Sun 23 Dec 23:59:49 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 1vqs-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vqs-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vqs-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqs-3.2-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/1vqs-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqs-3.2-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 ============================================================ Sun 23 Dec 23:59:54 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/1vqs-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqs-3.2-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 512 and 0 Target number of residues in the AU: 512 Target solvent content: 0.5928 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-3.2-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: 97 Cell parameters: 94.778 94.778 303.043 90.000 90.000 90.000 Input sequence file: 1vqs-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4640 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: 29.971 3.200 Wilson plot Bfac: 49.53 11899 reflections ( 99.69 % complete ) and 0 restraints for refining 5191 atoms. Observations/parameters ratio is 0.57 ------------------------------------------------------ Starting model: R = 0.3118 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3196 (Rfree = 0.000) for 5191 atoms. Found 46 (46 requested) and removed 54 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.96 2.81 Search for helices and strands: 0 residues in 0 chains, 5276 seeds are put forward NCS extension: 0 residues added, 5276 seeds are put forward Round 1: 318 peptides, 54 chains. Longest chain 12 peptides. Score 0.428 Round 2: 389 peptides, 53 chains. Longest chain 17 peptides. Score 0.581 Round 3: 408 peptides, 45 chains. Longest chain 30 peptides. Score 0.671 Round 4: 425 peptides, 43 chains. Longest chain 24 peptides. Score 0.708 Round 5: 419 peptides, 37 chains. Longest chain 32 peptides. Score 0.737 Taking the results from Round 5 Chains 40, Residues 382, Estimated correctness of the model 72.6 % 6 chains (139 residues) have been docked in sequence Building loops using Loopy2018 40 chains (382 residues) following loop building 6 chains (139 residues) in sequence following loop building ------------------------------------------------------ 11899 reflections ( 99.69 % complete ) and 7396 restraints for refining 4233 atoms. 5295 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2925 (Rfree = 0.000) for 4233 atoms. Found 38 (38 requested) and removed 34 (19 requested) atoms. Cycle 2: After refmac, R = 0.2716 (Rfree = 0.000) for 4193 atoms. Found 20 (36 requested) and removed 25 (18 requested) atoms. Cycle 3: After refmac, R = 0.2611 (Rfree = 0.000) for 4155 atoms. Found 25 (36 requested) and removed 22 (18 requested) atoms. Cycle 4: After refmac, R = 0.2504 (Rfree = 0.000) for 4144 atoms. Found 11 (35 requested) and removed 25 (18 requested) atoms. Cycle 5: After refmac, R = 0.2491 (Rfree = 0.000) for 4122 atoms. Found 18 (33 requested) and removed 22 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.97 2.82 Search for helices and strands: 0 residues in 0 chains, 4233 seeds are put forward NCS extension: 28 residues added (7 deleted due to clashes), 4261 seeds are put forward Round 1: 391 peptides, 41 chains. Longest chain 24 peptides. Score 0.674 Round 2: 423 peptides, 36 chains. Longest chain 45 peptides. Score 0.748 Round 3: 421 peptides, 37 chains. Longest chain 28 peptides. Score 0.740 Round 4: 432 peptides, 37 chains. Longest chain 32 peptides. Score 0.753 Round 5: 430 peptides, 39 chains. Longest chain 28 peptides. Score 0.739 Taking the results from Round 4 Chains 42, Residues 395, Estimated correctness of the model 75.6 % 6 chains (123 residues) have been docked in sequence Building loops using Loopy2018 42 chains (395 residues) following loop building 6 chains (123 residues) in sequence following loop building ------------------------------------------------------ 11899 reflections ( 99.69 % complete ) and 7558 restraints for refining 4234 atoms. 5421 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2954 (Rfree = 0.000) for 4234 atoms. Found 34 (34 requested) and removed 46 (19 requested) atoms. Cycle 7: After refmac, R = 0.2578 (Rfree = 0.000) for 4198 atoms. Found 20 (33 requested) and removed 27 (18 requested) atoms. Cycle 8: After refmac, R = 0.2528 (Rfree = 0.000) for 4170 atoms. Found 15 (32 requested) and removed 24 (18 requested) atoms. Cycle 9: After refmac, R = 0.2468 (Rfree = 0.000) for 4152 atoms. Found 12 (31 requested) and removed 23 (18 requested) atoms. Cycle 10: After refmac, R = 0.2466 (Rfree = 0.000) for 4132 atoms. Found 10 (30 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.97 2.82 Search for helices and strands: 0 residues in 0 chains, 4217 seeds are put forward NCS extension: 36 residues added (9 deleted due to clashes), 4253 seeds are put forward Round 1: 391 peptides, 39 chains. Longest chain 33 peptides. Score 0.687 Round 2: 420 peptides, 39 chains. Longest chain 29 peptides. Score 0.727 Round 3: 433 peptides, 36 chains. Longest chain 38 peptides. Score 0.760 Round 4: 425 peptides, 37 chains. Longest chain 35 peptides. Score 0.745 Round 5: 409 peptides, 38 chains. Longest chain 35 peptides. Score 0.719 Taking the results from Round 3 Chains 47, Residues 397, Estimated correctness of the model 76.9 % 8 chains (150 residues) have been docked in sequence Building loops using Loopy2018 47 chains (397 residues) following loop building 8 chains (150 residues) in sequence following loop building ------------------------------------------------------ 11899 reflections ( 99.69 % complete ) and 7261 restraints for refining 4236 atoms. 5060 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2802 (Rfree = 0.000) for 4236 atoms. Found 30 (30 requested) and removed 32 (19 requested) atoms. Cycle 12: After refmac, R = 0.2442 (Rfree = 0.000) for 4220 atoms. Found 15 (29 requested) and removed 20 (18 requested) atoms. Cycle 13: After refmac, R = 0.2355 (Rfree = 0.000) for 4203 atoms. Found 9 (28 requested) and removed 20 (18 requested) atoms. Cycle 14: After refmac, R = 0.2338 (Rfree = 0.000) for 4188 atoms. Found 12 (27 requested) and removed 18 (18 requested) atoms. Cycle 15: After refmac, R = 0.2312 (Rfree = 0.000) for 4177 atoms. Found 12 (27 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.97 2.82 Search for helices and strands: 0 residues in 0 chains, 4281 seeds are put forward NCS extension: 14 residues added (13 deleted due to clashes), 4295 seeds are put forward Round 1: 396 peptides, 36 chains. Longest chain 43 peptides. Score 0.714 Round 2: 412 peptides, 39 chains. Longest chain 28 peptides. Score 0.716 Round 3: 422 peptides, 34 chains. Longest chain 38 peptides. Score 0.758 Round 4: 418 peptides, 37 chains. Longest chain 38 peptides. Score 0.736 Round 5: 406 peptides, 34 chains. Longest chain 41 peptides. Score 0.739 Taking the results from Round 3 Chains 39, Residues 388, Estimated correctness of the model 76.5 % 5 chains (126 residues) have been docked in sequence Building loops using Loopy2018 39 chains (388 residues) following loop building 5 chains (126 residues) in sequence following loop building ------------------------------------------------------ 11899 reflections ( 99.69 % complete ) and 7551 restraints for refining 4235 atoms. 5447 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2639 (Rfree = 0.000) for 4235 atoms. Found 27 (27 requested) and removed 33 (19 requested) atoms. Cycle 17: After refmac, R = 0.2443 (Rfree = 0.000) for 4217 atoms. Found 22 (25 requested) and removed 21 (18 requested) atoms. Cycle 18: After refmac, R = 0.2369 (Rfree = 0.000) for 4214 atoms. Found 17 (24 requested) and removed 19 (18 requested) atoms. Cycle 19: After refmac, R = 0.2326 (Rfree = 0.000) for 4209 atoms. Found 10 (24 requested) and removed 22 (18 requested) atoms. Cycle 20: After refmac, R = 0.2289 (Rfree = 0.000) for 4193 atoms. Found 11 (23 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.95 2.80 Search for helices and strands: 0 residues in 0 chains, 4318 seeds are put forward NCS extension: 27 residues added (12 deleted due to clashes), 4345 seeds are put forward Round 1: 381 peptides, 39 chains. Longest chain 30 peptides. Score 0.673 Round 2: 402 peptides, 33 chains. Longest chain 44 peptides. Score 0.740 Round 3: 399 peptides, 38 chains. Longest chain 28 peptides. Score 0.705 Round 4: 405 peptides, 42 chains. Longest chain 32 peptides. Score 0.687 Round 5: 400 peptides, 34 chains. Longest chain 43 peptides. Score 0.732 Taking the results from Round 2 Chains 37, Residues 369, Estimated correctness of the model 73.2 % 6 chains (130 residues) have been docked in sequence Building loops using Loopy2018 37 chains (369 residues) following loop building 6 chains (130 residues) in sequence following loop building ------------------------------------------------------ 11899 reflections ( 99.69 % complete ) and 7651 restraints for refining 4235 atoms. 5636 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2514 (Rfree = 0.000) for 4235 atoms. Found 23 (23 requested) and removed 29 (19 requested) atoms. Cycle 22: After refmac, R = 0.2376 (Rfree = 0.000) for 4211 atoms. Found 20 (21 requested) and removed 20 (18 requested) atoms. Cycle 23: After refmac, R = 0.2358 (Rfree = 0.000) for 4200 atoms. Found 18 (21 requested) and removed 19 (18 requested) atoms. Cycle 24: After refmac, R = 0.2328 (Rfree = 0.000) for 4194 atoms. Found 19 (20 requested) and removed 20 (18 requested) atoms. Cycle 25: After refmac, R = 0.2321 (Rfree = 0.000) for 4193 atoms. Found 8 (19 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.96 2.81 Search for helices and strands: 0 residues in 0 chains, 4307 seeds are put forward NCS extension: 9 residues added (10 deleted due to clashes), 4316 seeds are put forward Round 1: 384 peptides, 41 chains. Longest chain 30 peptides. Score 0.663 Round 2: 403 peptides, 39 chains. Longest chain 38 peptides. Score 0.704 Round 3: 397 peptides, 35 chains. Longest chain 33 peptides. Score 0.722 Round 4: 390 peptides, 37 chains. Longest chain 29 peptides. Score 0.699 Round 5: 380 peptides, 40 chains. Longest chain 29 peptides. Score 0.664 Taking the results from Round 3 Chains 40, Residues 362, Estimated correctness of the model 69.7 % 6 chains (119 residues) have been docked in sequence Building loops using Loopy2018 40 chains (362 residues) following loop building 6 chains (119 residues) in sequence following loop building ------------------------------------------------------ 11899 reflections ( 99.69 % complete ) and 7754 restraints for refining 4236 atoms. 5801 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2646 (Rfree = 0.000) for 4236 atoms. Found 19 (19 requested) and removed 38 (19 requested) atoms. Cycle 27: After refmac, R = 0.2526 (Rfree = 0.000) for 4211 atoms. Found 18 (18 requested) and removed 24 (18 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2477 (Rfree = 0.000) for 4196 atoms. Found 18 (18 requested) and removed 21 (18 requested) atoms. Cycle 29: After refmac, R = 0.2469 (Rfree = 0.000) for 4186 atoms. Found 18 (18 requested) and removed 19 (18 requested) atoms. Cycle 30: After refmac, R = 0.2461 (Rfree = 0.000) for 4178 atoms. Found 18 (18 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.00 2.84 Search for helices and strands: 0 residues in 0 chains, 4298 seeds are put forward NCS extension: 22 residues added (9 deleted due to clashes), 4320 seeds are put forward Round 1: 355 peptides, 42 chains. Longest chain 25 peptides. Score 0.608 Round 2: 359 peptides, 40 chains. Longest chain 26 peptides. Score 0.631 Round 3: 360 peptides, 37 chains. Longest chain 21 peptides. Score 0.655 Round 4: 359 peptides, 38 chains. Longest chain 27 peptides. Score 0.646 Round 5: 369 peptides, 41 chains. Longest chain 23 peptides. Score 0.639 Taking the results from Round 3 Chains 39, Residues 323, Estimated correctness of the model 55.0 % 5 chains (76 residues) have been docked in sequence ------------------------------------------------------ 11899 reflections ( 99.69 % complete ) and 8611 restraints for refining 4233 atoms. 7011 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2529 (Rfree = 0.000) for 4233 atoms. Found 19 (19 requested) and removed 24 (19 requested) atoms. Cycle 32: After refmac, R = 0.2389 (Rfree = 0.000) for 4216 atoms. Found 10 (18 requested) and removed 23 (18 requested) atoms. Cycle 33: After refmac, R = 0.2438 (Rfree = 0.000) for 4198 atoms. Found 18 (18 requested) and removed 22 (18 requested) atoms. Cycle 34: After refmac, R = 0.2338 (Rfree = 0.000) for 4186 atoms. Found 16 (18 requested) and removed 20 (18 requested) atoms. Cycle 35: After refmac, R = 0.2250 (Rfree = 0.000) for 4181 atoms. Found 12 (18 requested) and removed 19 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.99 2.83 Search for helices and strands: 0 residues in 0 chains, 4270 seeds are put forward NCS extension: 13 residues added (7 deleted due to clashes), 4283 seeds are put forward Round 1: 322 peptides, 38 chains. Longest chain 22 peptides. Score 0.582 Round 2: 346 peptides, 34 chains. Longest chain 23 peptides. Score 0.655 Round 3: 342 peptides, 38 chains. Longest chain 23 peptides. Score 0.617 Round 4: 348 peptides, 36 chains. Longest chain 28 peptides. Score 0.643 Round 5: 354 peptides, 34 chains. Longest chain 26 peptides. Score 0.667 Taking the results from Round 5 Chains 38, Residues 320, Estimated correctness of the model 57.9 % 4 chains (66 residues) have been docked in sequence ------------------------------------------------------ 11899 reflections ( 99.69 % complete ) and 8582 restraints for refining 4235 atoms. 7022 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2758 (Rfree = 0.000) for 4235 atoms. Found 19 (19 requested) and removed 31 (19 requested) atoms. Cycle 37: After refmac, R = 0.2466 (Rfree = 0.000) for 4208 atoms. Found 18 (18 requested) and removed 23 (18 requested) atoms. Cycle 38: After refmac, R = 0.2488 (Rfree = 0.000) for 4197 atoms. Found 18 (18 requested) and removed 24 (18 requested) atoms. Cycle 39: After refmac, R = 0.2325 (Rfree = 0.000) for 4184 atoms. Found 18 (18 requested) and removed 23 (18 requested) atoms. Cycle 40: After refmac, R = 0.2313 (Rfree = 0.000) for 4169 atoms. Found 18 (18 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.00 2.84 Search for helices and strands: 0 residues in 0 chains, 4289 seeds are put forward NCS extension: 16 residues added (5 deleted due to clashes), 4305 seeds are put forward Round 1: 301 peptides, 39 chains. Longest chain 22 peptides. Score 0.533 Round 2: 338 peptides, 35 chains. Longest chain 23 peptides. Score 0.634 Round 3: 345 peptides, 37 chains. Longest chain 22 peptides. Score 0.630 Round 4: 321 peptides, 35 chains. Longest chain 23 peptides. Score 0.605 Round 5: 342 peptides, 37 chains. Longest chain 23 peptides. Score 0.625 Taking the results from Round 2 Chains 35, Residues 303, Estimated correctness of the model 49.9 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 11899 reflections ( 99.69 % complete ) and 9338 restraints for refining 4233 atoms. 8107 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3224 (Rfree = 0.000) for 4233 atoms. Found 18 (18 requested) and removed 62 (18 requested) atoms. Cycle 42: After refmac, R = 0.2522 (Rfree = 0.000) for 4177 atoms. Found 18 (18 requested) and removed 29 (18 requested) atoms. Cycle 43: After refmac, R = 0.2491 (Rfree = 0.000) for 4159 atoms. Found 18 (18 requested) and removed 26 (18 requested) atoms. Cycle 44: After refmac, R = 0.2498 (Rfree = 0.000) for 4149 atoms. Found 18 (18 requested) and removed 22 (18 requested) atoms. Cycle 45: After refmac, R = 0.2493 (Rfree = 0.000) for 4139 atoms. Found 18 (18 requested) and removed 24 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.97 2.82 Search for helices and strands: 0 residues in 0 chains, 4216 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 4239 seeds are put forward Round 1: 290 peptides, 40 chains. Longest chain 23 peptides. Score 0.501 Round 2: 336 peptides, 39 chains. Longest chain 23 peptides. Score 0.599 Round 3: 349 peptides, 35 chains. Longest chain 22 peptides. Score 0.652 Round 4: 351 peptides, 35 chains. Longest chain 23 peptides. Score 0.655 Round 5: 337 peptides, 37 chains. Longest chain 25 peptides. Score 0.617 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 316, Estimated correctness of the model 55.0 % 3 chains (41 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 1vqs-3_warpNtrace.pdb as input Building loops using Loopy2018 35 chains (316 residues) following loop building 3 chains (41 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11899 reflections ( 99.69 % complete ) and 8836 restraints for refining 4236 atoms. 7425 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2778 (Rfree = 0.000) for 4236 atoms. Found 0 (19 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.2589 (Rfree = 0.000) for 4208 atoms. Found 0 (18 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.2381 (Rfree = 0.000) for 4186 atoms. Found 0 (18 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.2347 (Rfree = 0.000) for 4166 atoms. Found 0 (18 requested) and removed 18 (18 requested) atoms. Writing output files ... TimeTaking 67.57