Mon 24 Dec 00:00:55 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vl0-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vl0-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vl0-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl0-3.6-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vl0-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl0-3.6-parrot-mrncs ############### 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 00:00:59 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vl0-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl0-3.6-parrot-mrncs/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-mrncs.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-mrncs.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 7733 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3772 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3451 (Rfree = 0.000) for 7733 atoms. Found 49 (49 requested) and removed 218 (24 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.40 3.18 Search for helices and strands: 0 residues in 0 chains, 7594 seeds are put forward NCS extension: 0 residues added, 7594 seeds are put forward Round 1: 229 peptides, 48 chains. Longest chain 8 peptides. Score 0.244 Round 2: 306 peptides, 60 chains. Longest chain 9 peptides. Score 0.292 Round 3: 350 peptides, 67 chains. Longest chain 10 peptides. Score 0.316 Round 4: 354 peptides, 66 chains. Longest chain 13 peptides. Score 0.330 Round 5: 356 peptides, 67 chains. Longest chain 10 peptides. Score 0.327 Taking the results from Round 4 Chains 66, Residues 288, Estimated correctness of the model 0.0 % 4 chains (16 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 12426 reflections ( 98.98 % complete ) and 14303 restraints for refining 6353 atoms. 13161 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3010 (Rfree = 0.000) for 6353 atoms. Found 40 (40 requested) and removed 52 (20 requested) atoms. Cycle 2: After refmac, R = 0.3024 (Rfree = 0.000) for 6255 atoms. Found 40 (40 requested) and removed 49 (20 requested) atoms. Cycle 3: After refmac, R = 0.2925 (Rfree = 0.000) for 6201 atoms. Found 40 (40 requested) and removed 47 (20 requested) atoms. Cycle 4: After refmac, R = 0.2803 (Rfree = 0.000) for 6160 atoms. Found 39 (39 requested) and removed 41 (19 requested) atoms. Cycle 5: After refmac, R = 0.2754 (Rfree = 0.000) for 6133 atoms. Found 39 (39 requested) and removed 39 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.30 3.09 Search for helices and strands: 0 residues in 0 chains, 6266 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 6284 seeds are put forward Round 1: 326 peptides, 72 chains. Longest chain 9 peptides. Score 0.238 Round 2: 381 peptides, 76 chains. Longest chain 12 peptides. Score 0.304 Round 3: 375 peptides, 67 chains. Longest chain 11 peptides. Score 0.358 Round 4: 366 peptides, 66 chains. Longest chain 13 peptides. Score 0.350 Round 5: 389 peptides, 69 chains. Longest chain 14 peptides. Score 0.366 Taking the results from Round 5 Chains 69, Residues 320, Estimated correctness of the model 0.0 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 12426 reflections ( 98.98 % complete ) and 13906 restraints for refining 6352 atoms. 12577 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2831 (Rfree = 0.000) for 6352 atoms. Found 40 (40 requested) and removed 55 (20 requested) atoms. Cycle 7: After refmac, R = 0.2667 (Rfree = 0.000) for 6292 atoms. Found 40 (40 requested) and removed 40 (20 requested) atoms. Cycle 8: After refmac, R = 0.2242 (Rfree = 0.000) for 6266 atoms. Found 17 (40 requested) and removed 28 (20 requested) atoms. Cycle 9: After refmac, R = 0.2394 (Rfree = 0.000) for 6237 atoms. Found 40 (40 requested) and removed 39 (20 requested) atoms. Cycle 10: After refmac, R = 0.2503 (Rfree = 0.000) for 6230 atoms. Found 40 (40 requested) and removed 30 (20 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.15 Search for helices and strands: 0 residues in 0 chains, 6314 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 6329 seeds are put forward Round 1: 333 peptides, 65 chains. Longest chain 12 peptides. Score 0.302 Round 2: 390 peptides, 70 chains. Longest chain 12 peptides. Score 0.361 Round 3: 387 peptides, 67 chains. Longest chain 15 peptides. Score 0.377 Round 4: 394 peptides, 67 chains. Longest chain 14 peptides. Score 0.388 Round 5: 405 peptides, 68 chains. Longest chain 16 peptides. Score 0.398 Taking the results from Round 5 Chains 68, Residues 337, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 12426 reflections ( 98.98 % complete ) and 14263 restraints for refining 6353 atoms. 12971 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2600 (Rfree = 0.000) for 6353 atoms. Found 40 (40 requested) and removed 47 (20 requested) atoms. Cycle 12: After refmac, R = 0.2566 (Rfree = 0.000) for 6300 atoms. Found 40 (40 requested) and removed 47 (20 requested) atoms. Cycle 13: After refmac, R = 0.2489 (Rfree = 0.000) for 6270 atoms. Found 40 (40 requested) and removed 34 (20 requested) atoms. Cycle 14: After refmac, R = 0.2510 (Rfree = 0.000) for 6257 atoms. Found 40 (40 requested) and removed 39 (20 requested) atoms. Cycle 15: After refmac, R = 0.2531 (Rfree = 0.000) for 6246 atoms. Found 40 (40 requested) and removed 31 (20 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.33 3.11 Search for helices and strands: 0 residues in 0 chains, 6366 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 6381 seeds are put forward Round 1: 340 peptides, 72 chains. Longest chain 8 peptides. Score 0.263 Round 2: 404 peptides, 73 chains. Longest chain 14 peptides. Score 0.363 Round 3: 412 peptides, 75 chains. Longest chain 14 peptides. Score 0.362 Round 4: 419 peptides, 72 chains. Longest chain 14 peptides. Score 0.393 Round 5: 421 peptides, 67 chains. Longest chain 11 peptides. Score 0.429 Taking the results from Round 5 Chains 67, Residues 354, Estimated correctness of the model 0.0 % 4 chains (22 residues) have been docked in sequence ------------------------------------------------------ 12426 reflections ( 98.98 % complete ) and 13831 restraints for refining 6353 atoms. 12406 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2475 (Rfree = 0.000) for 6353 atoms. Found 40 (40 requested) and removed 42 (20 requested) atoms. Cycle 17: After refmac, R = 0.2416 (Rfree = 0.000) for 6308 atoms. Found 40 (40 requested) and removed 31 (20 requested) atoms. Cycle 18: After refmac, R = 0.2449 (Rfree = 0.000) for 6296 atoms. Found 40 (40 requested) and removed 32 (20 requested) atoms. Cycle 19: After refmac, R = 0.2387 (Rfree = 0.000) for 6276 atoms. Found 34 (40 requested) and removed 26 (20 requested) atoms. Cycle 20: After refmac, R = 0.2359 (Rfree = 0.000) for 6261 atoms. Found 40 (40 requested) and removed 32 (20 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.32 3.11 Search for helices and strands: 0 residues in 0 chains, 6363 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 6375 seeds are put forward Round 1: 334 peptides, 69 chains. Longest chain 13 peptides. Score 0.274 Round 2: 395 peptides, 69 chains. Longest chain 13 peptides. Score 0.376 Round 3: 387 peptides, 65 chains. Longest chain 14 peptides. Score 0.391 Round 4: 401 peptides, 68 chains. Longest chain 15 peptides. Score 0.392 Round 5: 428 peptides, 70 chains. Longest chain 14 peptides. Score 0.420 Taking the results from Round 5 Chains 70, Residues 358, Estimated correctness of the model 0.0 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 12426 reflections ( 98.98 % complete ) and 13675 restraints for refining 6353 atoms. 12240 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2489 (Rfree = 0.000) for 6353 atoms. Found 31 (40 requested) and removed 33 (20 requested) atoms. Cycle 22: After refmac, R = 0.2382 (Rfree = 0.000) for 6316 atoms. Found 27 (40 requested) and removed 32 (20 requested) atoms. Cycle 23: After refmac, R = 0.2324 (Rfree = 0.000) for 6295 atoms. Found 22 (40 requested) and removed 27 (20 requested) atoms. Cycle 24: After refmac, R = 0.2260 (Rfree = 0.000) for 6277 atoms. Found 32 (40 requested) and removed 26 (20 requested) atoms. Cycle 25: After refmac, R = 0.2231 (Rfree = 0.000) for 6277 atoms. Found 31 (40 requested) and removed 30 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.35 3.13 Search for helices and strands: 0 residues in 0 chains, 6349 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 6366 seeds are put forward Round 1: 365 peptides, 73 chains. Longest chain 12 peptides. Score 0.299 Round 2: 389 peptides, 67 chains. Longest chain 12 peptides. Score 0.380 Round 3: 394 peptides, 65 chains. Longest chain 14 peptides. Score 0.402 Round 4: 396 peptides, 65 chains. Longest chain 16 peptides. Score 0.405 Round 5: 410 peptides, 65 chains. Longest chain 16 peptides. Score 0.426 Taking the results from Round 5 Chains 67, Residues 345, Estimated correctness of the model 0.0 % 5 chains (35 residues) have been docked in sequence ------------------------------------------------------ 12426 reflections ( 98.98 % complete ) and 13843 restraints for refining 6353 atoms. 12420 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2384 (Rfree = 0.000) for 6353 atoms. Found 23 (40 requested) and removed 38 (20 requested) atoms. Cycle 27: After refmac, R = 0.2317 (Rfree = 0.000) for 6310 atoms. Found 39 (40 requested) and removed 27 (20 requested) atoms. Cycle 28: After refmac, R = 0.2010 (Rfree = 0.000) for 6305 atoms. Found 15 (40 requested) and removed 25 (20 requested) atoms. Cycle 29: After refmac, R = 0.1960 (Rfree = 0.000) for 6286 atoms. Found 13 (40 requested) and removed 25 (20 requested) atoms. Cycle 30: After refmac, R = 0.1951 (Rfree = 0.000) for 6272 atoms. Found 10 (40 requested) and removed 24 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.16 Search for helices and strands: 0 residues in 0 chains, 6341 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 6353 seeds are put forward Round 1: 363 peptides, 71 chains. Longest chain 11 peptides. Score 0.310 Round 2: 385 peptides, 70 chains. Longest chain 12 peptides. Score 0.353 Round 3: 406 peptides, 66 chains. Longest chain 18 peptides. Score 0.413 Round 4: 399 peptides, 67 chains. Longest chain 13 peptides. Score 0.396 Round 5: 395 peptides, 63 chains. Longest chain 15 peptides. Score 0.417 Taking the results from Round 5 Chains 63, Residues 332, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 12426 reflections ( 98.98 % complete ) and 14155 restraints for refining 6353 atoms. 12857 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2323 (Rfree = 0.000) for 6353 atoms. Found 35 (40 requested) and removed 29 (20 requested) atoms. Cycle 32: After refmac, R = 0.2385 (Rfree = 0.000) for 6341 atoms. Found 39 (40 requested) and removed 29 (20 requested) atoms. Cycle 33: After refmac, R = 0.2240 (Rfree = 0.000) for 6336 atoms. Found 37 (40 requested) and removed 29 (20 requested) atoms. Cycle 34: After refmac, R = 0.1928 (Rfree = 0.000) for 6333 atoms. Found 9 (40 requested) and removed 23 (20 requested) atoms. Cycle 35: After refmac, R = 0.2047 (Rfree = 0.000) for 6315 atoms. Found 21 (40 requested) and removed 22 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 3.18 Search for helices and strands: 0 residues in 0 chains, 6435 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 6449 seeds are put forward Round 1: 339 peptides, 75 chains. Longest chain 7 peptides. Score 0.239 Round 2: 354 peptides, 65 chains. Longest chain 12 peptides. Score 0.338 Round 3: 364 peptides, 67 chains. Longest chain 12 peptides. Score 0.340 Round 4: 373 peptides, 71 chains. Longest chain 12 peptides. Score 0.326 Round 5: 382 peptides, 69 chains. Longest chain 14 peptides. Score 0.355 Taking the results from Round 5 Chains 69, Residues 313, Estimated correctness of the model 0.0 % 5 chains (20 residues) have been docked in sequence ------------------------------------------------------ 12426 reflections ( 98.98 % complete ) and 14155 restraints for refining 6352 atoms. 12920 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2295 (Rfree = 0.000) for 6352 atoms. Found 28 (40 requested) and removed 24 (20 requested) atoms. Cycle 37: After refmac, R = 0.2319 (Rfree = 0.000) for 6335 atoms. Found 40 (40 requested) and removed 24 (20 requested) atoms. Cycle 38: After refmac, R = 0.2351 (Rfree = 0.000) for 6338 atoms. Found 40 (40 requested) and removed 28 (20 requested) atoms. Cycle 39: After refmac, R = 0.2255 (Rfree = 0.000) for 6341 atoms. Found 40 (40 requested) and removed 26 (20 requested) atoms. Cycle 40: After refmac, R = 0.1950 (Rfree = 0.000) for 6340 atoms. Found 14 (40 requested) and removed 29 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.34 3.12 Search for helices and strands: 0 residues in 0 chains, 6447 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 6470 seeds are put forward Round 1: 308 peptides, 67 chains. Longest chain 9 peptides. Score 0.243 Round 2: 343 peptides, 64 chains. Longest chain 13 peptides. Score 0.326 Round 3: 349 peptides, 62 chains. Longest chain 11 peptides. Score 0.351 Round 4: 383 peptides, 68 chains. Longest chain 18 peptides. Score 0.364 Round 5: 367 peptides, 63 chains. Longest chain 14 peptides. Score 0.373 Taking the results from Round 5 Chains 63, Residues 304, Estimated correctness of the model 0.0 % 5 chains (24 residues) have been docked in sequence ------------------------------------------------------ 12426 reflections ( 98.98 % complete ) and 14074 restraints for refining 6353 atoms. 12857 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2404 (Rfree = 0.000) for 6353 atoms. Found 40 (40 requested) and removed 26 (20 requested) atoms. Cycle 42: After refmac, R = 0.2338 (Rfree = 0.000) for 6347 atoms. Found 40 (40 requested) and removed 28 (20 requested) atoms. Cycle 43: After refmac, R = 0.2343 (Rfree = 0.000) for 6352 atoms. Found 40 (40 requested) and removed 23 (20 requested) atoms. Cycle 44: After refmac, R = 0.2113 (Rfree = 0.000) for 6353 atoms. Found 13 (40 requested) and removed 22 (20 requested) atoms. Cycle 45: After refmac, R = 0.2095 (Rfree = 0.000) for 6340 atoms. Found 15 (40 requested) and removed 22 (20 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.40 3.18 Search for helices and strands: 0 residues in 0 chains, 6418 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 6438 seeds are put forward Round 1: 291 peptides, 65 chains. Longest chain 11 peptides. Score 0.227 Round 2: 314 peptides, 59 chains. Longest chain 12 peptides. Score 0.314 Round 3: 333 peptides, 58 chains. Longest chain 11 peptides. Score 0.353 Round 4: 327 peptides, 57 chains. Longest chain 11 peptides. Score 0.350 Round 5: 335 peptides, 51 chains. Longest chain 16 peptides. Score 0.406 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 51, Residues 284, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 1vl0-3_warpNtrace.pdb as input Building loops using Loopy2018 51 chains (284 residues) following loop building 2 chains (13 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12426 reflections ( 98.98 % complete ) and 14238 restraints for refining 6353 atoms. 13108 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2367 (Rfree = 0.000) for 6353 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 47: After refmac, R = 0.2447 (Rfree = 0.000) for 6312 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 48: After refmac, R = 0.2404 (Rfree = 0.000) for 6284 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 49: After refmac, R = 0.2118 (Rfree = 0.000) for 6250 atoms. TimeTaking 68.13