null Mon 24 Dec 00:02:43 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vqy-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vqy-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vqy-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqy-3.4-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vqy-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqy-3.4-parrot-mrncs ############### 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 00:02:47 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vqy-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqy-3.4-parrot-mrncs/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 795 and 0 Target number of residues in the AU: 795 Target solvent content: 0.5608 Checking the provided sequence file Detected sequence length: 116 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 8 Adjusted target number of residues: 928 Adjusted target solvent content: 0.49 Input MTZ file: 1vqy-3.4-parrot-mrncs.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: 68.026 110.931 129.804 90.000 90.000 90.000 Input sequence file: 1vqy-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 7424 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: 29.074 3.400 Wilson plot Bfac: 38.67 13838 reflections ( 98.37 % complete ) and 0 restraints for refining 8260 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.2793 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2614 (Rfree = 0.000) for 8260 atoms. Found 62 (62 requested) and removed 50 (31 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.89 2.93 Search for helices and strands: 0 residues in 0 chains, 8437 seeds are put forward NCS extension: 0 residues added, 8437 seeds are put forward Round 1: 459 peptides, 78 chains. Longest chain 12 peptides. Score 0.428 Round 2: 579 peptides, 81 chains. Longest chain 24 peptides. Score 0.579 Round 3: 603 peptides, 70 chains. Longest chain 25 peptides. Score 0.663 Round 4: 609 peptides, 69 chains. Longest chain 31 peptides. Score 0.674 Round 5: 620 peptides, 63 chains. Longest chain 32 peptides. Score 0.711 Taking the results from Round 5 Chains 65, Residues 557, Estimated correctness of the model 60.7 % 4 chains (59 residues) have been docked in sequence Building loops using Loopy2018 65 chains (557 residues) following loop building 4 chains (59 residues) in sequence following loop building ------------------------------------------------------ 13838 reflections ( 98.37 % complete ) and 13959 restraints for refining 6749 atoms. 11555 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2582 (Rfree = 0.000) for 6749 atoms. Found 35 (50 requested) and removed 46 (25 requested) atoms. Cycle 2: After refmac, R = 0.2452 (Rfree = 0.000) for 6645 atoms. Found 33 (49 requested) and removed 48 (25 requested) atoms. Cycle 3: After refmac, R = 0.2247 (Rfree = 0.000) for 6581 atoms. Found 11 (48 requested) and removed 39 (25 requested) atoms. Cycle 4: After refmac, R = 0.2251 (Rfree = 0.000) for 6527 atoms. Found 30 (46 requested) and removed 37 (24 requested) atoms. Cycle 5: After refmac, R = 0.2025 (Rfree = 0.000) for 6500 atoms. Found 16 (45 requested) and removed 37 (24 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.88 2.92 Search for helices and strands: 0 residues in 0 chains, 6738 seeds are put forward NCS extension: 17 residues added (14 deleted due to clashes), 6755 seeds are put forward Round 1: 573 peptides, 74 chains. Longest chain 29 peptides. Score 0.609 Round 2: 639 peptides, 69 chains. Longest chain 31 peptides. Score 0.703 Round 3: 636 peptides, 66 chains. Longest chain 29 peptides. Score 0.713 Round 4: 649 peptides, 73 chains. Longest chain 29 peptides. Score 0.695 Round 5: 650 peptides, 69 chains. Longest chain 26 peptides. Score 0.713 Taking the results from Round 5 Chains 74, Residues 581, Estimated correctness of the model 61.1 % 5 chains (81 residues) have been docked in sequence Building loops using Loopy2018 74 chains (581 residues) following loop building 5 chains (81 residues) in sequence following loop building ------------------------------------------------------ 13838 reflections ( 98.37 % complete ) and 13807 restraints for refining 6750 atoms. 11213 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2624 (Rfree = 0.000) for 6750 atoms. Found 38 (45 requested) and removed 63 (25 requested) atoms. Cycle 7: After refmac, R = 0.2652 (Rfree = 0.000) for 6681 atoms. Found 38 (44 requested) and removed 70 (25 requested) atoms. Cycle 8: After refmac, R = 0.2587 (Rfree = 0.000) for 6617 atoms. Found 31 (43 requested) and removed 56 (25 requested) atoms. Cycle 9: After refmac, R = 0.2449 (Rfree = 0.000) for 6575 atoms. Found 34 (41 requested) and removed 48 (24 requested) atoms. Cycle 10: After refmac, R = 0.2183 (Rfree = 0.000) for 6545 atoms. Found 18 (40 requested) and removed 28 (24 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.82 2.86 Search for helices and strands: 0 residues in 0 chains, 6732 seeds are put forward NCS extension: 9 residues added (16 deleted due to clashes), 6741 seeds are put forward Round 1: 539 peptides, 80 chains. Longest chain 19 peptides. Score 0.532 Round 2: 588 peptides, 72 chains. Longest chain 24 peptides. Score 0.637 Round 3: 596 peptides, 72 chains. Longest chain 22 peptides. Score 0.645 Round 4: 599 peptides, 70 chains. Longest chain 20 peptides. Score 0.658 Round 5: 597 peptides, 71 chains. Longest chain 24 peptides. Score 0.651 Taking the results from Round 4 Chains 71, Residues 529, Estimated correctness of the model 46.5 % 3 chains (41 residues) have been docked in sequence ------------------------------------------------------ 13838 reflections ( 98.37 % complete ) and 14595 restraints for refining 6748 atoms. 12372 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2616 (Rfree = 0.000) for 6748 atoms. Found 40 (40 requested) and removed 63 (25 requested) atoms. Cycle 12: After refmac, R = 0.2496 (Rfree = 0.000) for 6698 atoms. Found 29 (40 requested) and removed 61 (25 requested) atoms. Cycle 13: After refmac, R = 0.2432 (Rfree = 0.000) for 6643 atoms. Found 36 (40 requested) and removed 39 (25 requested) atoms. Cycle 14: After refmac, R = 0.2410 (Rfree = 0.000) for 6626 atoms. Found 40 (40 requested) and removed 38 (25 requested) atoms. Cycle 15: After refmac, R = 0.2357 (Rfree = 0.000) for 6613 atoms. Found 40 (40 requested) and removed 38 (25 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.84 2.88 Search for helices and strands: 0 residues in 0 chains, 6840 seeds are put forward NCS extension: 8 residues added (8 deleted due to clashes), 6848 seeds are put forward Round 1: 510 peptides, 79 chains. Longest chain 16 peptides. Score 0.498 Round 2: 545 peptides, 71 chains. Longest chain 17 peptides. Score 0.592 Round 3: 537 peptides, 69 chains. Longest chain 17 peptides. Score 0.593 Round 4: 553 peptides, 72 chains. Longest chain 22 peptides. Score 0.596 Round 5: 563 peptides, 69 chains. Longest chain 26 peptides. Score 0.624 Taking the results from Round 5 Chains 71, Residues 494, Estimated correctness of the model 36.3 % 4 chains (47 residues) have been docked in sequence ------------------------------------------------------ 13838 reflections ( 98.37 % complete ) and 14766 restraints for refining 6748 atoms. 12672 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2688 (Rfree = 0.000) for 6748 atoms. Found 33 (40 requested) and removed 64 (25 requested) atoms. Cycle 17: After refmac, R = 0.2553 (Rfree = 0.000) for 6681 atoms. Found 38 (40 requested) and removed 53 (25 requested) atoms. Cycle 18: After refmac, R = 0.2495 (Rfree = 0.000) for 6643 atoms. Found 40 (40 requested) and removed 41 (25 requested) atoms. Cycle 19: After refmac, R = 0.2439 (Rfree = 0.000) for 6628 atoms. Found 40 (40 requested) and removed 31 (25 requested) atoms. Cycle 20: After refmac, R = 0.2123 (Rfree = 0.000) for 6628 atoms. Found 26 (40 requested) and removed 31 (25 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.84 2.88 Search for helices and strands: 0 residues in 0 chains, 6817 seeds are put forward NCS extension: 33 residues added (9 deleted due to clashes), 6850 seeds are put forward Round 1: 474 peptides, 81 chains. Longest chain 16 peptides. Score 0.431 Round 2: 561 peptides, 78 chains. Longest chain 19 peptides. Score 0.573 Round 3: 553 peptides, 71 chains. Longest chain 22 peptides. Score 0.601 Round 4: 566 peptides, 69 chains. Longest chain 22 peptides. Score 0.627 Round 5: 560 peptides, 71 chains. Longest chain 21 peptides. Score 0.610 Taking the results from Round 4 Chains 71, Residues 497, Estimated correctness of the model 37.2 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 13838 reflections ( 98.37 % complete ) and 14620 restraints for refining 6750 atoms. 12604 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2669 (Rfree = 0.000) for 6750 atoms. Found 40 (40 requested) and removed 55 (25 requested) atoms. Cycle 22: After refmac, R = 0.2648 (Rfree = 0.000) for 6712 atoms. Found 40 (40 requested) and removed 48 (25 requested) atoms. Cycle 23: After refmac, R = 0.2471 (Rfree = 0.000) for 6677 atoms. Found 40 (40 requested) and removed 39 (25 requested) atoms. Cycle 24: After refmac, R = 0.2477 (Rfree = 0.000) for 6652 atoms. Found 40 (40 requested) and removed 36 (25 requested) atoms. Cycle 25: After refmac, R = 0.2499 (Rfree = 0.000) for 6648 atoms. Found 40 (40 requested) and removed 41 (25 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.94 2.98 Search for helices and strands: 0 residues in 0 chains, 6837 seeds are put forward NCS extension: 22 residues added (10 deleted due to clashes), 6859 seeds are put forward Round 1: 496 peptides, 84 chains. Longest chain 12 peptides. Score 0.445 Round 2: 565 peptides, 79 chains. Longest chain 20 peptides. Score 0.572 Round 3: 575 peptides, 81 chains. Longest chain 18 peptides. Score 0.574 Round 4: 566 peptides, 72 chains. Longest chain 22 peptides. Score 0.611 Round 5: 547 peptides, 76 chains. Longest chain 17 peptides. Score 0.566 Taking the results from Round 4 Chains 73, Residues 494, Estimated correctness of the model 32.2 % 3 chains (36 residues) have been docked in sequence ------------------------------------------------------ 13838 reflections ( 98.37 % complete ) and 14293 restraints for refining 6749 atoms. 12228 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2693 (Rfree = 0.000) for 6749 atoms. Found 40 (40 requested) and removed 66 (25 requested) atoms. Cycle 27: After refmac, R = 0.2377 (Rfree = 0.000) for 6681 atoms. Found 33 (40 requested) and removed 37 (25 requested) atoms. Cycle 28: After refmac, R = 0.2214 (Rfree = 0.000) for 6660 atoms. Found 11 (40 requested) and removed 34 (25 requested) atoms. Cycle 29: After refmac, R = 0.2137 (Rfree = 0.000) for 6623 atoms. Found 16 (40 requested) and removed 32 (25 requested) atoms. Cycle 30: After refmac, R = 0.2347 (Rfree = 0.000) for 6601 atoms. Found 39 (39 requested) and removed 32 (24 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.90 2.94 Search for helices and strands: 0 residues in 0 chains, 6789 seeds are put forward NCS extension: 18 residues added (10 deleted due to clashes), 6807 seeds are put forward Round 1: 445 peptides, 79 chains. Longest chain 12 peptides. Score 0.399 Round 2: 505 peptides, 75 chains. Longest chain 22 peptides. Score 0.516 Round 3: 479 peptides, 67 chains. Longest chain 20 peptides. Score 0.529 Round 4: 488 peptides, 73 chains. Longest chain 20 peptides. Score 0.504 Round 5: 474 peptides, 64 chains. Longest chain 26 peptides. Score 0.540 Taking the results from Round 5 Chains 66, Residues 410, Estimated correctness of the model 7.9 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 13838 reflections ( 98.37 % complete ) and 14895 restraints for refining 6748 atoms. 13202 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2618 (Rfree = 0.000) for 6748 atoms. Found 38 (40 requested) and removed 65 (25 requested) atoms. Cycle 32: After refmac, R = 0.2353 (Rfree = 0.000) for 6697 atoms. Found 40 (40 requested) and removed 32 (25 requested) atoms. Cycle 33: After refmac, R = 0.2427 (Rfree = 0.000) for 6689 atoms. Found 40 (40 requested) and removed 42 (25 requested) atoms. Cycle 34: After refmac, R = 0.2443 (Rfree = 0.000) for 6665 atoms. Found 40 (40 requested) and removed 40 (25 requested) atoms. Cycle 35: After refmac, R = 0.2757 (Rfree = 0.000) for 6660 atoms. Found 40 (40 requested) and removed 63 (25 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.87 2.91 Search for helices and strands: 0 residues in 0 chains, 6854 seeds are put forward NCS extension: 33 residues added (4 deleted due to clashes), 6887 seeds are put forward Round 1: 382 peptides, 73 chains. Longest chain 14 peptides. Score 0.336 Round 2: 418 peptides, 62 chains. Longest chain 16 peptides. Score 0.472 Round 3: 423 peptides, 67 chains. Longest chain 17 peptides. Score 0.446 Round 4: 461 peptides, 67 chains. Longest chain 16 peptides. Score 0.503 Round 5: 444 peptides, 63 chains. Longest chain 22 peptides. Score 0.504 Taking the results from Round 5 Chains 63, Residues 381, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 13838 reflections ( 98.37 % complete ) and 15251 restraints for refining 6748 atoms. 13790 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2591 (Rfree = 0.000) for 6748 atoms. Found 40 (40 requested) and removed 81 (25 requested) atoms. Cycle 37: After refmac, R = 0.2488 (Rfree = 0.000) for 6688 atoms. Found 40 (40 requested) and removed 52 (25 requested) atoms. Cycle 38: After refmac, R = 0.2394 (Rfree = 0.000) for 6653 atoms. Found 40 (40 requested) and removed 36 (25 requested) atoms. Cycle 39: After refmac, R = 0.2102 (Rfree = 0.000) for 6646 atoms. Found 34 (40 requested) and removed 37 (25 requested) atoms. Cycle 40: After refmac, R = 0.1989 (Rfree = 0.000) for 6635 atoms. Found 23 (40 requested) and removed 29 (25 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.86 2.90 Search for helices and strands: 0 residues in 0 chains, 6782 seeds are put forward NCS extension: 22 residues added (5 deleted due to clashes), 6804 seeds are put forward Round 1: 356 peptides, 69 chains. Longest chain 12 peptides. Score 0.320 Round 2: 414 peptides, 66 chains. Longest chain 18 peptides. Score 0.439 Round 3: 419 peptides, 64 chains. Longest chain 16 peptides. Score 0.460 Round 4: 419 peptides, 64 chains. Longest chain 16 peptides. Score 0.460 Round 5: 426 peptides, 66 chains. Longest chain 18 peptides. Score 0.458 Taking the results from Round 4 Chains 64, Residues 355, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 13838 reflections ( 98.37 % complete ) and 15194 restraints for refining 6702 atoms. 13811 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2513 (Rfree = 0.000) for 6702 atoms. Found 40 (40 requested) and removed 74 (25 requested) atoms. Cycle 42: After refmac, R = 0.2331 (Rfree = 0.000) for 6650 atoms. Found 37 (40 requested) and removed 47 (25 requested) atoms. Cycle 43: After refmac, R = 0.2383 (Rfree = 0.000) for 6634 atoms. Found 40 (40 requested) and removed 46 (25 requested) atoms. Cycle 44: After refmac, R = 0.2462 (Rfree = 0.000) for 6627 atoms. Found 40 (40 requested) and removed 34 (25 requested) atoms. Cycle 45: After refmac, R = 0.2432 (Rfree = 0.000) for 6627 atoms. Found 40 (40 requested) and removed 39 (25 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.87 2.91 Search for helices and strands: 0 residues in 0 chains, 6812 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 6826 seeds are put forward Round 1: 340 peptides, 65 chains. Longest chain 10 peptides. Score 0.322 Round 2: 376 peptides, 61 chains. Longest chain 13 peptides. Score 0.413 Round 3: 401 peptides, 64 chains. Longest chain 13 peptides. Score 0.432 Round 4: 393 peptides, 64 chains. Longest chain 13 peptides. Score 0.419 Round 5: 390 peptides, 64 chains. Longest chain 14 peptides. Score 0.415 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 64, Residues 337, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vqy-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13838 reflections ( 98.37 % complete ) and 14610 restraints for refining 6608 atoms. 13326 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2624 (Rfree = 0.000) for 6608 atoms. Found 0 (39 requested) and removed 24 (24 requested) atoms. Cycle 47: After refmac, R = 0.2420 (Rfree = 0.000) for 6569 atoms. Found 0 (39 requested) and removed 24 (24 requested) atoms. Cycle 48: After refmac, R = 0.2166 (Rfree = 0.000) for 6539 atoms. Found 0 (39 requested) and removed 24 (24 requested) atoms. Cycle 49: After refmac, R = 0.2036 (Rfree = 0.000) for 6508 atoms. Found 0 (39 requested) and removed 24 (24 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:12:01 GMT 2018 Job finished. TimeTaking 69.31 Used memory is bytes: 22203008