 27 (27 requested) and removed 17 (13 requested) atoms. Cycle 33: After refmac, R = 0.2391 (Rfree = 0.000) for 4180 atoms. Found 26 (26 requested) and removed 22 (13 requested) atoms. Cycle 34: After refmac, R = 0.2227 (Rfree = 0.000) for 4165 atoms. Found 26 (26 requested) and removed 18 (13 requested) atoms. Cycle 35: After refmac, R = 0.2228 (Rfree = 0.000) for 4165 atoms. Found 26 (26 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.33 3.16 Search for helices and strands: 0 residues in 0 chains, 4300 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 4324 seeds are put forward Round 1: 226 peptides, 44 chains. Longest chain 11 peptides. Score 0.308 Round 2: 252 peptides, 39 chains. Longest chain 14 peptides. Score 0.426 Round 3: 274 peptides, 45 chains. Longest chain 19 peptides. Score 0.416 Round 4: 268 peptides, 40 chains. Longest chain 13 peptides. Score 0.453 Round 5: 277 peptides, 42 chains. Longest chain 17 peptides. Score 0.453 Taking the results from Round 5 Chains 42, Residues 235, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 8432 reflections ( 99.56 % complete ) and 9724 restraints for refining 4205 atoms. 8803 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2368 (Rfree = 0.000) for 4205 atoms. Found 20 (26 requested) and removed 19 (13 requested) atoms. Cycle 37: After refmac, R = 0.2395 (Rfree = 0.000) for 4190 atoms. Found 26 (26 requested) and removed 19 (13 requested) atoms. Cycle 38: After refmac, R = 0.2230 (Rfree = 0.000) for 4176 atoms. Found 22 (26 requested) and removed 17 (13 requested) atoms. Cycle 39: After refmac, R = 0.2174 (Rfree = 0.000) for 4166 atoms. Found 26 (26 requested) and removed 18 (13 requested) atoms. Cycle 40: After refmac, R = 0.2069 (Rfree = 0.000) for 4170 atoms. Found 23 (26 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.42 3.24 Search for helices and strands: 0 residues in 0 chains, 4276 seeds are put forward NCS extension: 22 residues added (4 deleted due to clashes), 4298 seeds are put forward Round 1: 224 peptides, 42 chains. Longest chain 10 peptides. Score 0.325 Round 2: 267 peptides, 43 chains. Longest chain 15 peptides. Score 0.420 Round 3: 263 peptides, 39 chains. Longest chain 17 peptides. Score 0.452 Round 4: 263 peptides, 39 chains. Longest chain 17 peptides. Score 0.452 Round 5: 265 peptides, 40 chains. Longest chain 17 peptides. Score 0.446 Taking the results from Round 4 Chains 39, Residues 224, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8432 reflections ( 99.56 % complete ) and 9793 restraints for refining 4206 atoms. 8936 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2520 (Rfree = 0.000) for 4206 atoms. Found 26 (26 requested) and removed 26 (13 requested) atoms. Cycle 42: After refmac, R = 0.2297 (Rfree = 0.000) for 4189 atoms. Found 26 (26 requested) and removed 18 (13 requested) atoms. Cycle 43: After refmac, R = 0.2218 (Rfree = 0.000) for 4184 atoms. Found 26 (26 requested) and removed 22 (13 requested) atoms. Cycle 44: After refmac, R = 0.2137 (Rfree = 0.000) for 4181 atoms. Found 19 (26 requested) and removed 15 (13 requested) atoms. Cycle 45: After refmac, R = 0.2139 (Rfree = 0.000) for 4176 atoms. Found 24 (26 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.38 3.20 Search for helices and strands: 0 residues in 0 chains, 4291 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 4315 seeds are put forward Round 1: 224 peptides, 42 chains. Longest chain 12 peptides. Score 0.325 Round 2: 260 peptides, 42 chains. Longest chain 15 peptides. Score 0.414 Round 3: 273 peptides, 44 chains. Longest chain 14 peptides. Score 0.424 Round 4: 269 peptides, 42 chains. Longest chain 16 peptides. Score 0.435 Round 5: 257 peptides, 42 chains. Longest chain 13 peptides. Score 0.407 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 42, Residues 227, 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 9836 restraints for refining 4206 atoms. 8970 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2352 (Rfree = 0.000) for 4206 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2252 (Rfree = 0.000) for 4178 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2207 (Rfree = 0.000) for 4157 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.2039 (Rfree = 0.000) for 4139 atoms. TimeTaking 50.25