null Sun 23 Dec 22:23:02 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 1vlu-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vlu-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vlu-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlu-3.8-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/1vlu-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlu-3.8-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 22:23:12 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/1vlu-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlu-3.8-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 938 and 0 Target number of residues in the AU: 938 Target solvent content: 0.6546 Checking the provided sequence file Detected sequence length: 468 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 936 Adjusted target solvent content: 0.66 Input MTZ file: 1vlu-3.8-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: 20 Cell parameters: 123.109 190.784 125.153 90.000 90.000 90.000 Input sequence file: 1vlu-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 7488 target number of atoms Had to go as low as 0.90 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: 44.569 3.800 Wilson plot Bfac: 81.10 14859 reflections ( 99.83 % complete ) and 0 restraints for refining 8241 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3363 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3124 (Rfree = 0.000) for 8241 atoms. Found 45 (45 requested) and removed 54 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.65 2.93 Search for helices and strands: 0 residues in 0 chains, 8427 seeds are put forward NCS extension: 0 residues added, 8427 seeds are put forward Round 1: 455 peptides, 69 chains. Longest chain 15 peptides. Score 0.403 Round 2: 538 peptides, 60 chains. Longest chain 29 peptides. Score 0.533 Round 3: 546 peptides, 54 chains. Longest chain 28 peptides. Score 0.566 Round 4: 570 peptides, 54 chains. Longest chain 32 peptides. Score 0.588 Round 5: 576 peptides, 59 chains. Longest chain 29 peptides. Score 0.572 Taking the results from Round 4 Chains 61, Residues 516, Estimated correctness of the model 0.0 % 11 chains (125 residues) have been docked in sequence ------------------------------------------------------ 14859 reflections ( 99.83 % complete ) and 14025 restraints for refining 6770 atoms. 11587 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2490 (Rfree = 0.000) for 6770 atoms. Found 32 (37 requested) and removed 68 (18 requested) atoms. Cycle 2: After refmac, R = 0.2363 (Rfree = 0.000) for 6552 atoms. Found 34 (37 requested) and removed 61 (18 requested) atoms. Cycle 3: After refmac, R = 0.2260 (Rfree = 0.000) for 6454 atoms. Found 26 (35 requested) and removed 32 (17 requested) atoms. Cycle 4: After refmac, R = 0.2230 (Rfree = 0.000) for 6400 atoms. Found 28 (35 requested) and removed 40 (17 requested) atoms. Cycle 5: After refmac, R = 0.2183 (Rfree = 0.000) for 6355 atoms. Found 19 (35 requested) and removed 30 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.60 2.89 Search for helices and strands: 0 residues in 0 chains, 6596 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 6617 seeds are put forward Round 1: 535 peptides, 68 chains. Longest chain 19 peptides. Score 0.493 Round 2: 566 peptides, 56 chains. Longest chain 36 peptides. Score 0.576 Round 3: 558 peptides, 58 chains. Longest chain 34 peptides. Score 0.560 Round 4: 552 peptides, 58 chains. Longest chain 28 peptides. Score 0.554 Round 5: 553 peptides, 54 chains. Longest chain 28 peptides. Score 0.573 Taking the results from Round 2 Chains 61, Residues 510, Estimated correctness of the model 0.0 % 8 chains (107 residues) have been docked in sequence ------------------------------------------------------ 14859 reflections ( 99.83 % complete ) and 13675 restraints for refining 6740 atoms. 11314 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2479 (Rfree = 0.000) for 6740 atoms. Found 37 (37 requested) and removed 98 (18 requested) atoms. Cycle 7: After refmac, R = 0.2407 (Rfree = 0.000) for 6607 atoms. Found 36 (36 requested) and removed 62 (18 requested) atoms. Cycle 8: After refmac, R = 0.2314 (Rfree = 0.000) for 6520 atoms. Found 36 (36 requested) and removed 50 (18 requested) atoms. Cycle 9: After refmac, R = 0.2241 (Rfree = 0.000) for 6468 atoms. Found 26 (35 requested) and removed 37 (17 requested) atoms. Cycle 10: After refmac, R = 0.2198 (Rfree = 0.000) for 6418 atoms. Found 32 (35 requested) and removed 43 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.62 2.90 Search for helices and strands: 0 residues in 0 chains, 6661 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 6691 seeds are put forward Round 1: 521 peptides, 65 chains. Longest chain 22 peptides. Score 0.493 Round 2: 559 peptides, 53 chains. Longest chain 31 peptides. Score 0.582 Round 3: 546 peptides, 60 chains. Longest chain 29 peptides. Score 0.540 Round 4: 563 peptides, 54 chains. Longest chain 35 peptides. Score 0.581 Round 5: 563 peptides, 57 chains. Longest chain 38 peptides. Score 0.569 Taking the results from Round 2 Chains 63, Residues 506, Estimated correctness of the model 0.0 % 9 chains (99 residues) have been docked in sequence ------------------------------------------------------ 14859 reflections ( 99.83 % complete ) and 13659 restraints for refining 6673 atoms. 11368 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2411 (Rfree = 0.000) for 6673 atoms. Found 36 (36 requested) and removed 79 (18 requested) atoms. Cycle 12: After refmac, R = 0.2284 (Rfree = 0.000) for 6568 atoms. Found 35 (36 requested) and removed 42 (18 requested) atoms. Cycle 13: After refmac, R = 0.2258 (Rfree = 0.000) for 6535 atoms. Found 26 (36 requested) and removed 39 (18 requested) atoms. Cycle 14: After refmac, R = 0.2174 (Rfree = 0.000) for 6499 atoms. Found 32 (35 requested) and removed 40 (17 requested) atoms. Cycle 15: After refmac, R = 0.2139 (Rfree = 0.000) for 6468 atoms. Found 17 (35 requested) and removed 32 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.60 2.89 Search for helices and strands: 0 residues in 0 chains, 6691 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 6703 seeds are put forward Round 1: 507 peptides, 66 chains. Longest chain 19 peptides. Score 0.474 Round 2: 526 peptides, 60 chains. Longest chain 23 peptides. Score 0.521 Round 3: 543 peptides, 58 chains. Longest chain 49 peptides. Score 0.546 Round 4: 532 peptides, 59 chains. Longest chain 30 peptides. Score 0.531 Round 5: 542 peptides, 55 chains. Longest chain 33 peptides. Score 0.558 Taking the results from Round 5 Chains 57, Residues 487, Estimated correctness of the model 0.0 % 6 chains (72 residues) have been docked in sequence ------------------------------------------------------ 14859 reflections ( 99.83 % complete ) and 14513 restraints for refining 6773 atoms. 12374 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2470 (Rfree = 0.000) for 6773 atoms. Found 37 (37 requested) and removed 70 (18 requested) atoms. Cycle 17: After refmac, R = 0.2315 (Rfree = 0.000) for 6646 atoms. Found 28 (37 requested) and removed 46 (18 requested) atoms. Cycle 18: After refmac, R = 0.2279 (Rfree = 0.000) for 6596 atoms. Found 23 (36 requested) and removed 42 (18 requested) atoms. Cycle 19: After refmac, R = 0.2253 (Rfree = 0.000) for 6549 atoms. Found 28 (36 requested) and removed 39 (18 requested) atoms. Cycle 20: After refmac, R = 0.2227 (Rfree = 0.000) for 6513 atoms. Found 31 (35 requested) and removed 26 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.63 2.91 Search for helices and strands: 0 residues in 0 chains, 6778 seeds are put forward NCS extension: 15 residues added (11 deleted due to clashes), 6793 seeds are put forward Round 1: 518 peptides, 67 chains. Longest chain 22 peptides. Score 0.481 Round 2: 549 peptides, 54 chains. Longest chain 51 peptides. Score 0.569 Round 3: 549 peptides, 59 chains. Longest chain 32 peptides. Score 0.547 Round 4: 548 peptides, 58 chains. Longest chain 28 peptides. Score 0.551 Round 5: 553 peptides, 51 chains. Longest chain 40 peptides. Score 0.585 Taking the results from Round 5 Chains 56, Residues 502, Estimated correctness of the model 0.0 % 4 chains (62 residues) have been docked in sequence ------------------------------------------------------ 14859 reflections ( 99.83 % complete ) and 14187 restraints for refining 6772 atoms. 11979 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2488 (Rfree = 0.000) for 6772 atoms. Found 37 (37 requested) and removed 60 (18 requested) atoms. Cycle 22: After refmac, R = 0.2309 (Rfree = 0.000) for 6694 atoms. Found 37 (37 requested) and removed 37 (18 requested) atoms. Cycle 23: After refmac, R = 0.2283 (Rfree = 0.000) for 6661 atoms. Found 29 (36 requested) and removed 39 (18 requested) atoms. Cycle 24: After refmac, R = 0.2203 (Rfree = 0.000) for 6628 atoms. Found 18 (36 requested) and removed 36 (18 requested) atoms. Cycle 25: After refmac, R = 0.2253 (Rfree = 0.000) for 6599 atoms. Found 36 (36 requested) and removed 30 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.61 2.89 Search for helices and strands: 0 residues in 0 chains, 6885 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 6910 seeds are put forward Round 1: 501 peptides, 68 chains. Longest chain 30 peptides. Score 0.458 Round 2: 529 peptides, 55 chains. Longest chain 42 peptides. Score 0.546 Round 3: 530 peptides, 60 chains. Longest chain 26 peptides. Score 0.525 Round 4: 548 peptides, 61 chains. Longest chain 21 peptides. Score 0.538 Round 5: 543 peptides, 57 chains. Longest chain 39 peptides. Score 0.551 Taking the results from Round 5 Chains 68, Residues 486, Estimated correctness of the model 0.0 % 11 chains (111 residues) have been docked in sequence ------------------------------------------------------ 14859 reflections ( 99.83 % complete ) and 14075 restraints for refining 6770 atoms. 11823 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2489 (Rfree = 0.000) for 6770 atoms. Found 37 (37 requested) and removed 62 (18 requested) atoms. Cycle 27: After refmac, R = 0.2285 (Rfree = 0.000) for 6675 atoms. Found 36 (37 requested) and removed 38 (18 requested) atoms. Cycle 28: After refmac, R = 0.2214 (Rfree = 0.000) for 6648 atoms. Found 16 (36 requested) and removed 40 (18 requested) atoms. Cycle 29: After refmac, R = 0.2109 (Rfree = 0.000) for 6608 atoms. Found 21 (36 requested) and removed 42 (18 requested) atoms. Cycle 30: After refmac, R = 0.2101 (Rfree = 0.000) for 6571 atoms. Found 33 (36 requested) and removed 34 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.60 2.89 Search for helices and strands: 0 residues in 0 chains, 6815 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 6845 seeds are put forward Round 1: 475 peptides, 71 chains. Longest chain 24 peptides. Score 0.415 Round 2: 522 peptides, 68 chains. Longest chain 21 peptides. Score 0.480 Round 3: 519 peptides, 65 chains. Longest chain 35 peptides. Score 0.491 Round 4: 501 peptides, 61 chains. Longest chain 28 peptides. Score 0.492 Round 5: 504 peptides, 61 chains. Longest chain 25 peptides. Score 0.495 Taking the results from Round 5 Chains 66, Residues 443, Estimated correctness of the model 0.0 % 6 chains (79 residues) have been docked in sequence ------------------------------------------------------ 14859 reflections ( 99.83 % complete ) and 14497 restraints for refining 6771 atoms. 12483 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2395 (Rfree = 0.000) for 6771 atoms. Found 31 (37 requested) and removed 40 (18 requested) atoms. Cycle 32: After refmac, R = 0.2280 (Rfree = 0.000) for 6697 atoms. Found 26 (37 requested) and removed 37 (18 requested) atoms. Cycle 33: After refmac, R = 0.2197 (Rfree = 0.000) for 6662 atoms. Found 33 (36 requested) and removed 32 (18 requested) atoms. Cycle 34: After refmac, R = 0.2138 (Rfree = 0.000) for 6633 atoms. Found 27 (36 requested) and removed 33 (18 requested) atoms. Cycle 35: After refmac, R = 0.2109 (Rfree = 0.000) for 6609 atoms. Found 26 (36 requested) and removed 31 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.65 2.93 Search for helices and strands: 0 residues in 0 chains, 6862 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 6885 seeds are put forward Round 1: 469 peptides, 78 chains. Longest chain 16 peptides. Score 0.373 Round 2: 497 peptides, 69 chains. Longest chain 23 peptides. Score 0.449 Round 3: 497 peptides, 67 chains. Longest chain 28 peptides. Score 0.459 Round 4: 497 peptides, 64 chains. Longest chain 23 peptides. Score 0.473 Round 5: 506 peptides, 64 chains. Longest chain 34 peptides. Score 0.483 Taking the results from Round 5 Chains 70, Residues 442, Estimated correctness of the model 0.0 % 5 chains (87 residues) have been docked in sequence ------------------------------------------------------ 14859 reflections ( 99.83 % complete ) and 14383 restraints for refining 6773 atoms. 12358 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2366 (Rfree = 0.000) for 6773 atoms. Found 33 (37 requested) and removed 41 (18 requested) atoms. Cycle 37: After refmac, R = 0.2232 (Rfree = 0.000) for 6678 atoms. Found 31 (37 requested) and removed 28 (18 requested) atoms. Cycle 38: After refmac, R = 0.2188 (Rfree = 0.000) for 6628 atoms. Found 34 (36 requested) and removed 32 (18 requested) atoms. Cycle 39: After refmac, R = 0.2166 (Rfree = 0.000) for 6602 atoms. Found 35 (36 requested) and removed 30 (18 requested) atoms. Cycle 40: After refmac, R = 0.2146 (Rfree = 0.000) for 6588 atoms. Found 31 (36 requested) and removed 31 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.65 2.93 Search for helices and strands: 0 residues in 0 chains, 6866 seeds are put forward NCS extension: 45 residues added (0 deleted due to clashes), 6911 seeds are put forward Round 1: 428 peptides, 72 chains. Longest chain 14 peptides. Score 0.356 Round 2: 495 peptides, 67 chains. Longest chain 22 peptides. Score 0.457 Round 3: 493 peptides, 65 chains. Longest chain 24 peptides. Score 0.464 Round 4: 513 peptides, 67 chains. Longest chain 28 peptides. Score 0.475 Round 5: 522 peptides, 63 chains. Longest chain 28 peptides. Score 0.503 Taking the results from Round 5 Chains 71, Residues 459, Estimated correctness of the model 0.0 % 8 chains (105 residues) have been docked in sequence ------------------------------------------------------ 14859 reflections ( 99.83 % complete ) and 14191 restraints for refining 6772 atoms. 12034 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2399 (Rfree = 0.000) for 6772 atoms. Found 37 (37 requested) and removed 69 (18 requested) atoms. Cycle 42: After refmac, R = 0.2229 (Rfree = 0.000) for 6677 atoms. Found 24 (37 requested) and removed 32 (18 requested) atoms. Cycle 43: After refmac, R = 0.2206 (Rfree = 0.000) for 6634 atoms. Found 14 (36 requested) and removed 35 (18 requested) atoms. Cycle 44: After refmac, R = 0.2218 (Rfree = 0.000) for 6593 atoms. Found 22 (36 requested) and removed 27 (18 requested) atoms. Cycle 45: After refmac, R = 0.2142 (Rfree = 0.000) for 6574 atoms. Found 13 (36 requested) and removed 24 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.63 2.91 Search for helices and strands: 0 residues in 0 chains, 6836 seeds are put forward NCS extension: 41 residues added (1 deleted due to clashes), 6877 seeds are put forward Round 1: 416 peptides, 70 chains. Longest chain 13 peptides. Score 0.352 Round 2: 447 peptides, 63 chains. Longest chain 19 peptides. Score 0.425 Round 3: 463 peptides, 68 chains. Longest chain 22 peptides. Score 0.417 Round 4: 489 peptides, 67 chains. Longest chain 22 peptides. Score 0.450 Round 5: 479 peptides, 67 chains. Longest chain 23 peptides. Score 0.440 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 78, Residues 422, Estimated correctness of the model 0.0 % 9 chains (89 residues) have been docked in sequence Sequence coverage is 21 % Consider running further cycles of model building using 1vlu-3_warpNtrace.pdb as input Building loops using Loopy2018 78 chains (422 residues) following loop building 9 chains (89 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14859 reflections ( 99.83 % complete ) and 14789 restraints for refining 6772 atoms. 12881 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2402 (Rfree = 0.000) for 6772 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2326 (Rfree = 0.000) for 6696 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.2280 (Rfree = 0.000) for 6652 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.2240 (Rfree = 0.000) for 6608 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:56:50 GMT 2018 Job finished. TimeTaking 93.81 Used memory is bytes: 17427104