null Mon 24 Dec 07:59:17 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 1vqs-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vqs-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vqs-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqs-3.2-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/1vqs-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqs-3.2-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 07:59:21 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/1vqs-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqs-3.2-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 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-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: 97 Cell parameters: 94.778 94.778 303.043 90.000 90.000 90.000 Input sequence file: 1vqs-3.2-parrot-noncs.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 5120 atoms. Observations/parameters ratio is 0.58 ------------------------------------------------------ Starting model: R = 0.3219 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3253 (Rfree = 0.000) for 5120 atoms. Found 45 (45 requested) and removed 44 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.02 2.86 Search for helices and strands: 0 residues in 0 chains, 5213 seeds are put forward NCS extension: 0 residues added, 5213 seeds are put forward Round 1: 307 peptides, 51 chains. Longest chain 14 peptides. Score 0.432 Round 2: 372 peptides, 46 chains. Longest chain 24 peptides. Score 0.606 Round 3: 383 peptides, 39 chains. Longest chain 27 peptides. Score 0.676 Round 4: 383 peptides, 40 chains. Longest chain 26 peptides. Score 0.669 Round 5: 388 peptides, 40 chains. Longest chain 24 peptides. Score 0.676 Taking the results from Round 5 Chains 40, Residues 348, Estimated correctness of the model 59.9 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 11899 reflections ( 99.69 % complete ) and 8515 restraints for refining 4234 atoms. 7042 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2812 (Rfree = 0.000) for 4234 atoms. Found 36 (38 requested) and removed 25 (19 requested) atoms. Cycle 2: After refmac, R = 0.2673 (Rfree = 0.000) for 4195 atoms. Found 32 (38 requested) and removed 22 (19 requested) atoms. Cycle 3: After refmac, R = 0.2633 (Rfree = 0.000) for 4183 atoms. Found 30 (37 requested) and removed 24 (18 requested) atoms. Cycle 4: After refmac, R = 0.2619 (Rfree = 0.000) for 4172 atoms. Found 24 (37 requested) and removed 23 (18 requested) atoms. Cycle 5: After refmac, R = 0.2565 (Rfree = 0.000) for 4160 atoms. Found 27 (37 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.03 2.87 Search for helices and strands: 0 residues in 0 chains, 4277 seeds are put forward NCS extension: 9 residues added (10 deleted due to clashes), 4286 seeds are put forward Round 1: 359 peptides, 42 chains. Longest chain 20 peptides. Score 0.615 Round 2: 374 peptides, 41 chains. Longest chain 29 peptides. Score 0.647 Round 3: 397 peptides, 41 chains. Longest chain 24 peptides. Score 0.682 Round 4: 396 peptides, 42 chains. Longest chain 21 peptides. Score 0.674 Round 5: 398 peptides, 39 chains. Longest chain 32 peptides. Score 0.697 Taking the results from Round 5 Chains 43, Residues 359, Estimated correctness of the model 64.5 % 2 chains (37 residues) have been docked in sequence ------------------------------------------------------ 11899 reflections ( 99.69 % complete ) and 8573 restraints for refining 4236 atoms. 7025 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2724 (Rfree = 0.000) for 4236 atoms. Found 38 (38 requested) and removed 27 (19 requested) atoms. Cycle 7: After refmac, R = 0.2634 (Rfree = 0.000) for 4229 atoms. Found 25 (38 requested) and removed 22 (19 requested) atoms. Cycle 8: After refmac, R = 0.2555 (Rfree = 0.000) for 4218 atoms. Found 25 (37 requested) and removed 26 (18 requested) atoms. Cycle 9: After refmac, R = 0.2499 (Rfree = 0.000) for 4207 atoms. Found 14 (37 requested) and removed 21 (18 requested) atoms. Cycle 10: After refmac, R = 0.2490 (Rfree = 0.000) for 4187 atoms. Found 29 (37 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.05 2.89 Search for helices and strands: 0 residues in 0 chains, 4331 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 4347 seeds are put forward Round 1: 366 peptides, 43 chains. Longest chain 27 peptides. Score 0.619 Round 2: 408 peptides, 39 chains. Longest chain 27 peptides. Score 0.711 Round 3: 423 peptides, 45 chains. Longest chain 25 peptides. Score 0.693 Round 4: 413 peptides, 39 chains. Longest chain 30 peptides. Score 0.717 Round 5: 406 peptides, 41 chains. Longest chain 40 peptides. Score 0.695 Taking the results from Round 4 Chains 44, Residues 374, Estimated correctness of the model 68.7 % 8 chains (125 residues) have been docked in sequence Building loops using Loopy2018 44 chains (374 residues) following loop building 8 chains (125 residues) in sequence following loop building ------------------------------------------------------ 11899 reflections ( 99.69 % complete ) and 7356 restraints for refining 4235 atoms. 5316 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2792 (Rfree = 0.000) for 4235 atoms. Found 38 (38 requested) and removed 34 (19 requested) atoms. Cycle 12: After refmac, R = 0.2670 (Rfree = 0.000) for 4205 atoms. Found 26 (37 requested) and removed 29 (19 requested) atoms. Cycle 13: After refmac, R = 0.2577 (Rfree = 0.000) for 4182 atoms. Found 24 (36 requested) and removed 21 (18 requested) atoms. Cycle 14: After refmac, R = 0.2479 (Rfree = 0.000) for 4171 atoms. Found 10 (35 requested) and removed 18 (18 requested) atoms. Cycle 15: After refmac, R = 0.2425 (Rfree = 0.000) for 4154 atoms. Found 7 (34 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.07 2.91 Search for helices and strands: 0 residues in 0 chains, 4239 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 4263 seeds are put forward Round 1: 361 peptides, 43 chains. Longest chain 29 peptides. Score 0.611 Round 2: 378 peptides, 39 chains. Longest chain 29 peptides. Score 0.668 Round 3: 384 peptides, 42 chains. Longest chain 27 peptides. Score 0.656 Round 4: 407 peptides, 40 chains. Longest chain 29 peptides. Score 0.703 Round 5: 383 peptides, 42 chains. Longest chain 27 peptides. Score 0.654 Taking the results from Round 4 Chains 44, Residues 367, Estimated correctness of the model 65.8 % 6 chains (113 residues) have been docked in sequence Building loops using Loopy2018 44 chains (367 residues) following loop building 6 chains (113 residues) in sequence following loop building ------------------------------------------------------ 11899 reflections ( 99.69 % complete ) and 7812 restraints for refining 4234 atoms. 5882 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2825 (Rfree = 0.000) for 4234 atoms. Found 34 (34 requested) and removed 34 (19 requested) atoms. Cycle 17: After refmac, R = 0.2676 (Rfree = 0.000) for 4213 atoms. Found 18 (33 requested) and removed 21 (18 requested) atoms. Cycle 18: After refmac, R = 0.2650 (Rfree = 0.000) for 4189 atoms. Found 30 (32 requested) and removed 25 (18 requested) atoms. Cycle 19: After refmac, R = 0.2563 (Rfree = 0.000) for 4182 atoms. Found 24 (31 requested) and removed 25 (18 requested) atoms. Cycle 20: After refmac, R = 0.2568 (Rfree = 0.000) for 4175 atoms. Found 23 (30 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.99 2.83 Search for helices and strands: 0 residues in 0 chains, 4254 seeds are put forward NCS extension: 26 residues added (9 deleted due to clashes), 4280 seeds are put forward Round 1: 377 peptides, 42 chains. Longest chain 28 peptides. Score 0.645 Round 2: 386 peptides, 41 chains. Longest chain 28 peptides. Score 0.666 Round 3: 395 peptides, 38 chains. Longest chain 29 peptides. Score 0.700 Round 4: 390 peptides, 40 chains. Longest chain 26 peptides. Score 0.679 Round 5: 385 peptides, 39 chains. Longest chain 28 peptides. Score 0.679 Taking the results from Round 3 Chains 40, Residues 357, Estimated correctness of the model 65.2 % 3 chains (66 residues) have been docked in sequence ------------------------------------------------------ 11899 reflections ( 99.69 % complete ) and 8249 restraints for refining 4236 atoms. 6578 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2664 (Rfree = 0.000) for 4236 atoms. Found 30 (30 requested) and removed 32 (19 requested) atoms. Cycle 22: After refmac, R = 0.2516 (Rfree = 0.000) for 4215 atoms. Found 23 (30 requested) and removed 21 (18 requested) atoms. Cycle 23: After refmac, R = 0.2444 (Rfree = 0.000) for 4208 atoms. Found 15 (30 requested) and removed 24 (18 requested) atoms. Cycle 24: After refmac, R = 0.2426 (Rfree = 0.000) for 4194 atoms. Found 16 (30 requested) and removed 22 (18 requested) atoms. Cycle 25: After refmac, R = 0.2355 (Rfree = 0.000) for 4183 atoms. Found 13 (30 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, 4243 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 4260 seeds are put forward Round 1: 352 peptides, 37 chains. Longest chain 26 peptides. Score 0.642 Round 2: 373 peptides, 37 chains. Longest chain 26 peptides. Score 0.675 Round 3: 375 peptides, 39 chains. Longest chain 34 peptides. Score 0.663 Round 4: 368 peptides, 36 chains. Longest chain 26 peptides. Score 0.674 Round 5: 365 peptides, 36 chains. Longest chain 31 peptides. Score 0.670 Taking the results from Round 2 Chains 38, Residues 336, Estimated correctness of the model 59.7 % 4 chains (72 residues) have been docked in sequence ------------------------------------------------------ 11899 reflections ( 99.69 % complete ) and 8291 restraints for refining 4235 atoms. 6638 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2708 (Rfree = 0.000) for 4235 atoms. Found 30 (30 requested) and removed 28 (19 requested) atoms. Cycle 27: After refmac, R = 0.2542 (Rfree = 0.000) for 4224 atoms. Found 30 (30 requested) and removed 26 (19 requested) atoms. Cycle 28: After refmac, R = 0.2435 (Rfree = 0.000) for 4218 atoms. Found 12 (30 requested) and removed 24 (18 requested) atoms. Cycle 29: After refmac, R = 0.2404 (Rfree = 0.000) for 4200 atoms. Found 28 (30 requested) and removed 23 (18 requested) atoms. Cycle 30: After refmac, R = 0.2357 (Rfree = 0.000) for 4197 atoms. Found 19 (30 requested) and removed 19 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.07 2.91 Search for helices and strands: 0 residues in 0 chains, 4289 seeds are put forward NCS extension: 13 residues added (5 deleted due to clashes), 4302 seeds are put forward Round 1: 326 peptides, 37 chains. Longest chain 37 peptides. Score 0.598 Round 2: 360 peptides, 43 chains. Longest chain 23 peptides. Score 0.609 Round 3: 368 peptides, 40 chains. Longest chain 22 peptides. Score 0.645 Round 4: 363 peptides, 41 chains. Longest chain 23 peptides. Score 0.630 Round 5: 382 peptides, 43 chains. Longest chain 23 peptides. Score 0.645 Taking the results from Round 5 Chains 46, Residues 339, Estimated correctness of the model 52.6 % 5 chains (59 residues) have been docked in sequence ------------------------------------------------------ 11899 reflections ( 99.69 % complete ) and 8326 restraints for refining 4236 atoms. 6702 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2732 (Rfree = 0.000) for 4236 atoms. Found 30 (30 requested) and removed 28 (19 requested) atoms. Cycle 32: After refmac, R = 0.2620 (Rfree = 0.000) for 4218 atoms. Found 29 (30 requested) and removed 21 (19 requested) atoms. Cycle 33: After refmac, R = 0.2547 (Rfree = 0.000) for 4218 atoms. Found 18 (30 requested) and removed 24 (18 requested) atoms. Cycle 34: After refmac, R = 0.2549 (Rfree = 0.000) for 4201 atoms. Found 26 (30 requested) and removed 21 (18 requested) atoms. Cycle 35: After refmac, R = 0.2537 (Rfree = 0.000) for 4200 atoms. Found 22 (30 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.04 2.88 Search for helices and strands: 0 residues in 0 chains, 4331 seeds are put forward NCS extension: 14 residues added (4 deleted due to clashes), 4345 seeds are put forward Round 1: 337 peptides, 46 chains. Longest chain 24 peptides. Score 0.542 Round 2: 354 peptides, 36 chains. Longest chain 27 peptides. Score 0.653 Round 3: 342 peptides, 43 chains. Longest chain 31 peptides. Score 0.577 Round 4: 344 peptides, 38 chains. Longest chain 22 peptides. Score 0.621 Round 5: 335 peptides, 39 chains. Longest chain 25 peptides. Score 0.597 Taking the results from Round 2 Chains 37, Residues 318, Estimated correctness of the model 54.6 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 11899 reflections ( 99.69 % complete ) and 8884 restraints for refining 4235 atoms. 7489 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2652 (Rfree = 0.000) for 4235 atoms. Found 28 (30 requested) and removed 23 (19 requested) atoms. Cycle 37: After refmac, R = 0.2598 (Rfree = 0.000) for 4230 atoms. Found 29 (30 requested) and removed 20 (19 requested) atoms. Cycle 38: After refmac, R = 0.2530 (Rfree = 0.000) for 4233 atoms. Found 19 (30 requested) and removed 20 (19 requested) atoms. Cycle 39: After refmac, R = 0.2527 (Rfree = 0.000) for 4223 atoms. Found 19 (30 requested) and removed 21 (18 requested) atoms. Cycle 40: After refmac, R = 0.2374 (Rfree = 0.000) for 4210 atoms. Found 10 (30 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.02 2.86 Search for helices and strands: 0 residues in 0 chains, 4304 seeds are put forward NCS extension: 12 residues added (5 deleted due to clashes), 4316 seeds are put forward Round 1: 303 peptides, 41 chains. Longest chain 20 peptides. Score 0.518 Round 2: 340 peptides, 38 chains. Longest chain 24 peptides. Score 0.614 Round 3: 323 peptides, 39 chains. Longest chain 22 peptides. Score 0.575 Round 4: 337 peptides, 40 chains. Longest chain 20 peptides. Score 0.592 Round 5: 343 peptides, 42 chains. Longest chain 23 peptides. Score 0.587 Taking the results from Round 2 Chains 40, Residues 302, Estimated correctness of the model 44.8 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 11899 reflections ( 99.69 % complete ) and 9000 restraints for refining 4236 atoms. 7672 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2693 (Rfree = 0.000) for 4236 atoms. Found 30 (30 requested) and removed 25 (19 requested) atoms. Cycle 42: After refmac, R = 0.2617 (Rfree = 0.000) for 4235 atoms. Found 30 (30 requested) and removed 20 (19 requested) atoms. Cycle 43: After refmac, R = 0.2578 (Rfree = 0.000) for 4235 atoms. Found 30 (30 requested) and removed 21 (19 requested) atoms. Cycle 44: After refmac, R = 0.2568 (Rfree = 0.000) for 4236 atoms. Found 25 (30 requested) and removed 22 (19 requested) atoms. Cycle 45: After refmac, R = 0.2505 (Rfree = 0.000) for 4227 atoms. Found 30 (30 requested) and removed 24 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.00 2.84 Search for helices and strands: 0 residues in 0 chains, 4322 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 4334 seeds are put forward Round 1: 310 peptides, 46 chains. Longest chain 19 peptides. Score 0.487 Round 2: 325 peptides, 46 chains. Longest chain 20 peptides. Score 0.518 Round 3: 365 peptides, 43 chains. Longest chain 29 peptides. Score 0.617 Round 4: 371 peptides, 42 chains. Longest chain 30 peptides. Score 0.635 Round 5: 364 peptides, 40 chains. Longest chain 30 peptides. Score 0.639 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 40, Residues 324, Estimated correctness of the model 51.1 % 1 chains (16 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 8964 restraints for refining 4236 atoms. 7614 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2651 (Rfree = 0.000) for 4236 atoms. Found 0 (30 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.2600 (Rfree = 0.000) for 4205 atoms. Found 0 (30 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.2587 (Rfree = 0.000) for 4175 atoms. Found 0 (30 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.2558 (Rfree = 0.000) for 4153 atoms. Found 0 (30 requested) and removed 18 (18 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:55:01 GMT 2018 Job finished. TimeTaking 55.74 Used memory is bytes: 12194120