null Sun 23 Dec 22:22:56 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 1vl4-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vl4-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vl4-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl4-3.4-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/1vl4-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl4-3.4-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 22:23:06 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/1vl4-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl4-3.4-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 734 and 0 Target number of residues in the AU: 734 Target solvent content: 0.6140 Checking the provided sequence file Detected sequence length: 447 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 894 Adjusted target solvent content: 0.53 Input MTZ file: 1vl4-3.4-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: 19 Cell parameters: 80.171 107.117 119.834 90.000 90.000 90.000 Input sequence file: 1vl4-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 7152 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: 79.862 3.400 Wilson plot Bfac: 58.63 14660 reflections ( 99.46 % complete ) and 0 restraints for refining 7968 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.2988 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2960 (Rfree = 0.000) for 7968 atoms. Found 60 (60 requested) and removed 68 (30 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.21 3.08 Search for helices and strands: 0 residues in 0 chains, 8078 seeds are put forward NCS extension: 0 residues added, 8078 seeds are put forward Round 1: 418 peptides, 70 chains. Longest chain 14 peptides. Score 0.409 Round 2: 553 peptides, 72 chains. Longest chain 22 peptides. Score 0.582 Round 3: 627 peptides, 77 chains. Longest chain 34 peptides. Score 0.640 Round 4: 613 peptides, 66 chains. Longest chain 37 peptides. Score 0.677 Round 5: 626 peptides, 65 chains. Longest chain 32 peptides. Score 0.693 Taking the results from Round 5 Chains 74, Residues 561, Estimated correctness of the model 56.1 % 8 chains (120 residues) have been docked in sequence ------------------------------------------------------ 14660 reflections ( 99.46 % complete ) and 12747 restraints for refining 6503 atoms. 10118 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2608 (Rfree = 0.000) for 6503 atoms. Found 39 (49 requested) and removed 57 (24 requested) atoms. Cycle 2: After refmac, R = 0.2606 (Rfree = 0.000) for 6346 atoms. Found 28 (48 requested) and removed 42 (24 requested) atoms. Cycle 3: After refmac, R = 0.2406 (Rfree = 0.000) for 6288 atoms. Found 18 (47 requested) and removed 35 (23 requested) atoms. Cycle 4: After refmac, R = 0.2521 (Rfree = 0.000) for 6242 atoms. Found 25 (47 requested) and removed 47 (23 requested) atoms. Cycle 5: After refmac, R = 0.2324 (Rfree = 0.000) for 6188 atoms. Found 26 (46 requested) and removed 39 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.17 3.05 Search for helices and strands: 0 residues in 0 chains, 6352 seeds are put forward NCS extension: 16 residues added (13 deleted due to clashes), 6368 seeds are put forward Round 1: 574 peptides, 74 chains. Longest chain 25 peptides. Score 0.596 Round 2: 628 peptides, 62 chains. Longest chain 30 peptides. Score 0.708 Round 3: 615 peptides, 68 chains. Longest chain 27 peptides. Score 0.670 Round 4: 625 peptides, 65 chains. Longest chain 27 peptides. Score 0.692 Round 5: 618 peptides, 64 chains. Longest chain 37 peptides. Score 0.690 Taking the results from Round 2 Chains 72, Residues 566, Estimated correctness of the model 59.9 % 11 chains (130 residues) have been docked in sequence Building loops using Loopy2018 72 chains (566 residues) following loop building 11 chains (130 residues) in sequence following loop building ------------------------------------------------------ 14660 reflections ( 99.46 % complete ) and 12534 restraints for refining 6464 atoms. 9822 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2819 (Rfree = 0.000) for 6464 atoms. Found 44 (48 requested) and removed 73 (24 requested) atoms. Cycle 7: After refmac, R = 0.2522 (Rfree = 0.000) for 6366 atoms. Found 46 (47 requested) and removed 47 (24 requested) atoms. Cycle 8: After refmac, R = 0.2384 (Rfree = 0.000) for 6323 atoms. Found 22 (46 requested) and removed 38 (24 requested) atoms. Cycle 9: After refmac, R = 0.2290 (Rfree = 0.000) for 6286 atoms. Found 10 (44 requested) and removed 29 (23 requested) atoms. Cycle 10: After refmac, R = 0.2276 (Rfree = 0.000) for 6259 atoms. Found 12 (43 requested) and removed 37 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.17 3.05 Search for helices and strands: 0 residues in 0 chains, 6403 seeds are put forward NCS extension: 18 residues added (9 deleted due to clashes), 6421 seeds are put forward Round 1: 547 peptides, 76 chains. Longest chain 19 peptides. Score 0.553 Round 2: 604 peptides, 70 chains. Longest chain 25 peptides. Score 0.649 Round 3: 591 peptides, 61 chains. Longest chain 34 peptides. Score 0.678 Round 4: 607 peptides, 63 chains. Longest chain 27 peptides. Score 0.684 Round 5: 618 peptides, 68 chains. Longest chain 26 peptides. Score 0.672 Taking the results from Round 4 Chains 67, Residues 544, Estimated correctness of the model 53.7 % 7 chains (85 residues) have been docked in sequence ------------------------------------------------------ 14660 reflections ( 99.46 % complete ) and 13318 restraints for refining 6502 atoms. 10897 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2501 (Rfree = 0.000) for 6502 atoms. Found 34 (44 requested) and removed 43 (24 requested) atoms. Cycle 12: After refmac, R = 0.2378 (Rfree = 0.000) for 6455 atoms. Found 17 (44 requested) and removed 38 (24 requested) atoms. Cycle 13: After refmac, R = 0.2256 (Rfree = 0.000) for 6416 atoms. Found 16 (43 requested) and removed 36 (24 requested) atoms. Cycle 14: After refmac, R = 0.2242 (Rfree = 0.000) for 6390 atoms. Found 14 (43 requested) and removed 32 (24 requested) atoms. Cycle 15: After refmac, R = 0.2149 (Rfree = 0.000) for 6360 atoms. Found 12 (43 requested) and removed 32 (24 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.21 3.08 Search for helices and strands: 0 residues in 0 chains, 6492 seeds are put forward NCS extension: 13 residues added (4 deleted due to clashes), 6505 seeds are put forward Round 1: 497 peptides, 68 chains. Longest chain 21 peptides. Score 0.534 Round 2: 550 peptides, 59 chains. Longest chain 30 peptides. Score 0.646 Round 3: 564 peptides, 64 chains. Longest chain 39 peptides. Score 0.636 Round 4: 586 peptides, 67 chains. Longest chain 30 peptides. Score 0.645 Round 5: 568 peptides, 58 chains. Longest chain 33 peptides. Score 0.669 Taking the results from Round 5 Chains 60, Residues 510, Estimated correctness of the model 49.6 % 7 chains (140 residues) have been docked in sequence ------------------------------------------------------ 14660 reflections ( 99.46 % complete ) and 12897 restraints for refining 6502 atoms. 10343 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2680 (Rfree = 0.000) for 6502 atoms. Found 33 (44 requested) and removed 56 (24 requested) atoms. Cycle 17: After refmac, R = 0.2422 (Rfree = 0.000) for 6441 atoms. Found 24 (43 requested) and removed 38 (24 requested) atoms. Cycle 18: After refmac, R = 0.2303 (Rfree = 0.000) for 6392 atoms. Found 27 (43 requested) and removed 33 (24 requested) atoms. Cycle 19: After refmac, R = 0.2450 (Rfree = 0.000) for 6376 atoms. Found 34 (43 requested) and removed 36 (24 requested) atoms. Cycle 20: After refmac, R = 0.2246 (Rfree = 0.000) for 6349 atoms. Found 25 (43 requested) and removed 32 (24 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.16 3.04 Search for helices and strands: 0 residues in 0 chains, 6527 seeds are put forward NCS extension: 20 residues added (5 deleted due to clashes), 6547 seeds are put forward Round 1: 499 peptides, 69 chains. Longest chain 30 peptides. Score 0.531 Round 2: 534 peptides, 63 chains. Longest chain 40 peptides. Score 0.608 Round 3: 563 peptides, 62 chains. Longest chain 35 peptides. Score 0.645 Round 4: 579 peptides, 65 chains. Longest chain 35 peptides. Score 0.647 Round 5: 564 peptides, 64 chains. Longest chain 31 peptides. Score 0.636 Taking the results from Round 4 Chains 69, Residues 514, Estimated correctness of the model 43.3 % 10 chains (119 residues) have been docked in sequence ------------------------------------------------------ 14660 reflections ( 99.46 % complete ) and 13050 restraints for refining 6503 atoms. 10630 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2636 (Rfree = 0.000) for 6503 atoms. Found 44 (44 requested) and removed 40 (24 requested) atoms. Cycle 22: After refmac, R = 0.2721 (Rfree = 0.000) for 6468 atoms. Found 44 (44 requested) and removed 43 (24 requested) atoms. Cycle 23: After refmac, R = 0.2392 (Rfree = 0.000) for 6438 atoms. Found 37 (43 requested) and removed 29 (24 requested) atoms. Cycle 24: After refmac, R = 0.2321 (Rfree = 0.000) for 6429 atoms. Found 33 (43 requested) and removed 31 (24 requested) atoms. Cycle 25: After refmac, R = 0.2333 (Rfree = 0.000) for 6420 atoms. Found 33 (43 requested) and removed 36 (24 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.17 3.05 Search for helices and strands: 0 residues in 0 chains, 6554 seeds are put forward NCS extension: 49 residues added (3 deleted due to clashes), 6603 seeds are put forward Round 1: 501 peptides, 76 chains. Longest chain 25 peptides. Score 0.492 Round 2: 523 peptides, 66 chains. Longest chain 26 peptides. Score 0.579 Round 3: 519 peptides, 64 chains. Longest chain 26 peptides. Score 0.585 Round 4: 573 peptides, 63 chains. Longest chain 29 peptides. Score 0.650 Round 5: 551 peptides, 65 chains. Longest chain 29 peptides. Score 0.617 Taking the results from Round 4 Chains 68, Residues 510, Estimated correctness of the model 44.1 % 6 chains (83 residues) have been docked in sequence ------------------------------------------------------ 14660 reflections ( 99.46 % complete ) and 13205 restraints for refining 6502 atoms. 10896 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2378 (Rfree = 0.000) for 6502 atoms. Found 33 (44 requested) and removed 31 (24 requested) atoms. Cycle 27: After refmac, R = 0.2357 (Rfree = 0.000) for 6476 atoms. Found 20 (44 requested) and removed 32 (24 requested) atoms. Cycle 28: After refmac, R = 0.2252 (Rfree = 0.000) for 6445 atoms. Found 14 (43 requested) and removed 30 (24 requested) atoms. Cycle 29: After refmac, R = 0.2375 (Rfree = 0.000) for 6421 atoms. Found 28 (43 requested) and removed 35 (24 requested) atoms. Cycle 30: After refmac, R = 0.2252 (Rfree = 0.000) for 6397 atoms. Found 22 (43 requested) and removed 29 (24 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 3.05 Search for helices and strands: 0 residues in 0 chains, 6546 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 6571 seeds are put forward Round 1: 477 peptides, 73 chains. Longest chain 17 peptides. Score 0.477 Round 2: 523 peptides, 66 chains. Longest chain 23 peptides. Score 0.579 Round 3: 535 peptides, 70 chains. Longest chain 23 peptides. Score 0.571 Round 4: 545 peptides, 68 chains. Longest chain 37 peptides. Score 0.594 Round 5: 520 peptides, 65 chains. Longest chain 24 peptides. Score 0.580 Taking the results from Round 4 Chains 72, Residues 477, Estimated correctness of the model 26.7 % 7 chains (79 residues) have been docked in sequence ------------------------------------------------------ 14660 reflections ( 99.46 % complete ) and 13482 restraints for refining 6503 atoms. 11324 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2416 (Rfree = 0.000) for 6503 atoms. Found 41 (44 requested) and removed 38 (24 requested) atoms. Cycle 32: After refmac, R = 0.2439 (Rfree = 0.000) for 6476 atoms. Found 37 (44 requested) and removed 32 (24 requested) atoms. Cycle 33: After refmac, R = 0.2134 (Rfree = 0.000) for 6463 atoms. Found 14 (43 requested) and removed 27 (24 requested) atoms. Cycle 34: After refmac, R = 0.2252 (Rfree = 0.000) for 6444 atoms. Found 23 (43 requested) and removed 29 (24 requested) atoms. Cycle 35: After refmac, R = 0.2167 (Rfree = 0.000) for 6433 atoms. Found 22 (43 requested) and removed 27 (24 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.19 3.06 Search for helices and strands: 0 residues in 0 chains, 6594 seeds are put forward NCS extension: 36 residues added (2 deleted due to clashes), 6630 seeds are put forward Round 1: 446 peptides, 69 chains. Longest chain 28 peptides. Score 0.458 Round 2: 483 peptides, 63 chains. Longest chain 23 peptides. Score 0.545 Round 3: 489 peptides, 63 chains. Longest chain 21 peptides. Score 0.553 Round 4: 502 peptides, 63 chains. Longest chain 36 peptides. Score 0.569 Round 5: 497 peptides, 62 chains. Longest chain 26 peptides. Score 0.569 Taking the results from Round 5 Chains 68, Residues 435, Estimated correctness of the model 18.2 % 10 chains (85 residues) have been docked in sequence ------------------------------------------------------ 14660 reflections ( 99.46 % complete ) and 13711 restraints for refining 6503 atoms. 11707 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2395 (Rfree = 0.000) for 6503 atoms. Found 38 (44 requested) and removed 34 (24 requested) atoms. Cycle 37: After refmac, R = 0.2438 (Rfree = 0.000) for 6473 atoms. Found 39 (44 requested) and removed 31 (24 requested) atoms. Cycle 38: After refmac, R = 0.2210 (Rfree = 0.000) for 6468 atoms. Found 29 (43 requested) and removed 33 (24 requested) atoms. Cycle 39: After refmac, R = 0.2111 (Rfree = 0.000) for 6453 atoms. Found 25 (43 requested) and removed 28 (24 requested) atoms. Cycle 40: After refmac, R = 0.2101 (Rfree = 0.000) for 6435 atoms. Found 24 (43 requested) and removed 27 (24 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.21 3.08 Search for helices and strands: 0 residues in 0 chains, 6541 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 6558 seeds are put forward Round 1: 456 peptides, 76 chains. Longest chain 22 peptides. Score 0.427 Round 2: 511 peptides, 74 chains. Longest chain 27 peptides. Score 0.518 Round 3: 489 peptides, 70 chains. Longest chain 17 peptides. Score 0.512 Round 4: 500 peptides, 66 chains. Longest chain 20 peptides. Score 0.550 Round 5: 494 peptides, 68 chains. Longest chain 18 peptides. Score 0.530 Taking the results from Round 4 Chains 69, Residues 434, Estimated correctness of the model 11.5 % 5 chains (52 residues) have been docked in sequence ------------------------------------------------------ 14660 reflections ( 99.46 % complete ) and 14116 restraints for refining 6503 atoms. 12225 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2392 (Rfree = 0.000) for 6503 atoms. Found 42 (44 requested) and removed 35 (24 requested) atoms. Cycle 42: After refmac, R = 0.2110 (Rfree = 0.000) for 6487 atoms. Found 19 (44 requested) and removed 32 (24 requested) atoms. Cycle 43: After refmac, R = 0.2073 (Rfree = 0.000) for 6453 atoms. Found 20 (43 requested) and removed 24 (24 requested) atoms. Cycle 44: After refmac, R = 0.2109 (Rfree = 0.000) for 6433 atoms. Found 23 (43 requested) and removed 27 (24 requested) atoms. Cycle 45: After refmac, R = 0.1925 (Rfree = 0.000) for 6419 atoms. Found 13 (43 requested) and removed 26 (24 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.22 3.09 Search for helices and strands: 0 residues in 0 chains, 6527 seeds are put forward NCS extension: 26 residues added (6 deleted due to clashes), 6553 seeds are put forward Round 1: 432 peptides, 78 chains. Longest chain 20 peptides. Score 0.377 Round 2: 481 peptides, 69 chains. Longest chain 23 peptides. Score 0.507 Round 3: 478 peptides, 71 chains. Longest chain 24 peptides. Score 0.491 Round 4: 461 peptides, 68 chains. Longest chain 18 peptides. Score 0.485 Round 5: 462 peptides, 62 chains. Longest chain 23 peptides. Score 0.524 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 66, Residues 400, Estimated correctness of the model 1.9 % 5 chains (52 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 1vl4-3_warpNtrace.pdb as input Building loops using Loopy2018 66 chains (400 residues) following loop building 5 chains (52 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14660 reflections ( 99.46 % complete ) and 14173 restraints for refining 6503 atoms. 12402 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2360 (Rfree = 0.000) for 6503 atoms. Found 0 (44 requested) and removed 24 (24 requested) atoms. Cycle 47: After refmac, R = 0.2292 (Rfree = 0.000) for 6466 atoms. Found 0 (43 requested) and removed 24 (24 requested) atoms. Cycle 48: After refmac, R = 0.2438 (Rfree = 0.000) for 6433 atoms. Found 0 (43 requested) and removed 24 (24 requested) atoms. Cycle 49: After refmac, R = 0.2018 (Rfree = 0.000) for 6402 atoms. Found 0 (43 requested) and removed 24 (24 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:48:35 GMT 2018 Job finished. TimeTaking 85.66 Used memory is bytes: 10486464