null Tue 25 Dec 19:27:55 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 1vl0-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vl0-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vl0-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl0-3.6-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/1vl0-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl0-3.6-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 19:28:05 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/1vl0-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl0-3.6-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 714 and 0 Target number of residues in the AU: 714 Target solvent content: 0.6326 Checking the provided sequence file Detected sequence length: 292 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 876 Adjusted target solvent content: 0.55 Input MTZ file: 1vl0-3.6-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: 20 Cell parameters: 106.471 130.661 151.225 90.000 90.000 90.000 Input sequence file: 1vl0-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 7008 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: 29.987 3.600 Wilson plot Bfac: 67.85 12426 reflections ( 98.98 % complete ) and 0 restraints for refining 7736 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3779 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3558 (Rfree = 0.000) for 7736 atoms. Found 49 (49 requested) and removed 152 (24 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.42 3.20 Search for helices and strands: 0 residues in 0 chains, 7671 seeds are put forward NCS extension: 0 residues added, 7671 seeds are put forward Round 1: 219 peptides, 48 chains. Longest chain 9 peptides. Score 0.224 Round 2: 289 peptides, 60 chains. Longest chain 10 peptides. Score 0.262 Round 3: 321 peptides, 63 chains. Longest chain 11 peptides. Score 0.296 Round 4: 326 peptides, 60 chains. Longest chain 13 peptides. Score 0.327 Round 5: 343 peptides, 64 chains. Longest chain 10 peptides. Score 0.326 Taking the results from Round 4 Chains 60, Residues 266, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 12426 reflections ( 98.98 % complete ) and 14591 restraints for refining 6352 atoms. 13570 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2926 (Rfree = 0.000) for 6352 atoms. Found 39 (40 requested) and removed 51 (20 requested) atoms. Cycle 2: After refmac, R = 0.2818 (Rfree = 0.000) for 6258 atoms. Found 40 (40 requested) and removed 45 (20 requested) atoms. Cycle 3: After refmac, R = 0.2321 (Rfree = 0.000) for 6209 atoms. Found 25 (40 requested) and removed 32 (20 requested) atoms. Cycle 4: After refmac, R = 0.2207 (Rfree = 0.000) for 6173 atoms. Found 21 (39 requested) and removed 25 (19 requested) atoms. Cycle 5: After refmac, R = 0.2138 (Rfree = 0.000) for 6154 atoms. Found 17 (39 requested) and removed 28 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.31 3.10 Search for helices and strands: 0 residues in 0 chains, 6255 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 6277 seeds are put forward Round 1: 368 peptides, 81 chains. Longest chain 8 peptides. Score 0.246 Round 2: 425 peptides, 79 chains. Longest chain 12 peptides. Score 0.356 Round 3: 435 peptides, 80 chains. Longest chain 10 peptides. Score 0.365 Round 4: 436 peptides, 79 chains. Longest chain 11 peptides. Score 0.373 Round 5: 436 peptides, 70 chains. Longest chain 16 peptides. Score 0.432 Taking the results from Round 5 Chains 70, Residues 366, Estimated correctness of the model 0.0 % 5 chains (25 residues) have been docked in sequence ------------------------------------------------------ 12426 reflections ( 98.98 % complete ) and 13899 restraints for refining 6352 atoms. 12443 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2795 (Rfree = 0.000) for 6352 atoms. Found 40 (40 requested) and removed 58 (20 requested) atoms. Cycle 7: After refmac, R = 0.2698 (Rfree = 0.000) for 6286 atoms. Found 40 (40 requested) and removed 37 (20 requested) atoms. Cycle 8: After refmac, R = 0.2665 (Rfree = 0.000) for 6246 atoms. Found 40 (40 requested) and removed 39 (20 requested) atoms. Cycle 9: After refmac, R = 0.2503 (Rfree = 0.000) for 6221 atoms. Found 40 (40 requested) and removed 30 (20 requested) atoms. Cycle 10: After refmac, R = 0.2486 (Rfree = 0.000) for 6211 atoms. Found 39 (39 requested) and removed 35 (19 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.33 3.11 Search for helices and strands: 0 residues in 0 chains, 6327 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 6344 seeds are put forward Round 1: 348 peptides, 69 chains. Longest chain 10 peptides. Score 0.299 Round 2: 433 peptides, 71 chains. Longest chain 16 peptides. Score 0.421 Round 3: 454 peptides, 76 chains. Longest chain 14 peptides. Score 0.420 Round 4: 432 peptides, 71 chains. Longest chain 14 peptides. Score 0.420 Round 5: 443 peptides, 73 chains. Longest chain 16 peptides. Score 0.423 Taking the results from Round 5 Chains 73, Residues 370, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 12426 reflections ( 98.98 % complete ) and 14068 restraints for refining 6353 atoms. 12620 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2774 (Rfree = 0.000) for 6353 atoms. Found 40 (40 requested) and removed 37 (20 requested) atoms. Cycle 12: After refmac, R = 0.2701 (Rfree = 0.000) for 6312 atoms. Found 40 (40 requested) and removed 37 (20 requested) atoms. Cycle 13: After refmac, R = 0.2540 (Rfree = 0.000) for 6287 atoms. Found 40 (40 requested) and removed 32 (20 requested) atoms. Cycle 14: After refmac, R = 0.2655 (Rfree = 0.000) for 6270 atoms. Found 40 (40 requested) and removed 39 (20 requested) atoms. Cycle 15: After refmac, R = 0.2474 (Rfree = 0.000) for 6249 atoms. Found 40 (40 requested) and removed 37 (20 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.33 3.11 Search for helices and strands: 0 residues in 0 chains, 6362 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 6382 seeds are put forward Round 1: 331 peptides, 69 chains. Longest chain 8 peptides. Score 0.269 Round 2: 401 peptides, 70 chains. Longest chain 15 peptides. Score 0.379 Round 3: 408 peptides, 71 chains. Longest chain 13 peptides. Score 0.383 Round 4: 428 peptides, 69 chains. Longest chain 17 peptides. Score 0.427 Round 5: 411 peptides, 66 chains. Longest chain 17 peptides. Score 0.421 Taking the results from Round 4 Chains 69, Residues 359, Estimated correctness of the model 0.0 % 5 chains (29 residues) have been docked in sequence ------------------------------------------------------ 12426 reflections ( 98.98 % complete ) and 13738 restraints for refining 6352 atoms. 12284 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2676 (Rfree = 0.000) for 6352 atoms. Found 40 (40 requested) and removed 40 (20 requested) atoms. Cycle 17: After refmac, R = 0.2521 (Rfree = 0.000) for 6310 atoms. Found 40 (40 requested) and removed 30 (20 requested) atoms. Cycle 18: After refmac, R = 0.2490 (Rfree = 0.000) for 6299 atoms. Found 40 (40 requested) and removed 39 (20 requested) atoms. Cycle 19: After refmac, R = 0.2448 (Rfree = 0.000) for 6283 atoms. Found 40 (40 requested) and removed 43 (20 requested) atoms. Cycle 20: After refmac, R = 0.2369 (Rfree = 0.000) for 6261 atoms. Found 40 (40 requested) and removed 32 (20 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.34 3.12 Search for helices and strands: 0 residues in 0 chains, 6393 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 6410 seeds are put forward Round 1: 339 peptides, 70 chains. Longest chain 10 peptides. Score 0.276 Round 2: 397 peptides, 72 chains. Longest chain 13 peptides. Score 0.359 Round 3: 388 peptides, 66 chains. Longest chain 23 peptides. Score 0.385 Round 4: 411 peptides, 70 chains. Longest chain 17 peptides. Score 0.394 Round 5: 417 peptides, 70 chains. Longest chain 14 peptides. Score 0.404 Taking the results from Round 5 Chains 70, Residues 347, Estimated correctness of the model 0.0 % 5 chains (19 residues) have been docked in sequence ------------------------------------------------------ 12426 reflections ( 98.98 % complete ) and 13833 restraints for refining 6352 atoms. 12465 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2408 (Rfree = 0.000) for 6352 atoms. Found 40 (40 requested) and removed 37 (20 requested) atoms. Cycle 22: After refmac, R = 0.2453 (Rfree = 0.000) for 6320 atoms. Found 40 (40 requested) and removed 30 (20 requested) atoms. Cycle 23: After refmac, R = 0.2346 (Rfree = 0.000) for 6301 atoms. Found 40 (40 requested) and removed 30 (20 requested) atoms. Cycle 24: After refmac, R = 0.2302 (Rfree = 0.000) for 6294 atoms. Found 40 (40 requested) and removed 27 (20 requested) atoms. Cycle 25: After refmac, R = 0.2327 (Rfree = 0.000) for 6291 atoms. Found 40 (40 requested) and removed 30 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.30 3.09 Search for helices and strands: 0 residues in 0 chains, 6427 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 6446 seeds are put forward Round 1: 328 peptides, 65 chains. Longest chain 14 peptides. Score 0.293 Round 2: 400 peptides, 74 chains. Longest chain 16 peptides. Score 0.350 Round 3: 373 peptides, 68 chains. Longest chain 15 peptides. Score 0.348 Round 4: 405 peptides, 71 chains. Longest chain 12 peptides. Score 0.378 Round 5: 421 peptides, 73 chains. Longest chain 15 peptides. Score 0.390 Taking the results from Round 5 Chains 73, Residues 348, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 12426 reflections ( 98.98 % complete ) and 13873 restraints for refining 6350 atoms. 12545 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2417 (Rfree = 0.000) for 6350 atoms. Found 40 (40 requested) and removed 28 (20 requested) atoms. Cycle 27: After refmac, R = 0.2449 (Rfree = 0.000) for 6324 atoms. Found 40 (40 requested) and removed 35 (20 requested) atoms. Cycle 28: After refmac, R = 0.2392 (Rfree = 0.000) for 6301 atoms. Found 40 (40 requested) and removed 30 (20 requested) atoms. Cycle 29: After refmac, R = 0.2340 (Rfree = 0.000) for 6295 atoms. Found 40 (40 requested) and removed 25 (20 requested) atoms. Cycle 30: After refmac, R = 0.2357 (Rfree = 0.000) for 6297 atoms. Found 40 (40 requested) and removed 32 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.28 3.07 Search for helices and strands: 0 residues in 0 chains, 6400 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 6414 seeds are put forward Round 1: 319 peptides, 68 chains. Longest chain 12 peptides. Score 0.255 Round 2: 358 peptides, 64 chains. Longest chain 15 peptides. Score 0.351 Round 3: 372 peptides, 64 chains. Longest chain 13 peptides. Score 0.374 Round 4: 364 peptides, 65 chains. Longest chain 15 peptides. Score 0.354 Round 5: 361 peptides, 62 chains. Longest chain 15 peptides. Score 0.370 Taking the results from Round 3 Chains 64, Residues 308, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12426 reflections ( 98.98 % complete ) and 13986 restraints for refining 6353 atoms. 12818 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2367 (Rfree = 0.000) for 6353 atoms. Found 38 (40 requested) and removed 29 (20 requested) atoms. Cycle 32: After refmac, R = 0.2286 (Rfree = 0.000) for 6334 atoms. Found 40 (40 requested) and removed 31 (20 requested) atoms. Cycle 33: After refmac, R = 0.2186 (Rfree = 0.000) for 6330 atoms. Found 38 (40 requested) and removed 25 (20 requested) atoms. Cycle 34: After refmac, R = 0.2168 (Rfree = 0.000) for 6331 atoms. Found 40 (40 requested) and removed 29 (20 requested) atoms. Cycle 35: After refmac, R = 0.2235 (Rfree = 0.000) for 6330 atoms. Found 40 (40 requested) and removed 27 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 3.06 Search for helices and strands: 0 residues in 0 chains, 6423 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 6442 seeds are put forward Round 1: 289 peptides, 65 chains. Longest chain 7 peptides. Score 0.223 Round 2: 302 peptides, 59 chains. Longest chain 12 peptides. Score 0.293 Round 3: 314 peptides, 60 chains. Longest chain 11 peptides. Score 0.306 Round 4: 319 peptides, 55 chains. Longest chain 13 peptides. Score 0.352 Round 5: 323 peptides, 60 chains. Longest chain 13 peptides. Score 0.322 Taking the results from Round 4 Chains 56, Residues 264, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 12426 reflections ( 98.98 % complete ) and 14194 restraints for refining 6353 atoms. 13153 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2448 (Rfree = 0.000) for 6353 atoms. Found 40 (40 requested) and removed 30 (20 requested) atoms. Cycle 37: After refmac, R = 0.2395 (Rfree = 0.000) for 6341 atoms. Found 40 (40 requested) and removed 28 (20 requested) atoms. Cycle 38: After refmac, R = 0.1937 (Rfree = 0.000) for 6336 atoms. Found 18 (40 requested) and removed 23 (20 requested) atoms. Cycle 39: After refmac, R = 0.1891 (Rfree = 0.000) for 6326 atoms. Found 11 (40 requested) and removed 24 (20 requested) atoms. Cycle 40: After refmac, R = 0.1855 (Rfree = 0.000) for 6306 atoms. Found 8 (40 requested) and removed 22 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 3.08 Search for helices and strands: 0 residues in 0 chains, 6350 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 6367 seeds are put forward Round 1: 279 peptides, 61 chains. Longest chain 11 peptides. Score 0.235 Round 2: 328 peptides, 64 chains. Longest chain 11 peptides. Score 0.301 Round 3: 324 peptides, 62 chains. Longest chain 9 peptides. Score 0.309 Round 4: 336 peptides, 59 chains. Longest chain 10 peptides. Score 0.351 Round 5: 346 peptides, 64 chains. Longest chain 12 peptides. Score 0.331 Taking the results from Round 4 Chains 59, Residues 277, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 12426 reflections ( 98.98 % complete ) and 13939 restraints for refining 6353 atoms. 12861 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2429 (Rfree = 0.000) for 6353 atoms. Found 40 (40 requested) and removed 33 (20 requested) atoms. Cycle 42: After refmac, R = 0.2401 (Rfree = 0.000) for 6324 atoms. Found 40 (40 requested) and removed 27 (20 requested) atoms. Cycle 43: After refmac, R = 0.2396 (Rfree = 0.000) for 6321 atoms. Found 40 (40 requested) and removed 29 (20 requested) atoms. Cycle 44: After refmac, R = 0.2473 (Rfree = 0.000) for 6318 atoms. Found 40 (40 requested) and removed 28 (20 requested) atoms. Cycle 45: After refmac, R = 0.2394 (Rfree = 0.000) for 6314 atoms. Found 40 (40 requested) and removed 30 (20 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.28 3.07 Search for helices and strands: 0 residues in 0 chains, 6427 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 6439 seeds are put forward Round 1: 237 peptides, 54 chains. Longest chain 7 peptides. Score 0.210 Round 2: 287 peptides, 55 chains. Longest chain 13 peptides. Score 0.296 Round 3: 290 peptides, 59 chains. Longest chain 9 peptides. Score 0.271 Round 4: 281 peptides, 54 chains. Longest chain 10 peptides. Score 0.293 Round 5: 276 peptides, 51 chains. Longest chain 11 peptides. Score 0.308 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 52, Residues 225, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vl0-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12426 reflections ( 98.98 % complete ) and 14291 restraints for refining 6353 atoms. 13417 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2550 (Rfree = 0.000) for 6353 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 47: After refmac, R = 0.2519 (Rfree = 0.000) for 6306 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 48: After refmac, R = 0.2058 (Rfree = 0.000) for 6272 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 49: After refmac, R = 0.1958 (Rfree = 0.000) for 6239 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:01:07 GMT 2018 Job finished. TimeTaking 93.2 Used memory is bytes: 14450352