Sun 23 Dec 22:22:50 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 2gvh-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gvh-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gvh-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvh-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/2gvh-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvh-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 22:22:59 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/hancs/ArpWArp/wArpResults/WorkingDir/2gvh-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvh-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 765 and 0 Target number of residues in the AU: 765 Target solvent content: 0.6556 Checking the provided sequence file Detected sequence length: 288 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 864 Adjusted target solvent content: 0.61 Input MTZ file: 2gvh-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: 78 Cell parameters: 121.211 121.211 81.834 90.000 90.000 90.000 Input sequence file: 2gvh-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 6912 target number of atoms Had to go as low as 0.85 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: 121.211 3.200 Wilson plot Bfac: 81.85 19717 reflections ( 99.66 % complete ) and 0 restraints for refining 7716 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Starting model: R = 0.3537 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3172 (Rfree = 0.000) for 7716 atoms. Found 69 (69 requested) and removed 198 (34 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.40 2.93 Search for helices and strands: 0 residues in 0 chains, 7700 seeds are put forward NCS extension: 0 residues added, 7700 seeds are put forward Round 1: 400 peptides, 66 chains. Longest chain 14 peptides. Score 0.382 Round 2: 490 peptides, 72 chains. Longest chain 16 peptides. Score 0.466 Round 3: 482 peptides, 59 chains. Longest chain 20 peptides. Score 0.528 Round 4: 516 peptides, 65 chains. Longest chain 22 peptides. Score 0.535 Round 5: 521 peptides, 65 chains. Longest chain 31 peptides. Score 0.541 Taking the results from Round 5 Chains 67, Residues 456, Estimated correctness of the model 24.2 % 8 chains (59 residues) have been docked in sequence ------------------------------------------------------ 19717 reflections ( 99.66 % complete ) and 13646 restraints for refining 6308 atoms. 11691 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2746 (Rfree = 0.000) for 6308 atoms. Found 52 (56 requested) and removed 57 (28 requested) atoms. Cycle 2: After refmac, R = 0.2632 (Rfree = 0.000) for 6243 atoms. Found 27 (56 requested) and removed 44 (28 requested) atoms. Cycle 3: After refmac, R = 0.2702 (Rfree = 0.000) for 6212 atoms. Found 28 (55 requested) and removed 31 (27 requested) atoms. Cycle 4: After refmac, R = 0.2956 (Rfree = 0.000) for 6199 atoms. Found 55 (55 requested) and removed 54 (27 requested) atoms. Cycle 5: After refmac, R = 0.2882 (Rfree = 0.000) for 6163 atoms. Found 52 (55 requested) and removed 51 (27 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.41 2.94 Search for helices and strands: 0 residues in 0 chains, 6321 seeds are put forward NCS extension: 41 residues added (2 deleted due to clashes), 6362 seeds are put forward Round 1: 464 peptides, 65 chains. Longest chain 22 peptides. Score 0.473 Round 2: 507 peptides, 65 chains. Longest chain 23 peptides. Score 0.525 Round 3: 514 peptides, 57 chains. Longest chain 22 peptides. Score 0.574 Round 4: 495 peptides, 52 chains. Longest chain 29 peptides. Score 0.578 Round 5: 515 peptides, 61 chains. Longest chain 30 peptides. Score 0.554 Taking the results from Round 4 Chains 57, Residues 443, Estimated correctness of the model 35.0 % 6 chains (52 residues) have been docked in sequence ------------------------------------------------------ 19717 reflections ( 99.66 % complete ) and 13452 restraints for refining 6309 atoms. 11561 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2914 (Rfree = 0.000) for 6309 atoms. Found 39 (56 requested) and removed 46 (28 requested) atoms. Cycle 7: After refmac, R = 0.2971 (Rfree = 0.000) for 6259 atoms. Found 56 (56 requested) and removed 55 (28 requested) atoms. Cycle 8: After refmac, R = 0.2897 (Rfree = 0.000) for 6214 atoms. Found 56 (56 requested) and removed 47 (28 requested) atoms. Cycle 9: After refmac, R = 0.2932 (Rfree = 0.000) for 6197 atoms. Found 55 (55 requested) and removed 55 (27 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2781 (Rfree = 0.000) for 6173 atoms. Found 55 (55 requested) and removed 47 (27 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 2.95 Search for helices and strands: 0 residues in 0 chains, 6336 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 6351 seeds are put forward Round 1: 498 peptides, 67 chains. Longest chain 22 peptides. Score 0.503 Round 2: 509 peptides, 61 chains. Longest chain 23 peptides. Score 0.548 Round 3: 524 peptides, 60 chains. Longest chain 51 peptides. Score 0.569 Round 4: 521 peptides, 57 chains. Longest chain 28 peptides. Score 0.581 Round 5: 534 peptides, 58 chains. Longest chain 23 peptides. Score 0.590 Taking the results from Round 5 Chains 59, Residues 476, Estimated correctness of the model 38.3 % 5 chains (49 residues) have been docked in sequence ------------------------------------------------------ 19717 reflections ( 99.66 % complete ) and 13364 restraints for refining 6310 atoms. 11335 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2653 (Rfree = 0.000) for 6310 atoms. Found 51 (56 requested) and removed 45 (28 requested) atoms. Cycle 12: After refmac, R = 0.2502 (Rfree = 0.000) for 6299 atoms. Found 16 (56 requested) and removed 39 (28 requested) atoms. Cycle 13: After refmac, R = 0.2677 (Rfree = 0.000) for 6256 atoms. Found 48 (56 requested) and removed 42 (28 requested) atoms. Cycle 14: After refmac, R = 0.2426 (Rfree = 0.000) for 6256 atoms. Found 16 (56 requested) and removed 40 (28 requested) atoms. Cycle 15: After refmac, R = 0.2342 (Rfree = 0.000) for 6209 atoms. Found 19 (55 requested) and removed 32 (27 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 2.97 Search for helices and strands: 0 residues in 0 chains, 6350 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 6368 seeds are put forward Round 1: 493 peptides, 71 chains. Longest chain 23 peptides. Score 0.476 Round 2: 493 peptides, 63 chains. Longest chain 28 peptides. Score 0.519 Round 3: 499 peptides, 62 chains. Longest chain 29 peptides. Score 0.531 Round 4: 516 peptides, 62 chains. Longest chain 31 peptides. Score 0.550 Round 5: 502 peptides, 56 chains. Longest chain 50 peptides. Score 0.566 Taking the results from Round 5 Chains 61, Residues 446, Estimated correctness of the model 31.6 % 5 chains (60 residues) have been docked in sequence ------------------------------------------------------ 19717 reflections ( 99.66 % complete ) and 13486 restraints for refining 6310 atoms. 11538 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2606 (Rfree = 0.000) for 6310 atoms. Found 34 (56 requested) and removed 40 (28 requested) atoms. Cycle 17: After refmac, R = 0.2430 (Rfree = 0.000) for 6287 atoms. Found 21 (56 requested) and removed 31 (28 requested) atoms. Cycle 18: After refmac, R = 0.2425 (Rfree = 0.000) for 6263 atoms. Found 19 (56 requested) and removed 28 (28 requested) atoms. Cycle 19: After refmac, R = 0.2393 (Rfree = 0.000) for 6240 atoms. Found 16 (56 requested) and removed 34 (28 requested) atoms. Cycle 20: After refmac, R = 0.2330 (Rfree = 0.000) for 6219 atoms. Found 12 (55 requested) and removed 35 (27 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 2.94 Search for helices and strands: 0 residues in 0 chains, 6366 seeds are put forward NCS extension: 34 residues added (0 deleted due to clashes), 6400 seeds are put forward Round 1: 450 peptides, 65 chains. Longest chain 25 peptides. Score 0.455 Round 2: 479 peptides, 55 chains. Longest chain 31 peptides. Score 0.545 Round 3: 498 peptides, 61 chains. Longest chain 26 peptides. Score 0.535 Round 4: 515 peptides, 62 chains. Longest chain 47 peptides. Score 0.549 Round 5: 510 peptides, 64 chains. Longest chain 47 peptides. Score 0.533 Taking the results from Round 4 Chains 66, Residues 453, Estimated correctness of the model 26.6 % 5 chains (64 residues) have been docked in sequence ------------------------------------------------------ 19717 reflections ( 99.66 % complete ) and 13418 restraints for refining 6310 atoms. 11432 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2521 (Rfree = 0.000) for 6310 atoms. Found 34 (56 requested) and removed 40 (28 requested) atoms. Cycle 22: After refmac, R = 0.2406 (Rfree = 0.000) for 6282 atoms. Found 19 (56 requested) and removed 35 (28 requested) atoms. Cycle 23: After refmac, R = 0.2288 (Rfree = 0.000) for 6258 atoms. Found 12 (56 requested) and removed 30 (28 requested) atoms. Cycle 24: After refmac, R = 0.2438 (Rfree = 0.000) for 6234 atoms. Found 33 (56 requested) and removed 28 (28 requested) atoms. Cycle 25: After refmac, R = 0.2286 (Rfree = 0.000) for 6236 atoms. Found 8 (55 requested) and removed 28 (27 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.46 2.98 Search for helices and strands: 0 residues in 0 chains, 6361 seeds are put forward NCS extension: 34 residues added (6 deleted due to clashes), 6395 seeds are put forward Round 1: 458 peptides, 69 chains. Longest chain 24 peptides. Score 0.443 Round 2: 494 peptides, 66 chains. Longest chain 37 peptides. Score 0.504 Round 3: 489 peptides, 59 chains. Longest chain 45 peptides. Score 0.536 Round 4: 478 peptides, 59 chains. Longest chain 31 peptides. Score 0.523 Round 5: 483 peptides, 58 chains. Longest chain 50 peptides. Score 0.534 Taking the results from Round 3 Chains 62, Residues 430, Estimated correctness of the model 22.7 % 6 chains (49 residues) have been docked in sequence ------------------------------------------------------ 19717 reflections ( 99.66 % complete ) and 13911 restraints for refining 6309 atoms. 12078 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2487 (Rfree = 0.000) for 6309 atoms. Found 43 (56 requested) and removed 31 (28 requested) atoms. Cycle 27: After refmac, R = 0.2338 (Rfree = 0.000) for 6302 atoms. Found 17 (56 requested) and removed 29 (28 requested) atoms. Cycle 28: After refmac, R = 0.2395 (Rfree = 0.000) for 6281 atoms. Found 20 (56 requested) and removed 30 (28 requested) atoms. Cycle 29: After refmac, R = 0.2418 (Rfree = 0.000) for 6266 atoms. Found 39 (56 requested) and removed 30 (28 requested) atoms. Cycle 30: After refmac, R = 0.2180 (Rfree = 0.000) for 6272 atoms. Found 9 (56 requested) and removed 28 (28 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.44 2.96 Search for helices and strands: 0 residues in 0 chains, 6379 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 6395 seeds are put forward Round 1: 469 peptides, 69 chains. Longest chain 23 peptides. Score 0.457 Round 2: 511 peptides, 65 chains. Longest chain 50 peptides. Score 0.529 Round 3: 511 peptides, 61 chains. Longest chain 31 peptides. Score 0.550 Round 4: 493 peptides, 56 chains. Longest chain 49 peptides. Score 0.556 Round 5: 498 peptides, 53 chains. Longest chain 47 peptides. Score 0.577 Taking the results from Round 5 Chains 64, Residues 445, Estimated correctness of the model 34.7 % 9 chains (89 residues) have been docked in sequence ------------------------------------------------------ 19717 reflections ( 99.66 % complete ) and 13167 restraints for refining 6310 atoms. 11118 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2639 (Rfree = 0.000) for 6310 atoms. Found 49 (56 requested) and removed 35 (28 requested) atoms. Cycle 32: After refmac, R = 0.2816 (Rfree = 0.000) for 6303 atoms. Found 56 (56 requested) and removed 38 (28 requested) atoms. Cycle 33: After refmac, R = 0.2281 (Rfree = 0.000) for 6305 atoms. Found 24 (56 requested) and removed 33 (28 requested) atoms. Cycle 34: After refmac, R = 0.2255 (Rfree = 0.000) for 6280 atoms. Found 20 (56 requested) and removed 33 (28 requested) atoms. Cycle 35: After refmac, R = 0.2210 (Rfree = 0.000) for 6262 atoms. Found 18 (56 requested) and removed 32 (28 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.43 2.96 Search for helices and strands: 0 residues in 0 chains, 6419 seeds are put forward NCS extension: 16 residues added (8 deleted due to clashes), 6435 seeds are put forward Round 1: 409 peptides, 63 chains. Longest chain 27 peptides. Score 0.413 Round 2: 431 peptides, 55 chains. Longest chain 32 peptides. Score 0.489 Round 3: 451 peptides, 59 chains. Longest chain 27 peptides. Score 0.491 Round 4: 451 peptides, 50 chains. Longest chain 51 peptides. Score 0.540 Round 5: 475 peptides, 59 chains. Longest chain 33 peptides. Score 0.519 Taking the results from Round 4 Chains 55, Residues 401, Estimated correctness of the model 23.9 % 7 chains (82 residues) have been docked in sequence ------------------------------------------------------ 19717 reflections ( 99.66 % complete ) and 13725 restraints for refining 6310 atoms. 11896 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2444 (Rfree = 0.000) for 6310 atoms. Found 54 (56 requested) and removed 32 (28 requested) atoms. Cycle 37: After refmac, R = 0.2314 (Rfree = 0.000) for 6317 atoms. Found 24 (56 requested) and removed 32 (28 requested) atoms. Cycle 38: After refmac, R = 0.2214 (Rfree = 0.000) for 6296 atoms. Found 10 (56 requested) and removed 34 (28 requested) atoms. Cycle 39: After refmac, R = 0.2174 (Rfree = 0.000) for 6267 atoms. Found 9 (56 requested) and removed 29 (28 requested) atoms. Cycle 40: After refmac, R = 0.2152 (Rfree = 0.000) for 6246 atoms. Found 8 (56 requested) and removed 29 (28 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.43 2.96 Search for helices and strands: 0 residues in 0 chains, 6393 seeds are put forward NCS extension: 31 residues added (6 deleted due to clashes), 6424 seeds are put forward Round 1: 401 peptides, 61 chains. Longest chain 19 peptides. Score 0.414 Round 2: 432 peptides, 51 chains. Longest chain 31 peptides. Score 0.512 Round 3: 441 peptides, 54 chains. Longest chain 47 peptides. Score 0.506 Round 4: 447 peptides, 55 chains. Longest chain 28 peptides. Score 0.508 Round 5: 454 peptides, 49 chains. Longest chain 35 peptides. Score 0.549 Taking the results from Round 5 Chains 50, Residues 405, Estimated correctness of the model 26.6 % 4 chains (62 residues) have been docked in sequence ------------------------------------------------------ 19717 reflections ( 99.66 % complete ) and 13642 restraints for refining 6310 atoms. 11840 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2472 (Rfree = 0.000) for 6310 atoms. Found 51 (56 requested) and removed 33 (28 requested) atoms. Cycle 42: After refmac, R = 0.2330 (Rfree = 0.000) for 6315 atoms. Found 17 (56 requested) and removed 30 (28 requested) atoms. Cycle 43: After refmac, R = 0.2278 (Rfree = 0.000) for 6294 atoms. Found 11 (56 requested) and removed 28 (28 requested) atoms. Cycle 44: After refmac, R = 0.2228 (Rfree = 0.000) for 6275 atoms. Found 8 (56 requested) and removed 28 (28 requested) atoms. Cycle 45: After refmac, R = 0.2203 (Rfree = 0.000) for 6254 atoms. Found 13 (56 requested) and removed 29 (28 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.46 2.98 Search for helices and strands: 0 residues in 0 chains, 6388 seeds are put forward NCS extension: 55 residues added (3 deleted due to clashes), 6443 seeds are put forward Round 1: 407 peptides, 63 chains. Longest chain 17 peptides. Score 0.410 Round 2: 449 peptides, 54 chains. Longest chain 23 peptides. Score 0.516 Round 3: 451 peptides, 49 chains. Longest chain 59 peptides. Score 0.546 Round 4: 457 peptides, 56 chains. Longest chain 33 peptides. Score 0.514 Round 5: 460 peptides, 55 chains. Longest chain 26 peptides. Score 0.523 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 52, Residues 402, Estimated correctness of the model 25.7 % 6 chains (110 residues) have been docked in sequence Sequence coverage is 27 % Consider running further cycles of model building using 2gvh-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 194 C and 205 C 53 chains (408 residues) following loop building 5 chains (120 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 19717 reflections ( 99.66 % complete ) and 13071 restraints for refining 6309 atoms. 11063 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2526 (Rfree = 0.000) for 6309 atoms. Found 0 (56 requested) and removed 21 (28 requested) atoms. Cycle 47: After refmac, R = 0.2381 (Rfree = 0.000) for 6275 atoms. Found 0 (56 requested) and removed 8 (28 requested) atoms. Cycle 48: After refmac, R = 0.2405 (Rfree = 0.000) for 6259 atoms. Found 0 (56 requested) and removed 5 (28 requested) atoms. Cycle 49: After refmac, R = 0.2682 (Rfree = 0.000) for 6249 atoms. TimeTaking 90.42