Mon 24 Dec 07:28:23 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 2pbl-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2pbl-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2pbl-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pbl-3.2-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/2pbl-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pbl-3.2-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 07:28:28 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/2pbl-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pbl-3.2-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 750 and 0 Target number of residues in the AU: 750 Target solvent content: 0.5980 Checking the provided sequence file Detected sequence length: 262 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1048 Adjusted target solvent content: 0.44 Input MTZ file: 2pbl-3.2-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: 4 Cell parameters: 77.197 74.438 95.727 90.000 113.394 90.000 Input sequence file: 2pbl-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 8384 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: 87.858 3.200 Wilson plot Bfac: 51.72 16523 reflections ( 99.29 % complete ) and 0 restraints for refining 9315 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3492 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4295 (Rfree = 0.000) for 9315 atoms. Found 83 (83 requested) and removed 159 (41 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.88 3.12 Search for helices and strands: 0 residues in 0 chains, 9449 seeds are put forward NCS extension: 0 residues added, 9449 seeds are put forward Round 1: 381 peptides, 78 chains. Longest chain 12 peptides. Score 0.294 Round 2: 492 peptides, 84 chains. Longest chain 17 peptides. Score 0.433 Round 3: 503 peptides, 84 chains. Longest chain 19 peptides. Score 0.450 Round 4: 523 peptides, 84 chains. Longest chain 17 peptides. Score 0.479 Round 5: 539 peptides, 86 chains. Longest chain 17 peptides. Score 0.489 Taking the results from Round 5 Chains 88, Residues 453, Estimated correctness of the model 7.7 % 15 chains (78 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 99.29 % complete ) and 16714 restraints for refining 7654 atoms. 14781 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3539 (Rfree = 0.000) for 7654 atoms. Found 68 (68 requested) and removed 102 (34 requested) atoms. Cycle 2: After refmac, R = 0.3187 (Rfree = 0.000) for 7508 atoms. Found 68 (68 requested) and removed 63 (34 requested) atoms. Cycle 3: After refmac, R = 0.3264 (Rfree = 0.000) for 7464 atoms. Found 67 (67 requested) and removed 46 (33 requested) atoms. Cycle 4: After refmac, R = 0.3241 (Rfree = 0.000) for 7456 atoms. Found 67 (67 requested) and removed 44 (33 requested) atoms. Cycle 5: After refmac, R = 0.3146 (Rfree = 0.000) for 7444 atoms. Found 67 (67 requested) and removed 43 (33 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.94 3.19 Search for helices and strands: 0 residues in 0 chains, 7798 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 7813 seeds are put forward Round 1: 477 peptides, 89 chains. Longest chain 15 peptides. Score 0.377 Round 2: 567 peptides, 85 chains. Longest chain 17 peptides. Score 0.533 Round 3: 595 peptides, 84 chains. Longest chain 20 peptides. Score 0.574 Round 4: 613 peptides, 83 chains. Longest chain 21 peptides. Score 0.600 Round 5: 612 peptides, 84 chains. Longest chain 19 peptides. Score 0.594 Taking the results from Round 4 Chains 83, Residues 530, Estimated correctness of the model 41.1 % 5 chains (39 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 99.29 % complete ) and 16495 restraints for refining 7522 atoms. 14334 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3100 (Rfree = 0.000) for 7522 atoms. Found 67 (67 requested) and removed 79 (33 requested) atoms. Cycle 7: After refmac, R = 0.2934 (Rfree = 0.000) for 7454 atoms. Found 67 (67 requested) and removed 52 (33 requested) atoms. Cycle 8: After refmac, R = 0.2897 (Rfree = 0.000) for 7434 atoms. Found 67 (67 requested) and removed 42 (33 requested) atoms. Cycle 9: After refmac, R = 0.2749 (Rfree = 0.000) for 7442 atoms. Found 66 (66 requested) and removed 44 (33 requested) atoms. Cycle 10: After refmac, R = 0.2703 (Rfree = 0.000) for 7452 atoms. Found 66 (66 requested) and removed 41 (33 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.98 3.23 Search for helices and strands: 0 residues in 0 chains, 7785 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 7798 seeds are put forward Round 1: 549 peptides, 95 chains. Longest chain 13 peptides. Score 0.448 Round 2: 631 peptides, 95 chains. Longest chain 21 peptides. Score 0.559 Round 3: 648 peptides, 91 chains. Longest chain 25 peptides. Score 0.600 Round 4: 648 peptides, 89 chains. Longest chain 22 peptides. Score 0.610 Round 5: 621 peptides, 89 chains. Longest chain 21 peptides. Score 0.579 Taking the results from Round 4 Chains 93, Residues 559, Estimated correctness of the model 43.7 % 7 chains (55 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 99.29 % complete ) and 16723 restraints for refining 7654 atoms. 14378 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2945 (Rfree = 0.000) for 7654 atoms. Found 68 (68 requested) and removed 93 (34 requested) atoms. Cycle 12: After refmac, R = 0.2645 (Rfree = 0.000) for 7589 atoms. Found 68 (68 requested) and removed 42 (34 requested) atoms. Cycle 13: After refmac, R = 0.2510 (Rfree = 0.000) for 7590 atoms. Found 68 (68 requested) and removed 37 (34 requested) atoms. Cycle 14: After refmac, R = 0.2368 (Rfree = 0.000) for 7606 atoms. Found 68 (68 requested) and removed 40 (34 requested) atoms. Cycle 15: After refmac, R = 0.2302 (Rfree = 0.000) for 7623 atoms. Found 63 (68 requested) and removed 44 (34 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.97 3.22 Search for helices and strands: 0 residues in 0 chains, 7899 seeds are put forward NCS extension: 4 residues added (10 deleted due to clashes), 7903 seeds are put forward Round 1: 553 peptides, 92 chains. Longest chain 16 peptides. Score 0.472 Round 2: 616 peptides, 87 chains. Longest chain 21 peptides. Score 0.583 Round 3: 637 peptides, 87 chains. Longest chain 27 peptides. Score 0.608 Round 4: 629 peptides, 86 chains. Longest chain 29 peptides. Score 0.604 Round 5: 615 peptides, 80 chains. Longest chain 25 peptides. Score 0.618 Taking the results from Round 5 Chains 82, Residues 535, Estimated correctness of the model 45.8 % 4 chains (46 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 99.29 % complete ) and 16864 restraints for refining 7653 atoms. 14641 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2849 (Rfree = 0.000) for 7653 atoms. Found 68 (68 requested) and removed 55 (34 requested) atoms. Cycle 17: After refmac, R = 0.2687 (Rfree = 0.000) for 7633 atoms. Found 68 (68 requested) and removed 43 (34 requested) atoms. Cycle 18: After refmac, R = 0.2597 (Rfree = 0.000) for 7639 atoms. Found 68 (68 requested) and removed 39 (34 requested) atoms. Cycle 19: After refmac, R = 0.2448 (Rfree = 0.000) for 7658 atoms. Found 68 (68 requested) and removed 40 (34 requested) atoms. Cycle 20: After refmac, R = 0.2361 (Rfree = 0.000) for 7676 atoms. Found 68 (68 requested) and removed 43 (34 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.96 3.21 Search for helices and strands: 0 residues in 0 chains, 8033 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 8046 seeds are put forward Round 1: 515 peptides, 79 chains. Longest chain 19 peptides. Score 0.498 Round 2: 576 peptides, 81 chains. Longest chain 20 peptides. Score 0.567 Round 3: 605 peptides, 80 chains. Longest chain 22 peptides. Score 0.607 Round 4: 623 peptides, 78 chains. Longest chain 28 peptides. Score 0.637 Round 5: 626 peptides, 80 chains. Longest chain 25 peptides. Score 0.630 Taking the results from Round 4 Chains 83, Residues 545, Estimated correctness of the model 50.7 % 8 chains (69 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 99.29 % complete ) and 16722 restraints for refining 7654 atoms. 14411 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2735 (Rfree = 0.000) for 7654 atoms. Found 68 (68 requested) and removed 62 (34 requested) atoms. Cycle 22: After refmac, R = 0.2511 (Rfree = 0.000) for 7634 atoms. Found 68 (68 requested) and removed 44 (34 requested) atoms. Cycle 23: After refmac, R = 0.2338 (Rfree = 0.000) for 7642 atoms. Found 68 (68 requested) and removed 38 (34 requested) atoms. Cycle 24: After refmac, R = 0.2212 (Rfree = 0.000) for 7661 atoms. Found 66 (68 requested) and removed 42 (34 requested) atoms. Cycle 25: After refmac, R = 0.2142 (Rfree = 0.000) for 7679 atoms. Found 68 (68 requested) and removed 39 (34 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.98 3.23 Search for helices and strands: 0 residues in 0 chains, 7970 seeds are put forward NCS extension: 6 residues added (13 deleted due to clashes), 7976 seeds are put forward Round 1: 543 peptides, 87 chains. Longest chain 19 peptides. Score 0.489 Round 2: 576 peptides, 80 chains. Longest chain 19 peptides. Score 0.572 Round 3: 574 peptides, 77 chains. Longest chain 30 peptides. Score 0.586 Round 4: 588 peptides, 79 chains. Longest chain 26 peptides. Score 0.592 Round 5: 603 peptides, 75 chains. Longest chain 30 peptides. Score 0.629 Taking the results from Round 5 Chains 82, Residues 528, Estimated correctness of the model 48.6 % 12 chains (103 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 99.29 % complete ) and 16379 restraints for refining 7653 atoms. 13980 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2834 (Rfree = 0.000) for 7653 atoms. Found 68 (68 requested) and removed 64 (34 requested) atoms. Cycle 27: After refmac, R = 0.2624 (Rfree = 0.000) for 7615 atoms. Found 68 (68 requested) and removed 41 (34 requested) atoms. Cycle 28: After refmac, R = 0.2484 (Rfree = 0.000) for 7616 atoms. Found 68 (68 requested) and removed 48 (34 requested) atoms. Cycle 29: After refmac, R = 0.2387 (Rfree = 0.000) for 7613 atoms. Found 68 (68 requested) and removed 37 (34 requested) atoms. Cycle 30: After refmac, R = 0.2299 (Rfree = 0.000) for 7630 atoms. Found 68 (68 requested) and removed 42 (34 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.00 3.25 Search for helices and strands: 0 residues in 0 chains, 7939 seeds are put forward NCS extension: 10 residues added (14 deleted due to clashes), 7949 seeds are put forward Round 1: 479 peptides, 83 chains. Longest chain 18 peptides. Score 0.420 Round 2: 536 peptides, 75 chains. Longest chain 28 peptides. Score 0.549 Round 3: 539 peptides, 77 chains. Longest chain 21 peptides. Score 0.542 Round 4: 558 peptides, 74 chains. Longest chain 21 peptides. Score 0.583 Round 5: 558 peptides, 74 chains. Longest chain 21 peptides. Score 0.583 Taking the results from Round 5 Chains 77, Residues 484, Estimated correctness of the model 36.4 % 8 chains (43 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 99.29 % complete ) and 17286 restraints for refining 7654 atoms. 15282 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2786 (Rfree = 0.000) for 7654 atoms. Found 68 (68 requested) and removed 53 (34 requested) atoms. Cycle 32: After refmac, R = 0.2710 (Rfree = 0.000) for 7644 atoms. Found 68 (68 requested) and removed 38 (34 requested) atoms. Cycle 33: After refmac, R = 0.2641 (Rfree = 0.000) for 7660 atoms. Found 68 (68 requested) and removed 39 (34 requested) atoms. Cycle 34: After refmac, R = 0.2545 (Rfree = 0.000) for 7679 atoms. Found 69 (69 requested) and removed 37 (34 requested) atoms. Cycle 35: After refmac, R = 0.2546 (Rfree = 0.000) for 7704 atoms. Found 69 (69 requested) and removed 39 (34 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.96 3.21 Search for helices and strands: 0 residues in 0 chains, 8061 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 8093 seeds are put forward Round 1: 459 peptides, 81 chains. Longest chain 17 peptides. Score 0.402 Round 2: 519 peptides, 76 chains. Longest chain 28 peptides. Score 0.521 Round 3: 527 peptides, 74 chains. Longest chain 25 peptides. Score 0.544 Round 4: 544 peptides, 74 chains. Longest chain 28 peptides. Score 0.565 Round 5: 526 peptides, 71 chains. Longest chain 24 peptides. Score 0.559 Taking the results from Round 4 Chains 78, Residues 470, Estimated correctness of the model 31.3 % 5 chains (37 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 99.29 % complete ) and 17329 restraints for refining 7652 atoms. 15410 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2764 (Rfree = 0.000) for 7652 atoms. Found 68 (68 requested) and removed 54 (34 requested) atoms. Cycle 37: After refmac, R = 0.2608 (Rfree = 0.000) for 7638 atoms. Found 68 (68 requested) and removed 39 (34 requested) atoms. Cycle 38: After refmac, R = 0.2494 (Rfree = 0.000) for 7654 atoms. Found 68 (68 requested) and removed 37 (34 requested) atoms. Cycle 39: After refmac, R = 0.2422 (Rfree = 0.000) for 7676 atoms. Found 68 (68 requested) and removed 39 (34 requested) atoms. Cycle 40: After refmac, R = 0.2394 (Rfree = 0.000) for 7692 atoms. Found 69 (69 requested) and removed 38 (34 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.99 3.24 Search for helices and strands: 0 residues in 0 chains, 7966 seeds are put forward NCS extension: 9 residues added (13 deleted due to clashes), 7975 seeds are put forward Round 1: 456 peptides, 82 chains. Longest chain 17 peptides. Score 0.391 Round 2: 550 peptides, 81 chains. Longest chain 22 peptides. Score 0.533 Round 3: 545 peptides, 82 chains. Longest chain 19 peptides. Score 0.521 Round 4: 546 peptides, 77 chains. Longest chain 37 peptides. Score 0.551 Round 5: 545 peptides, 78 chains. Longest chain 25 peptides. Score 0.544 Taking the results from Round 4 Chains 80, Residues 469, Estimated correctness of the model 27.2 % 8 chains (74 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 99.29 % complete ) and 16983 restraints for refining 7654 atoms. 14897 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2695 (Rfree = 0.000) for 7654 atoms. Found 68 (68 requested) and removed 75 (34 requested) atoms. Cycle 42: After refmac, R = 0.2602 (Rfree = 0.000) for 7622 atoms. Found 68 (68 requested) and removed 37 (34 requested) atoms. Cycle 43: After refmac, R = 0.2538 (Rfree = 0.000) for 7634 atoms. Found 68 (68 requested) and removed 45 (34 requested) atoms. Cycle 44: After refmac, R = 0.2407 (Rfree = 0.000) for 7647 atoms. Found 68 (68 requested) and removed 36 (34 requested) atoms. Cycle 45: After refmac, R = 0.2369 (Rfree = 0.000) for 7664 atoms. Found 68 (68 requested) and removed 40 (34 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.97 3.22 Search for helices and strands: 0 residues in 0 chains, 7948 seeds are put forward NCS extension: 19 residues added (6 deleted due to clashes), 7967 seeds are put forward Round 1: 409 peptides, 76 chains. Longest chain 11 peptides. Score 0.356 Round 2: 480 peptides, 70 chains. Longest chain 14 peptides. Score 0.504 Round 3: 479 peptides, 67 chains. Longest chain 21 peptides. Score 0.521 Round 4: 447 peptides, 57 chains. Longest chain 21 peptides. Score 0.539 Round 5: 480 peptides, 64 chains. Longest chain 23 peptides. Score 0.540 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 67, Residues 416, Estimated correctness of the model 23.9 % 6 chains (51 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 2pbl-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 79 A and 92 A 66 chains (416 residues) following loop building 5 chains (63 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16523 reflections ( 99.29 % complete ) and 17440 restraints for refining 7654 atoms. 15624 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2702 (Rfree = 0.000) for 7654 atoms. Found 0 (68 requested) and removed 34 (34 requested) atoms. Cycle 47: After refmac, R = 0.2657 (Rfree = 0.000) for 7595 atoms. Found 0 (68 requested) and removed 34 (34 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2607 (Rfree = 0.000) for 7554 atoms. Found 0 (67 requested) and removed 33 (33 requested) atoms. Cycle 49: After refmac, R = 0.2522 (Rfree = 0.000) for 7515 atoms. TimeTaking 84