null Mon 24 Dec 07:44:54 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 1vr0-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vr0-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vr0-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr0-3.4-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/1vr0-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr0-3.4-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 07:44:58 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/1vr0-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr0-3.4-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 510 and 0 Target number of residues in the AU: 510 Target solvent content: 0.6232 Checking the provided sequence file Detected sequence length: 247 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 741 Adjusted target solvent content: 0.45 Input MTZ file: 1vr0-3.4-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: 20 Cell parameters: 46.686 69.193 453.518 90.000 90.000 90.000 Input sequence file: 1vr0-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 5928 target number of atoms Had to go as low as 0.65 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: 226.759 3.400 Wilson plot Bfac: 62.77 10631 reflections ( 99.67 % complete ) and 0 restraints for refining 6596 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3167 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2723 (Rfree = 0.000) for 6596 atoms. Found 29 (49 requested) and removed 62 (24 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.25 3.47 Search for helices and strands: 0 residues in 0 chains, 6713 seeds are put forward NCS extension: 0 residues added, 6713 seeds are put forward Round 1: 315 peptides, 61 chains. Longest chain 11 peptides. Score 0.341 Round 2: 385 peptides, 59 chains. Longest chain 17 peptides. Score 0.506 Round 3: 391 peptides, 57 chains. Longest chain 12 peptides. Score 0.533 Round 4: 390 peptides, 58 chains. Longest chain 15 peptides. Score 0.523 Round 5: 419 peptides, 58 chains. Longest chain 16 peptides. Score 0.574 Taking the results from Round 5 Chains 59, Residues 361, Estimated correctness of the model 20.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 10631 reflections ( 99.67 % complete ) and 12470 restraints for refining 5389 atoms. 11055 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2442 (Rfree = 0.000) for 5389 atoms. Found 27 (40 requested) and removed 39 (20 requested) atoms. Cycle 2: After refmac, R = 0.2286 (Rfree = 0.000) for 5334 atoms. Found 5 (40 requested) and removed 32 (20 requested) atoms. Cycle 3: After refmac, R = 0.2209 (Rfree = 0.000) for 5289 atoms. Found 6 (40 requested) and removed 27 (20 requested) atoms. Cycle 4: After refmac, R = 0.2409 (Rfree = 0.000) for 5259 atoms. Found 17 (39 requested) and removed 40 (19 requested) atoms. Cycle 5: After refmac, R = 0.2289 (Rfree = 0.000) for 5218 atoms. Found 12 (39 requested) and removed 26 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.26 3.49 Search for helices and strands: 0 residues in 0 chains, 5395 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 5410 seeds are put forward Round 1: 367 peptides, 64 chains. Longest chain 15 peptides. Score 0.427 Round 2: 401 peptides, 58 chains. Longest chain 33 peptides. Score 0.543 Round 3: 416 peptides, 54 chains. Longest chain 20 peptides. Score 0.599 Round 4: 422 peptides, 56 chains. Longest chain 19 peptides. Score 0.594 Round 5: 424 peptides, 57 chains. Longest chain 23 peptides. Score 0.590 Taking the results from Round 3 Chains 55, Residues 362, Estimated correctness of the model 28.3 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 10631 reflections ( 99.67 % complete ) and 12238 restraints for refining 5389 atoms. 10776 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2350 (Rfree = 0.000) for 5389 atoms. Found 15 (40 requested) and removed 30 (20 requested) atoms. Cycle 7: After refmac, R = 0.2181 (Rfree = 0.000) for 5358 atoms. Found 8 (40 requested) and removed 23 (20 requested) atoms. Cycle 8: After refmac, R = 0.2125 (Rfree = 0.000) for 5332 atoms. Found 5 (40 requested) and removed 20 (20 requested) atoms. Cycle 9: After refmac, R = 0.2065 (Rfree = 0.000) for 5316 atoms. Found 3 (40 requested) and removed 20 (20 requested) atoms. Cycle 10: After refmac, R = 0.2034 (Rfree = 0.000) for 5290 atoms. Found 6 (40 requested) and removed 21 (20 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.24 3.46 Search for helices and strands: 0 residues in 0 chains, 5480 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 5501 seeds are put forward Round 1: 365 peptides, 63 chains. Longest chain 14 peptides. Score 0.432 Round 2: 397 peptides, 59 chains. Longest chain 21 peptides. Score 0.528 Round 3: 390 peptides, 55 chains. Longest chain 18 peptides. Score 0.547 Round 4: 387 peptides, 53 chains. Longest chain 16 peptides. Score 0.557 Round 5: 400 peptides, 57 chains. Longest chain 27 peptides. Score 0.549 Taking the results from Round 4 Chains 54, Residues 334, Estimated correctness of the model 14.0 % 3 chains (34 residues) have been docked in sequence ------------------------------------------------------ 10631 reflections ( 99.67 % complete ) and 12125 restraints for refining 5389 atoms. 10726 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2388 (Rfree = 0.000) for 5389 atoms. Found 23 (40 requested) and removed 35 (20 requested) atoms. Cycle 12: After refmac, R = 0.2251 (Rfree = 0.000) for 5367 atoms. Found 11 (40 requested) and removed 23 (20 requested) atoms. Cycle 13: After refmac, R = 0.2170 (Rfree = 0.000) for 5348 atoms. Found 2 (40 requested) and removed 21 (20 requested) atoms. Cycle 14: After refmac, R = 0.2138 (Rfree = 0.000) for 5326 atoms. Found 6 (40 requested) and removed 20 (20 requested) atoms. Cycle 15: After refmac, R = 0.2102 (Rfree = 0.000) for 5311 atoms. Found 3 (40 requested) and removed 20 (20 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 3.49 Search for helices and strands: 0 residues in 0 chains, 5486 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 5501 seeds are put forward Round 1: 340 peptides, 55 chains. Longest chain 17 peptides. Score 0.451 Round 2: 369 peptides, 51 chains. Longest chain 17 peptides. Score 0.541 Round 3: 388 peptides, 50 chains. Longest chain 19 peptides. Score 0.582 Round 4: 377 peptides, 51 chains. Longest chain 21 peptides. Score 0.555 Round 5: 399 peptides, 54 chains. Longest chain 18 peptides. Score 0.571 Taking the results from Round 3 Chains 51, Residues 338, Estimated correctness of the model 22.7 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 10631 reflections ( 99.67 % complete ) and 12451 restraints for refining 5390 atoms. 11115 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2431 (Rfree = 0.000) for 5390 atoms. Found 14 (40 requested) and removed 25 (20 requested) atoms. Cycle 17: After refmac, R = 0.2258 (Rfree = 0.000) for 5375 atoms. Found 8 (40 requested) and removed 22 (20 requested) atoms. Cycle 18: After refmac, R = 0.2191 (Rfree = 0.000) for 5359 atoms. Found 6 (40 requested) and removed 20 (20 requested) atoms. Cycle 19: After refmac, R = 0.2175 (Rfree = 0.000) for 5344 atoms. Found 5 (40 requested) and removed 20 (20 requested) atoms. Cycle 20: After refmac, R = 0.2142 (Rfree = 0.000) for 5328 atoms. Found 5 (40 requested) and removed 20 (20 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.27 3.50 Search for helices and strands: 0 residues in 0 chains, 5476 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 5493 seeds are put forward Round 1: 364 peptides, 60 chains. Longest chain 14 peptides. Score 0.456 Round 2: 378 peptides, 54 chains. Longest chain 19 peptides. Score 0.533 Round 3: 399 peptides, 53 chains. Longest chain 18 peptides. Score 0.578 Round 4: 391 peptides, 53 chains. Longest chain 17 peptides. Score 0.564 Round 5: 387 peptides, 51 chains. Longest chain 20 peptides. Score 0.573 Taking the results from Round 3 Chains 53, Residues 346, Estimated correctness of the model 21.3 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 10631 reflections ( 99.67 % complete ) and 12424 restraints for refining 5390 atoms. 11045 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2346 (Rfree = 0.000) for 5390 atoms. Found 16 (40 requested) and removed 24 (20 requested) atoms. Cycle 22: After refmac, R = 0.2253 (Rfree = 0.000) for 5373 atoms. Found 5 (40 requested) and removed 24 (20 requested) atoms. Cycle 23: After refmac, R = 0.2262 (Rfree = 0.000) for 5352 atoms. Found 3 (40 requested) and removed 20 (20 requested) atoms. Cycle 24: After refmac, R = 0.2232 (Rfree = 0.000) for 5334 atoms. Found 5 (40 requested) and removed 20 (20 requested) atoms. Cycle 25: After refmac, R = 0.2219 (Rfree = 0.000) for 5319 atoms. Found 5 (40 requested) and removed 20 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 3.50 Search for helices and strands: 0 residues in 0 chains, 5489 seeds are put forward NCS extension: 20 residues added (5 deleted due to clashes), 5509 seeds are put forward Round 1: 334 peptides, 54 chains. Longest chain 16 peptides. Score 0.448 Round 2: 380 peptides, 55 chains. Longest chain 18 peptides. Score 0.529 Round 3: 376 peptides, 56 chains. Longest chain 16 peptides. Score 0.513 Round 4: 398 peptides, 55 chains. Longest chain 17 peptides. Score 0.561 Round 5: 389 peptides, 54 chains. Longest chain 19 peptides. Score 0.553 Taking the results from Round 4 Chains 55, Residues 343, Estimated correctness of the model 15.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10631 reflections ( 99.67 % complete ) and 12547 restraints for refining 5389 atoms. 11230 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2662 (Rfree = 0.000) for 5389 atoms. Found 25 (40 requested) and removed 23 (20 requested) atoms. Cycle 27: After refmac, R = 0.2437 (Rfree = 0.000) for 5388 atoms. Found 5 (40 requested) and removed 21 (20 requested) atoms. Cycle 28: After refmac, R = 0.2366 (Rfree = 0.000) for 5368 atoms. Found 5 (40 requested) and removed 20 (20 requested) atoms. Cycle 29: After refmac, R = 0.2318 (Rfree = 0.000) for 5350 atoms. Found 6 (40 requested) and removed 20 (20 requested) atoms. Cycle 30: After refmac, R = 0.2275 (Rfree = 0.000) for 5335 atoms. Found 5 (40 requested) and removed 20 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.24 3.46 Search for helices and strands: 0 residues in 0 chains, 5491 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 5513 seeds are put forward Round 1: 336 peptides, 56 chains. Longest chain 16 peptides. Score 0.434 Round 2: 351 peptides, 50 chains. Longest chain 20 peptides. Score 0.516 Round 3: 373 peptides, 63 chains. Longest chain 21 peptides. Score 0.448 Round 4: 358 peptides, 53 chains. Longest chain 17 peptides. Score 0.504 Round 5: 371 peptides, 55 chains. Longest chain 20 peptides. Score 0.512 Taking the results from Round 2 Chains 50, Residues 301, Estimated correctness of the model 0.0 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 10631 reflections ( 99.67 % complete ) and 12588 restraints for refining 5387 atoms. 11361 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2422 (Rfree = 0.000) for 5387 atoms. Found 13 (40 requested) and removed 25 (20 requested) atoms. Cycle 32: After refmac, R = 0.2314 (Rfree = 0.000) for 5372 atoms. Found 5 (40 requested) and removed 20 (20 requested) atoms. Cycle 33: After refmac, R = 0.2383 (Rfree = 0.000) for 5355 atoms. Found 5 (40 requested) and removed 20 (20 requested) atoms. Cycle 34: After refmac, R = 0.2312 (Rfree = 0.000) for 5337 atoms. Found 4 (40 requested) and removed 20 (20 requested) atoms. Cycle 35: After refmac, R = 0.2267 (Rfree = 0.000) for 5319 atoms. Found 5 (40 requested) and removed 20 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 3.50 Search for helices and strands: 0 residues in 0 chains, 5462 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 5482 seeds are put forward Round 1: 339 peptides, 61 chains. Longest chain 16 peptides. Score 0.395 Round 2: 356 peptides, 56 chains. Longest chain 18 peptides. Score 0.475 Round 3: 368 peptides, 56 chains. Longest chain 21 peptides. Score 0.498 Round 4: 362 peptides, 55 chains. Longest chain 16 peptides. Score 0.495 Round 5: 357 peptides, 48 chains. Longest chain 16 peptides. Score 0.544 Taking the results from Round 5 Chains 48, Residues 309, Estimated correctness of the model 9.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10631 reflections ( 99.67 % complete ) and 12786 restraints for refining 5390 atoms. 11598 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2332 (Rfree = 0.000) for 5390 atoms. Found 10 (40 requested) and removed 22 (20 requested) atoms. Cycle 37: After refmac, R = 0.2206 (Rfree = 0.000) for 5369 atoms. Found 9 (40 requested) and removed 21 (20 requested) atoms. Cycle 38: After refmac, R = 0.2115 (Rfree = 0.000) for 5354 atoms. Found 6 (40 requested) and removed 20 (20 requested) atoms. Cycle 39: After refmac, R = 0.2154 (Rfree = 0.000) for 5339 atoms. Found 6 (40 requested) and removed 20 (20 requested) atoms. Cycle 40: After refmac, R = 0.2106 (Rfree = 0.000) for 5322 atoms. Found 5 (40 requested) and removed 20 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.26 3.49 Search for helices and strands: 0 residues in 0 chains, 5498 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 5514 seeds are put forward Round 1: 287 peptides, 58 chains. Longest chain 11 peptides. Score 0.305 Round 2: 332 peptides, 53 chains. Longest chain 20 peptides. Score 0.453 Round 3: 332 peptides, 58 chains. Longest chain 14 peptides. Score 0.407 Round 4: 351 peptides, 55 chains. Longest chain 15 peptides. Score 0.473 Round 5: 332 peptides, 52 chains. Longest chain 19 peptides. Score 0.462 Taking the results from Round 4 Chains 55, Residues 296, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10631 reflections ( 99.67 % complete ) and 12725 restraints for refining 5390 atoms. 11596 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2234 (Rfree = 0.000) for 5390 atoms. Found 11 (40 requested) and removed 21 (20 requested) atoms. Cycle 42: After refmac, R = 0.2202 (Rfree = 0.000) for 5372 atoms. Found 8 (40 requested) and removed 20 (20 requested) atoms. Cycle 43: After refmac, R = 0.2124 (Rfree = 0.000) for 5358 atoms. Found 5 (40 requested) and removed 20 (20 requested) atoms. Cycle 44: After refmac, R = 0.2103 (Rfree = 0.000) for 5342 atoms. Found 5 (40 requested) and removed 20 (20 requested) atoms. Cycle 45: After refmac, R = 0.2116 (Rfree = 0.000) for 5326 atoms. Found 3 (40 requested) and removed 20 (20 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.25 3.47 Search for helices and strands: 0 residues in 0 chains, 5510 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 5527 seeds are put forward Round 1: 280 peptides, 54 chains. Longest chain 10 peptides. Score 0.329 Round 2: 329 peptides, 55 chains. Longest chain 11 peptides. Score 0.428 Round 3: 356 peptides, 48 chains. Longest chain 24 peptides. Score 0.542 Round 4: 338 peptides, 50 chains. Longest chain 14 peptides. Score 0.491 Round 5: 324 peptides, 48 chains. Longest chain 14 peptides. Score 0.481 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 50, Residues 308, Estimated correctness of the model 8.6 % 1 chains (20 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 1vr0-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10631 reflections ( 99.67 % complete ) and 12353 restraints for refining 5389 atoms. 11082 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2235 (Rfree = 0.000) for 5389 atoms. Found 0 (40 requested) and removed 11 (20 requested) atoms. Cycle 47: After refmac, R = 0.2187 (Rfree = 0.000) for 5370 atoms. Found 0 (40 requested) and removed 6 (20 requested) atoms. Cycle 48: After refmac, R = 0.2253 (Rfree = 0.000) for 5362 atoms. Found 0 (40 requested) and removed 6 (20 requested) atoms. Cycle 49: After refmac, R = 0.2085 (Rfree = 0.000) for 5355 atoms. Found 0 (40 requested) and removed 5 (20 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:43:35 GMT 2018 Job finished. TimeTaking 58.68 Used memory is bytes: 12484224