null Sun 23 Dec 22:22:43 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 1vqs-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vqs-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vqs-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqs-3.2-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/1vqs-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqs-3.2-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 ============================================================ Sun 23 Dec 22:22:53 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/1vqs-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqs-3.2-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 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-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: 97 Cell parameters: 94.778 94.778 303.043 90.000 90.000 90.000 Input sequence file: 1vqs-3.2-parrot-hancs.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 5111 atoms. Observations/parameters ratio is 0.58 ------------------------------------------------------ Starting model: R = 0.3151 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3007 (Rfree = 0.000) for 5111 atoms. Found 45 (45 requested) and removed 38 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.00 2.84 Search for helices and strands: 0 residues in 0 chains, 5215 seeds are put forward NCS extension: 0 residues added, 5215 seeds are put forward Round 1: 309 peptides, 49 chains. Longest chain 17 peptides. Score 0.456 Round 2: 384 peptides, 44 chains. Longest chain 27 peptides. Score 0.641 Round 3: 392 peptides, 40 chains. Longest chain 33 peptides. Score 0.682 Round 4: 391 peptides, 38 chains. Longest chain 25 peptides. Score 0.694 Round 5: 396 peptides, 37 chains. Longest chain 27 peptides. Score 0.708 Taking the results from Round 5 Chains 38, Residues 359, Estimated correctness of the model 66.9 % 4 chains (91 residues) have been docked in sequence Building loops using Loopy2018 38 chains (359 residues) following loop building 4 chains (91 residues) in sequence following loop building ------------------------------------------------------ 11899 reflections ( 99.69 % complete ) and 7902 restraints for refining 4235 atoms. 6106 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2875 (Rfree = 0.000) for 4235 atoms. Found 38 (38 requested) and removed 32 (19 requested) atoms. Cycle 2: After refmac, R = 0.2767 (Rfree = 0.000) for 4166 atoms. Found 30 (37 requested) and removed 27 (19 requested) atoms. Cycle 3: After refmac, R = 0.2626 (Rfree = 0.000) for 4148 atoms. Found 18 (36 requested) and removed 20 (18 requested) atoms. Cycle 4: After refmac, R = 0.2589 (Rfree = 0.000) for 4129 atoms. Found 18 (35 requested) and removed 21 (18 requested) atoms. Cycle 5: After refmac, R = 0.2537 (Rfree = 0.000) for 4105 atoms. Found 23 (33 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.02 2.86 Search for helices and strands: 0 residues in 0 chains, 4230 seeds are put forward NCS extension: 23 residues added (14 deleted due to clashes), 4253 seeds are put forward Round 1: 404 peptides, 45 chains. Longest chain 25 peptides. Score 0.665 Round 2: 411 peptides, 39 chains. Longest chain 30 peptides. Score 0.715 Round 3: 431 peptides, 42 chains. Longest chain 51 peptides. Score 0.722 Round 4: 419 peptides, 39 chains. Longest chain 34 peptides. Score 0.725 Round 5: 427 peptides, 38 chains. Longest chain 43 peptides. Score 0.741 Taking the results from Round 5 Chains 42, Residues 389, Estimated correctness of the model 73.4 % 6 chains (105 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 59 B and 65 B 40 chains (391 residues) following loop building 5 chains (110 residues) in sequence following loop building ------------------------------------------------------ 11899 reflections ( 99.69 % complete ) and 7828 restraints for refining 4236 atoms. 5829 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2834 (Rfree = 0.000) for 4236 atoms. Found 34 (34 requested) and removed 33 (19 requested) atoms. Cycle 7: After refmac, R = 0.2687 (Rfree = 0.000) for 4211 atoms. Found 31 (33 requested) and removed 27 (19 requested) atoms. Cycle 8: After refmac, R = 0.2603 (Rfree = 0.000) for 4198 atoms. Found 25 (32 requested) and removed 23 (18 requested) atoms. Cycle 9: After refmac, R = 0.2561 (Rfree = 0.000) for 4189 atoms. Found 25 (31 requested) and removed 24 (18 requested) atoms. Cycle 10: After refmac, R = 0.2492 (Rfree = 0.000) for 4183 atoms. Found 20 (30 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.99 2.83 Search for helices and strands: 0 residues in 0 chains, 4304 seeds are put forward NCS extension: 23 residues added (19 deleted due to clashes), 4327 seeds are put forward Round 1: 404 peptides, 43 chains. Longest chain 26 peptides. Score 0.679 Round 2: 427 peptides, 33 chains. Longest chain 37 peptides. Score 0.770 Round 3: 409 peptides, 43 chains. Longest chain 31 peptides. Score 0.686 Round 4: 406 peptides, 44 chains. Longest chain 23 peptides. Score 0.675 Round 5: 395 peptides, 38 chains. Longest chain 26 peptides. Score 0.700 Taking the results from Round 2 Chains 39, Residues 394, Estimated correctness of the model 78.6 % 6 chains (126 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 42 A and 50 A 39 chains (396 residues) following loop building 5 chains (133 residues) in sequence following loop building ------------------------------------------------------ 11899 reflections ( 99.69 % complete ) and 7283 restraints for refining 4235 atoms. 5138 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2819 (Rfree = 0.000) for 4235 atoms. Found 30 (30 requested) and removed 43 (19 requested) atoms. Cycle 12: After refmac, R = 0.2640 (Rfree = 0.000) for 4186 atoms. Found 19 (29 requested) and removed 31 (18 requested) atoms. Cycle 13: After refmac, R = 0.2525 (Rfree = 0.000) for 4162 atoms. Found 12 (28 requested) and removed 22 (18 requested) atoms. Cycle 14: After refmac, R = 0.2493 (Rfree = 0.000) for 4143 atoms. Found 21 (27 requested) and removed 20 (18 requested) atoms. Cycle 15: After refmac, R = 0.2457 (Rfree = 0.000) for 4138 atoms. Found 19 (27 requested) and removed 19 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.01 2.85 Search for helices and strands: 0 residues in 0 chains, 4272 seeds are put forward NCS extension: 40 residues added (32 deleted due to clashes), 4312 seeds are put forward Round 1: 373 peptides, 41 chains. Longest chain 25 peptides. Score 0.646 Round 2: 408 peptides, 36 chains. Longest chain 25 peptides. Score 0.730 Round 3: 376 peptides, 39 chains. Longest chain 29 peptides. Score 0.665 Round 4: 379 peptides, 34 chains. Longest chain 27 peptides. Score 0.704 Round 5: 388 peptides, 37 chains. Longest chain 35 peptides. Score 0.697 Taking the results from Round 2 Chains 41, Residues 372, Estimated correctness of the model 71.3 % 9 chains (146 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 85 C and 93 C Built loop between residues 42 B and 51 B 37 chains (379 residues) following loop building 7 chains (161 residues) in sequence following loop building ------------------------------------------------------ 11899 reflections ( 99.69 % complete ) and 7197 restraints for refining 4236 atoms. 5041 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2876 (Rfree = 0.000) for 4236 atoms. Found 27 (27 requested) and removed 46 (19 requested) atoms. Cycle 17: After refmac, R = 0.2737 (Rfree = 0.000) for 4191 atoms. Found 25 (25 requested) and removed 22 (18 requested) atoms. Cycle 18: After refmac, R = 0.2628 (Rfree = 0.000) for 4181 atoms. Found 19 (24 requested) and removed 23 (18 requested) atoms. Cycle 19: After refmac, R = 0.2561 (Rfree = 0.000) for 4173 atoms. Found 19 (24 requested) and removed 25 (18 requested) atoms. Cycle 20: After refmac, R = 0.2520 (Rfree = 0.000) for 4161 atoms. Found 16 (23 requested) and removed 24 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.03 2.87 Search for helices and strands: 0 residues in 0 chains, 4266 seeds are put forward NCS extension: 48 residues added (36 deleted due to clashes), 4314 seeds are put forward Round 1: 358 peptides, 41 chains. Longest chain 27 peptides. Score 0.621 Round 2: 379 peptides, 39 chains. Longest chain 32 peptides. Score 0.670 Round 3: 378 peptides, 38 chains. Longest chain 26 peptides. Score 0.675 Round 4: 394 peptides, 39 chains. Longest chain 30 peptides. Score 0.692 Round 5: 389 peptides, 38 chains. Longest chain 30 peptides. Score 0.691 Taking the results from Round 4 Chains 41, Residues 355, Estimated correctness of the model 63.5 % 2 chains (42 residues) have been docked in sequence ------------------------------------------------------ 11899 reflections ( 99.69 % complete ) and 8571 restraints for refining 4236 atoms. 6991 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2868 (Rfree = 0.000) for 4236 atoms. Found 23 (23 requested) and removed 30 (19 requested) atoms. Cycle 22: After refmac, R = 0.2789 (Rfree = 0.000) for 4211 atoms. Found 22 (22 requested) and removed 23 (18 requested) atoms. Cycle 23: After refmac, R = 0.2723 (Rfree = 0.000) for 4192 atoms. Found 22 (22 requested) and removed 19 (18 requested) atoms. Cycle 24: After refmac, R = 0.2621 (Rfree = 0.000) for 4184 atoms. Found 22 (22 requested) and removed 21 (18 requested) atoms. Cycle 25: After refmac, R = 0.2583 (Rfree = 0.000) for 4176 atoms. Found 22 (22 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.99 2.83 Search for helices and strands: 0 residues in 0 chains, 4312 seeds are put forward NCS extension: 12 residues added (8 deleted due to clashes), 4324 seeds are put forward Round 1: 344 peptides, 41 chains. Longest chain 24 peptides. Score 0.597 Round 2: 368 peptides, 46 chains. Longest chain 25 peptides. Score 0.599 Round 3: 364 peptides, 44 chains. Longest chain 20 peptides. Score 0.608 Round 4: 356 peptides, 39 chains. Longest chain 23 peptides. Score 0.633 Round 5: 351 peptides, 40 chains. Longest chain 20 peptides. Score 0.617 Taking the results from Round 4 Chains 41, Residues 317, Estimated correctness of the model 49.7 % 2 chains (33 residues) have been docked in sequence ------------------------------------------------------ 11899 reflections ( 99.69 % complete ) and 8980 restraints for refining 4235 atoms. 7594 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2902 (Rfree = 0.000) for 4235 atoms. Found 23 (23 requested) and removed 26 (19 requested) atoms. Cycle 27: After refmac, R = 0.2681 (Rfree = 0.000) for 4224 atoms. Found 22 (22 requested) and removed 23 (18 requested) atoms. Cycle 28: After refmac, R = 0.2629 (Rfree = 0.000) for 4214 atoms. Found 22 (22 requested) and removed 27 (18 requested) atoms. Cycle 29: After refmac, R = 0.2390 (Rfree = 0.000) for 4199 atoms. Found 22 (22 requested) and removed 22 (18 requested) atoms. Cycle 30: After refmac, R = 0.2329 (Rfree = 0.000) for 4193 atoms. Found 14 (22 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, 4293 seeds are put forward NCS extension: 14 residues added (6 deleted due to clashes), 4307 seeds are put forward Round 1: 331 peptides, 45 chains. Longest chain 20 peptides. Score 0.539 Round 2: 357 peptides, 38 chains. Longest chain 27 peptides. Score 0.642 Round 3: 359 peptides, 38 chains. Longest chain 27 peptides. Score 0.646 Round 4: 359 peptides, 40 chains. Longest chain 21 peptides. Score 0.631 Round 5: 354 peptides, 36 chains. Longest chain 28 peptides. Score 0.653 Taking the results from Round 5 Chains 40, Residues 318, Estimated correctness of the model 54.6 % 4 chains (91 residues) have been docked in sequence ------------------------------------------------------ 11899 reflections ( 99.69 % complete ) and 8099 restraints for refining 4235 atoms. 6401 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2940 (Rfree = 0.000) for 4235 atoms. Found 23 (23 requested) and removed 45 (19 requested) atoms. Cycle 32: After refmac, R = 0.2753 (Rfree = 0.000) for 4186 atoms. Found 22 (22 requested) and removed 28 (18 requested) atoms. Cycle 33: After refmac, R = 0.2750 (Rfree = 0.000) for 4162 atoms. Found 22 (22 requested) and removed 22 (18 requested) atoms. Cycle 34: After refmac, R = 0.2685 (Rfree = 0.000) for 4156 atoms. Found 22 (22 requested) and removed 23 (18 requested) atoms. Cycle 35: After refmac, R = 0.2443 (Rfree = 0.000) for 4149 atoms. Found 17 (22 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.01 2.85 Search for helices and strands: 0 residues in 0 chains, 4279 seeds are put forward NCS extension: 31 residues added (2 deleted due to clashes), 4310 seeds are put forward Round 1: 336 peptides, 47 chains. Longest chain 25 peptides. Score 0.531 Round 2: 367 peptides, 43 chains. Longest chain 26 peptides. Score 0.621 Round 3: 359 peptides, 42 chains. Longest chain 25 peptides. Score 0.615 Round 4: 367 peptides, 40 chains. Longest chain 26 peptides. Score 0.644 Round 5: 355 peptides, 44 chains. Longest chain 19 peptides. Score 0.592 Taking the results from Round 4 Chains 41, Residues 327, Estimated correctness of the model 52.4 % 2 chains (37 residues) have been docked in sequence ------------------------------------------------------ 11899 reflections ( 99.69 % complete ) and 8672 restraints for refining 4236 atoms. 7203 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2762 (Rfree = 0.000) for 4236 atoms. Found 23 (23 requested) and removed 27 (19 requested) atoms. Cycle 37: After refmac, R = 0.2724 (Rfree = 0.000) for 4220 atoms. Found 22 (22 requested) and removed 21 (18 requested) atoms. Cycle 38: After refmac, R = 0.2640 (Rfree = 0.000) for 4216 atoms. Found 22 (22 requested) and removed 22 (18 requested) atoms. Cycle 39: After refmac, R = 0.2484 (Rfree = 0.000) for 4210 atoms. Found 22 (22 requested) and removed 19 (18 requested) atoms. Cycle 40: After refmac, R = 0.2428 (Rfree = 0.000) for 4207 atoms. Found 22 (22 requested) and removed 19 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.97 2.82 Search for helices and strands: 0 residues in 0 chains, 4328 seeds are put forward NCS extension: 10 residues added (8 deleted due to clashes), 4338 seeds are put forward Round 1: 315 peptides, 44 chains. Longest chain 21 peptides. Score 0.516 Round 2: 349 peptides, 43 chains. Longest chain 23 peptides. Score 0.589 Round 3: 344 peptides, 42 chains. Longest chain 20 peptides. Score 0.589 Round 4: 338 peptides, 40 chains. Longest chain 23 peptides. Score 0.594 Round 5: 328 peptides, 41 chains. Longest chain 22 peptides. Score 0.568 Taking the results from Round 4 Chains 40, Residues 298, Estimated correctness of the model 39.4 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 11899 reflections ( 99.69 % complete ) and 9102 restraints for refining 4236 atoms. 7823 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2871 (Rfree = 0.000) for 4236 atoms. Found 23 (23 requested) and removed 24 (19 requested) atoms. Cycle 42: After refmac, R = 0.2546 (Rfree = 0.000) for 4224 atoms. Found 22 (22 requested) and removed 21 (18 requested) atoms. Cycle 43: After refmac, R = 0.2583 (Rfree = 0.000) for 4220 atoms. Found 22 (22 requested) and removed 21 (18 requested) atoms. Cycle 44: After refmac, R = 0.2516 (Rfree = 0.000) for 4213 atoms. Found 22 (22 requested) and removed 22 (18 requested) atoms. Cycle 45: After refmac, R = 0.2273 (Rfree = 0.000) for 4209 atoms. Found 10 (22 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.96 2.81 Search for helices and strands: 0 residues in 0 chains, 4305 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 4330 seeds are put forward Round 1: 298 peptides, 46 chains. Longest chain 19 peptides. Score 0.461 Round 2: 340 peptides, 45 chains. Longest chain 29 peptides. Score 0.556 Round 3: 344 peptides, 44 chains. Longest chain 24 peptides. Score 0.572 Round 4: 342 peptides, 42 chains. Longest chain 24 peptides. Score 0.585 Round 5: 329 peptides, 46 chains. Longest chain 15 peptides. Score 0.526 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 42, Residues 300, Estimated correctness of the model 37.0 % 1 chains (14 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 1vqs-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11899 reflections ( 99.69 % complete ) and 9036 restraints for refining 4236 atoms. 7790 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2593 (Rfree = 0.000) for 4236 atoms. Found 0 (23 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.2541 (Rfree = 0.000) for 4215 atoms. Found 0 (22 requested) and removed 15 (18 requested) atoms. Cycle 48: After refmac, R = 0.2465 (Rfree = 0.000) for 4198 atoms. Found 0 (22 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.2427 (Rfree = 0.000) for 4175 atoms. Found 0 (22 requested) and removed 10 (18 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:38:25 GMT 2018 Job finished. TimeTaking 75.71 Used memory is bytes: 6256048