null Mon 24 Dec 07:26:41 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 1vlu-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vlu-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vlu-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.8-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/1vlu-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.8-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 07:26:45 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/1vlu-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.8-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 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-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: 20 Cell parameters: 123.109 190.784 125.153 90.000 90.000 90.000 Input sequence file: 1vlu-3.8-parrot-noncs.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 8315 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3436 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3156 (Rfree = 0.000) for 8315 atoms. Found 45 (45 requested) and removed 108 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.67 2.94 Search for helices and strands: 0 residues in 0 chains, 8435 seeds are put forward NCS extension: 0 residues added, 8435 seeds are put forward Round 1: 423 peptides, 73 chains. Longest chain 12 peptides. Score 0.344 Round 2: 501 peptides, 64 chains. Longest chain 25 peptides. Score 0.477 Round 3: 522 peptides, 63 chains. Longest chain 25 peptides. Score 0.503 Round 4: 538 peptides, 57 chains. Longest chain 34 peptides. Score 0.546 Round 5: 563 peptides, 61 chains. Longest chain 29 peptides. Score 0.551 Taking the results from Round 5 Chains 65, Residues 502, Estimated correctness of the model 0.0 % 8 chains (117 residues) have been docked in sequence ------------------------------------------------------ 14859 reflections ( 99.83 % complete ) and 14189 restraints for refining 6771 atoms. 11846 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2666 (Rfree = 0.000) for 6771 atoms. Found 37 (37 requested) and removed 92 (18 requested) atoms. Cycle 2: After refmac, R = 0.2435 (Rfree = 0.000) for 6579 atoms. Found 22 (36 requested) and removed 46 (18 requested) atoms. Cycle 3: After refmac, R = 0.2373 (Rfree = 0.000) for 6473 atoms. Found 24 (36 requested) and removed 37 (18 requested) atoms. Cycle 4: After refmac, R = 0.2349 (Rfree = 0.000) for 6398 atoms. Found 29 (35 requested) and removed 47 (17 requested) atoms. Cycle 5: After refmac, R = 0.2227 (Rfree = 0.000) for 6347 atoms. Found 15 (35 requested) and removed 45 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.62 2.90 Search for helices and strands: 0 residues in 0 chains, 6593 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 6623 seeds are put forward Round 1: 525 peptides, 72 chains. Longest chain 18 peptides. Score 0.464 Round 2: 549 peptides, 59 chains. Longest chain 27 peptides. Score 0.547 Round 3: 549 peptides, 58 chains. Longest chain 33 peptides. Score 0.552 Round 4: 568 peptides, 58 chains. Longest chain 38 peptides. Score 0.569 Round 5: 563 peptides, 59 chains. Longest chain 23 peptides. Score 0.560 Taking the results from Round 4 Chains 64, Residues 510, Estimated correctness of the model 0.0 % 8 chains (68 residues) have been docked in sequence ------------------------------------------------------ 14859 reflections ( 99.83 % complete ) and 14263 restraints for refining 6720 atoms. 12067 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2491 (Rfree = 0.000) for 6720 atoms. Found 36 (36 requested) and removed 87 (18 requested) atoms. Cycle 7: After refmac, R = 0.2295 (Rfree = 0.000) for 6588 atoms. Found 36 (36 requested) and removed 60 (18 requested) atoms. Cycle 8: After refmac, R = 0.2206 (Rfree = 0.000) for 6527 atoms. Found 16 (36 requested) and removed 39 (18 requested) atoms. Cycle 9: After refmac, R = 0.2128 (Rfree = 0.000) for 6478 atoms. Found 18 (35 requested) and removed 29 (17 requested) atoms. Cycle 10: After refmac, R = 0.2096 (Rfree = 0.000) for 6441 atoms. Found 9 (35 requested) and removed 35 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.58 2.87 Search for helices and strands: 0 residues in 0 chains, 6687 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 6712 seeds are put forward Round 1: 527 peptides, 73 chains. Longest chain 22 peptides. Score 0.462 Round 2: 561 peptides, 61 chains. Longest chain 31 peptides. Score 0.550 Round 3: 561 peptides, 53 chains. Longest chain 32 peptides. Score 0.584 Round 4: 548 peptides, 63 chains. Longest chain 34 peptides. Score 0.529 Round 5: 555 peptides, 57 chains. Longest chain 34 peptides. Score 0.562 Taking the results from Round 3 Chains 62, Residues 508, Estimated correctness of the model 0.0 % 9 chains (156 residues) have been docked in sequence ------------------------------------------------------ 14859 reflections ( 99.83 % complete ) and 13251 restraints for refining 6771 atoms. 10693 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2441 (Rfree = 0.000) for 6771 atoms. Found 37 (37 requested) and removed 74 (18 requested) atoms. Cycle 12: After refmac, R = 0.2262 (Rfree = 0.000) for 6641 atoms. Found 34 (37 requested) and removed 48 (18 requested) atoms. Cycle 13: After refmac, R = 0.2185 (Rfree = 0.000) for 6581 atoms. Found 16 (36 requested) and removed 37 (18 requested) atoms. Cycle 14: After refmac, R = 0.2136 (Rfree = 0.000) for 6528 atoms. Found 23 (36 requested) and removed 33 (18 requested) atoms. Cycle 15: After refmac, R = 0.2090 (Rfree = 0.000) for 6495 atoms. Found 16 (35 requested) and removed 28 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.60 2.89 Search for helices and strands: 0 residues in 0 chains, 6709 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 6734 seeds are put forward Round 1: 516 peptides, 72 chains. Longest chain 21 peptides. Score 0.455 Round 2: 531 peptides, 63 chains. Longest chain 25 peptides. Score 0.512 Round 3: 536 peptides, 57 chains. Longest chain 24 peptides. Score 0.544 Round 4: 551 peptides, 61 chains. Longest chain 23 peptides. Score 0.540 Round 5: 543 peptides, 62 chains. Longest chain 32 peptides. Score 0.528 Taking the results from Round 3 Chains 67, Residues 479, Estimated correctness of the model 0.0 % 9 chains (98 residues) have been docked in sequence ------------------------------------------------------ 14859 reflections ( 99.83 % complete ) and 14195 restraints for refining 6772 atoms. 12019 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2373 (Rfree = 0.000) for 6772 atoms. Found 37 (37 requested) and removed 73 (18 requested) atoms. Cycle 17: After refmac, R = 0.2242 (Rfree = 0.000) for 6668 atoms. Found 34 (37 requested) and removed 46 (18 requested) atoms. Cycle 18: After refmac, R = 0.2154 (Rfree = 0.000) for 6628 atoms. Found 24 (36 requested) and removed 35 (18 requested) atoms. Cycle 19: After refmac, R = 0.2090 (Rfree = 0.000) for 6595 atoms. Found 15 (36 requested) and removed 29 (18 requested) atoms. Cycle 20: After refmac, R = 0.2065 (Rfree = 0.000) for 6566 atoms. Found 17 (36 requested) and removed 33 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.62 2.90 Search for helices and strands: 0 residues in 0 chains, 6823 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 6842 seeds are put forward Round 1: 471 peptides, 66 chains. Longest chain 22 peptides. Score 0.436 Round 2: 519 peptides, 69 chains. Longest chain 20 peptides. Score 0.472 Round 3: 508 peptides, 66 chains. Longest chain 25 peptides. Score 0.475 Round 4: 501 peptides, 58 chains. Longest chain 29 peptides. Score 0.506 Round 5: 501 peptides, 58 chains. Longest chain 25 peptides. Score 0.506 Taking the results from Round 5 Chains 59, Residues 443, Estimated correctness of the model 0.0 % 4 chains (43 residues) have been docked in sequence ------------------------------------------------------ 14859 reflections ( 99.83 % complete ) and 14980 restraints for refining 6773 atoms. 13115 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2266 (Rfree = 0.000) for 6773 atoms. Found 17 (37 requested) and removed 62 (18 requested) atoms. Cycle 22: After refmac, R = 0.2107 (Rfree = 0.000) for 6664 atoms. Found 8 (36 requested) and removed 40 (18 requested) atoms. Cycle 23: After refmac, R = 0.2052 (Rfree = 0.000) for 6613 atoms. Found 9 (36 requested) and removed 35 (18 requested) atoms. Cycle 24: After refmac, R = 0.2092 (Rfree = 0.000) for 6573 atoms. Found 14 (36 requested) and removed 35 (18 requested) atoms. Cycle 25: After refmac, R = 0.2053 (Rfree = 0.000) for 6540 atoms. Found 19 (36 requested) and removed 36 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.58 2.87 Search for helices and strands: 0 residues in 0 chains, 6804 seeds are put forward NCS extension: 29 residues added (4 deleted due to clashes), 6833 seeds are put forward Round 1: 479 peptides, 71 chains. Longest chain 14 peptides. Score 0.420 Round 2: 519 peptides, 68 chains. Longest chain 28 peptides. Score 0.477 Round 3: 520 peptides, 63 chains. Longest chain 21 peptides. Score 0.501 Round 4: 531 peptides, 65 chains. Longest chain 31 peptides. Score 0.503 Round 5: 526 peptides, 65 chains. Longest chain 29 peptides. Score 0.498 Taking the results from Round 4 Chains 70, Residues 466, Estimated correctness of the model 0.0 % 8 chains (75 residues) have been docked in sequence ------------------------------------------------------ 14859 reflections ( 99.83 % complete ) and 14483 restraints for refining 6773 atoms. 12444 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2339 (Rfree = 0.000) for 6773 atoms. Found 37 (37 requested) and removed 47 (18 requested) atoms. Cycle 27: After refmac, R = 0.2202 (Rfree = 0.000) for 6707 atoms. Found 30 (37 requested) and removed 37 (18 requested) atoms. Cycle 28: After refmac, R = 0.2117 (Rfree = 0.000) for 6662 atoms. Found 28 (36 requested) and removed 33 (18 requested) atoms. Cycle 29: After refmac, R = 0.2063 (Rfree = 0.000) for 6633 atoms. Found 20 (36 requested) and removed 37 (18 requested) atoms. Cycle 30: After refmac, R = 0.1975 (Rfree = 0.000) for 6603 atoms. Found 12 (36 requested) and removed 33 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.62 2.90 Search for helices and strands: 0 residues in 0 chains, 6833 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 6848 seeds are put forward Round 1: 463 peptides, 69 chains. Longest chain 19 peptides. Score 0.412 Round 2: 492 peptides, 64 chains. Longest chain 23 peptides. Score 0.468 Round 3: 532 peptides, 65 chains. Longest chain 27 peptides. Score 0.504 Round 4: 529 peptides, 65 chains. Longest chain 23 peptides. Score 0.501 Round 5: 514 peptides, 61 chains. Longest chain 26 peptides. Score 0.505 Taking the results from Round 5 Chains 63, Residues 453, Estimated correctness of the model 0.0 % 4 chains (60 residues) have been docked in sequence ------------------------------------------------------ 14859 reflections ( 99.83 % complete ) and 14668 restraints for refining 6773 atoms. 12702 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2356 (Rfree = 0.000) for 6773 atoms. Found 30 (37 requested) and removed 37 (18 requested) atoms. Cycle 32: After refmac, R = 0.2184 (Rfree = 0.000) for 6687 atoms. Found 30 (37 requested) and removed 36 (18 requested) atoms. Cycle 33: After refmac, R = 0.2123 (Rfree = 0.000) for 6649 atoms. Found 19 (36 requested) and removed 31 (18 requested) atoms. Cycle 34: After refmac, R = 0.2073 (Rfree = 0.000) for 6617 atoms. Found 23 (36 requested) and removed 27 (18 requested) atoms. Cycle 35: After refmac, R = 0.2080 (Rfree = 0.000) for 6595 atoms. Found 25 (36 requested) and removed 32 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.60 2.89 Search for helices and strands: 0 residues in 0 chains, 6873 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 6900 seeds are put forward Round 1: 433 peptides, 76 chains. Longest chain 15 peptides. Score 0.341 Round 2: 493 peptides, 72 chains. Longest chain 17 peptides. Score 0.430 Round 3: 494 peptides, 70 chains. Longest chain 18 peptides. Score 0.441 Round 4: 481 peptides, 63 chains. Longest chain 22 peptides. Score 0.461 Round 5: 493 peptides, 66 chains. Longest chain 22 peptides. Score 0.459 Taking the results from Round 4 Chains 63, Residues 418, Estimated correctness of the model 0.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 14859 reflections ( 99.83 % complete ) and 15431 restraints for refining 6772 atoms. 13724 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2259 (Rfree = 0.000) for 6772 atoms. Found 37 (37 requested) and removed 39 (18 requested) atoms. Cycle 37: After refmac, R = 0.2110 (Rfree = 0.000) for 6715 atoms. Found 32 (37 requested) and removed 33 (18 requested) atoms. Cycle 38: After refmac, R = 0.2053 (Rfree = 0.000) for 6695 atoms. Found 11 (36 requested) and removed 29 (18 requested) atoms. Cycle 39: After refmac, R = 0.2026 (Rfree = 0.000) for 6663 atoms. Found 13 (36 requested) and removed 26 (18 requested) atoms. Cycle 40: After refmac, R = 0.2045 (Rfree = 0.000) for 6630 atoms. Found 21 (36 requested) and removed 25 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.60 2.89 Search for helices and strands: 0 residues in 0 chains, 6879 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 6895 seeds are put forward Round 1: 463 peptides, 78 chains. Longest chain 22 peptides. Score 0.366 Round 2: 475 peptides, 66 chains. Longest chain 18 peptides. Score 0.440 Round 3: 484 peptides, 65 chains. Longest chain 19 peptides. Score 0.455 Round 4: 478 peptides, 68 chains. Longest chain 25 peptides. Score 0.434 Round 5: 473 peptides, 64 chains. Longest chain 17 peptides. Score 0.448 Taking the results from Round 3 Chains 69, Residues 419, Estimated correctness of the model 0.0 % 8 chains (57 residues) have been docked in sequence ------------------------------------------------------ 14859 reflections ( 99.83 % complete ) and 14866 restraints for refining 6772 atoms. 13080 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2300 (Rfree = 0.000) for 6772 atoms. Found 37 (37 requested) and removed 53 (18 requested) atoms. Cycle 42: After refmac, R = 0.2161 (Rfree = 0.000) for 6723 atoms. Found 37 (37 requested) and removed 32 (18 requested) atoms. Cycle 43: After refmac, R = 0.2141 (Rfree = 0.000) for 6710 atoms. Found 30 (36 requested) and removed 35 (18 requested) atoms. Cycle 44: After refmac, R = 0.2199 (Rfree = 0.000) for 6677 atoms. Found 36 (36 requested) and removed 40 (18 requested) atoms. Cycle 45: After refmac, R = 0.2128 (Rfree = 0.000) for 6647 atoms. Found 35 (36 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.61 2.89 Search for helices and strands: 0 residues in 0 chains, 6903 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 6926 seeds are put forward Round 1: 413 peptides, 73 chains. Longest chain 13 peptides. Score 0.332 Round 2: 465 peptides, 66 chains. Longest chain 19 peptides. Score 0.429 Round 3: 466 peptides, 67 chains. Longest chain 18 peptides. Score 0.425 Round 4: 473 peptides, 65 chains. Longest chain 17 peptides. Score 0.443 Round 5: 461 peptides, 64 chains. Longest chain 26 peptides. Score 0.435 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 65, Residues 408, Estimated correctness of the model 0.0 % 4 chains (27 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 1vlu-3_warpNtrace.pdb as input Building loops using Loopy2018 65 chains (408 residues) following loop building 4 chains (27 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14859 reflections ( 99.83 % complete ) and 15213 restraints for refining 6772 atoms. 13576 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2167 (Rfree = 0.000) for 6772 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2228 (Rfree = 0.000) for 6713 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.2167 (Rfree = 0.000) for 6675 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.2110 (Rfree = 0.000) for 6639 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:47:46 GMT 2018 Job finished. TimeTaking 81.09 Used memory is bytes: 11820224