Mon 24 Dec 00:10:40 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 2pbl-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pbl-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pbl-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pbl-3.2-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/2pbl-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pbl-3.2-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 00:10:44 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/2pbl-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pbl-3.2-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 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-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: 4 Cell parameters: 77.197 74.438 95.727 90.000 113.394 90.000 Input sequence file: 2pbl-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 8384 target number of atoms Had to go as low as 0.70 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 9278 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3430 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4180 (Rfree = 0.000) for 9278 atoms. Found 83 (83 requested) and removed 169 (41 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.88 3.12 Search for helices and strands: 0 residues in 0 chains, 9400 seeds are put forward NCS extension: 0 residues added, 9400 seeds are put forward Round 1: 424 peptides, 88 chains. Longest chain 11 peptides. Score 0.296 Round 2: 527 peptides, 90 chains. Longest chain 12 peptides. Score 0.447 Round 3: 583 peptides, 91 chains. Longest chain 21 peptides. Score 0.519 Round 4: 573 peptides, 82 chains. Longest chain 22 peptides. Score 0.557 Round 5: 602 peptides, 81 chains. Longest chain 23 peptides. Score 0.598 Taking the results from Round 5 Chains 85, Residues 521, Estimated correctness of the model 40.5 % 10 chains (82 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 99.29 % complete ) and 15942 restraints for refining 7654 atoms. 13643 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3392 (Rfree = 0.000) for 7654 atoms. Found 68 (68 requested) and removed 103 (34 requested) atoms. Cycle 2: After refmac, R = 0.3083 (Rfree = 0.000) for 7501 atoms. Found 68 (68 requested) and removed 52 (34 requested) atoms. Cycle 3: After refmac, R = 0.2903 (Rfree = 0.000) for 7460 atoms. Found 67 (67 requested) and removed 53 (33 requested) atoms. Cycle 4: After refmac, R = 0.2766 (Rfree = 0.000) for 7443 atoms. Found 67 (67 requested) and removed 56 (33 requested) atoms. Cycle 5: After refmac, R = 0.2644 (Rfree = 0.000) for 7434 atoms. Found 66 (66 requested) and removed 44 (33 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.98 3.23 Search for helices and strands: 0 residues in 0 chains, 7750 seeds are put forward NCS extension: 18 residues added (5 deleted due to clashes), 7768 seeds are put forward Round 1: 568 peptides, 93 chains. Longest chain 20 peptides. Score 0.487 Round 2: 642 peptides, 91 chains. Longest chain 23 peptides. Score 0.593 Round 3: 660 peptides, 84 chains. Longest chain 25 peptides. Score 0.647 Round 4: 644 peptides, 80 chains. Longest chain 20 peptides. Score 0.649 Round 5: 676 peptides, 85 chains. Longest chain 32 peptides. Score 0.659 Taking the results from Round 5 Chains 91, Residues 591, Estimated correctness of the model 56.0 % 12 chains (141 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 99.29 % complete ) and 15372 restraints for refining 7654 atoms. 12545 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2997 (Rfree = 0.000) for 7654 atoms. Found 68 (68 requested) and removed 91 (34 requested) atoms. Cycle 7: After refmac, R = 0.2794 (Rfree = 0.000) for 7572 atoms. Found 68 (68 requested) and removed 50 (34 requested) atoms. Cycle 8: After refmac, R = 0.2667 (Rfree = 0.000) for 7554 atoms. Found 68 (68 requested) and removed 43 (34 requested) atoms. Cycle 9: After refmac, R = 0.2548 (Rfree = 0.000) for 7563 atoms. Found 68 (68 requested) and removed 47 (34 requested) atoms. Cycle 10: After refmac, R = 0.2475 (Rfree = 0.000) for 7567 atoms. Found 68 (68 requested) and removed 39 (34 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.97 3.22 Search for helices and strands: 0 residues in 0 chains, 7879 seeds are put forward NCS extension: 13 residues added (19 deleted due to clashes), 7892 seeds are put forward Round 1: 623 peptides, 89 chains. Longest chain 22 peptides. Score 0.581 Round 2: 662 peptides, 72 chains. Longest chain 31 peptides. Score 0.702 Round 3: 671 peptides, 76 chains. Longest chain 31 peptides. Score 0.694 Round 4: 663 peptides, 74 chains. Longest chain 26 peptides. Score 0.695 Round 5: 695 peptides, 77 chains. Longest chain 31 peptides. Score 0.711 Taking the results from Round 5 Chains 84, Residues 618, Estimated correctness of the model 67.5 % 14 chains (177 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 146 C and 155 C 83 chains (625 residues) following loop building 13 chains (185 residues) in sequence following loop building ------------------------------------------------------ 16523 reflections ( 99.29 % complete ) and 14789 restraints for refining 7654 atoms. 11637 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3027 (Rfree = 0.000) for 7654 atoms. Found 68 (68 requested) and removed 114 (34 requested) atoms. Cycle 12: After refmac, R = 0.2771 (Rfree = 0.000) for 7554 atoms. Found 67 (67 requested) and removed 47 (34 requested) atoms. Cycle 13: After refmac, R = 0.2612 (Rfree = 0.000) for 7543 atoms. Found 64 (64 requested) and removed 38 (33 requested) atoms. Cycle 14: After refmac, R = 0.2492 (Rfree = 0.000) for 7552 atoms. Found 63 (63 requested) and removed 46 (33 requested) atoms. Cycle 15: After refmac, R = 0.2405 (Rfree = 0.000) for 7544 atoms. Found 62 (62 requested) and removed 44 (33 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.97 3.22 Search for helices and strands: 0 residues in 0 chains, 7866 seeds are put forward NCS extension: 12 residues added (44 deleted due to clashes), 7878 seeds are put forward Round 1: 629 peptides, 88 chains. Longest chain 23 peptides. Score 0.593 Round 2: 675 peptides, 81 chains. Longest chain 36 peptides. Score 0.676 Round 3: 693 peptides, 74 chains. Longest chain 34 peptides. Score 0.721 Round 4: 713 peptides, 72 chains. Longest chain 35 peptides. Score 0.745 Round 5: 700 peptides, 80 chains. Longest chain 26 peptides. Score 0.703 Taking the results from Round 4 Chains 86, Residues 641, Estimated correctness of the model 74.1 % 16 chains (260 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 212 B and 219 B 85 chains (645 residues) following loop building 15 chains (266 residues) in sequence following loop building ------------------------------------------------------ 16523 reflections ( 99.29 % complete ) and 13660 restraints for refining 7654 atoms. 10098 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2973 (Rfree = 0.000) for 7654 atoms. Found 61 (61 requested) and removed 109 (34 requested) atoms. Cycle 17: After refmac, R = 0.2727 (Rfree = 0.000) for 7536 atoms. Found 60 (60 requested) and removed 48 (34 requested) atoms. Cycle 18: After refmac, R = 0.2570 (Rfree = 0.000) for 7520 atoms. Found 58 (58 requested) and removed 37 (33 requested) atoms. Cycle 19: After refmac, R = 0.2437 (Rfree = 0.000) for 7523 atoms. Found 56 (56 requested) and removed 39 (33 requested) atoms. Cycle 20: After refmac, R = 0.2353 (Rfree = 0.000) for 7523 atoms. Found 55 (55 requested) and removed 37 (33 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.00 3.25 Search for helices and strands: 0 residues in 0 chains, 7814 seeds are put forward NCS extension: 32 residues added (64 deleted due to clashes), 7846 seeds are put forward Round 1: 588 peptides, 83 chains. Longest chain 20 peptides. Score 0.571 Round 2: 643 peptides, 79 chains. Longest chain 21 peptides. Score 0.653 Round 3: 653 peptides, 73 chains. Longest chain 28 peptides. Score 0.690 Round 4: 652 peptides, 77 chains. Longest chain 33 peptides. Score 0.671 Round 5: 630 peptides, 77 chains. Longest chain 21 peptides. Score 0.649 Taking the results from Round 3 Chains 76, Residues 580, Estimated correctness of the model 63.0 % 9 chains (95 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 99.29 % complete ) and 16232 restraints for refining 7652 atoms. 13649 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2639 (Rfree = 0.000) for 7652 atoms. Found 54 (54 requested) and removed 55 (34 requested) atoms. Cycle 22: After refmac, R = 0.2487 (Rfree = 0.000) for 7628 atoms. Found 54 (54 requested) and removed 42 (34 requested) atoms. Cycle 23: After refmac, R = 0.2390 (Rfree = 0.000) for 7623 atoms. Found 54 (54 requested) and removed 39 (34 requested) atoms. Cycle 24: After refmac, R = 0.2293 (Rfree = 0.000) for 7630 atoms. Found 54 (54 requested) and removed 39 (34 requested) atoms. Cycle 25: After refmac, R = 0.2305 (Rfree = 0.000) for 7636 atoms. Found 54 (54 requested) and removed 39 (34 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.01 3.26 Search for helices and strands: 0 residues in 0 chains, 7936 seeds are put forward NCS extension: 9 residues added (8 deleted due to clashes), 7945 seeds are put forward Round 1: 574 peptides, 82 chains. Longest chain 27 peptides. Score 0.559 Round 2: 640 peptides, 75 chains. Longest chain 31 peptides. Score 0.668 Round 3: 643 peptides, 69 chains. Longest chain 23 peptides. Score 0.698 Round 4: 644 peptides, 72 chains. Longest chain 31 peptides. Score 0.685 Round 5: 636 peptides, 69 chains. Longest chain 30 peptides. Score 0.691 Taking the results from Round 3 Chains 73, Residues 574, Estimated correctness of the model 64.8 % 9 chains (117 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 99.29 % complete ) and 15944 restraints for refining 7654 atoms. 13268 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2614 (Rfree = 0.000) for 7654 atoms. Found 54 (54 requested) and removed 76 (34 requested) atoms. Cycle 27: After refmac, R = 0.2433 (Rfree = 0.000) for 7593 atoms. Found 54 (54 requested) and removed 37 (34 requested) atoms. Cycle 28: After refmac, R = 0.2397 (Rfree = 0.000) for 7584 atoms. Found 54 (54 requested) and removed 40 (34 requested) atoms. Cycle 29: After refmac, R = 0.2313 (Rfree = 0.000) for 7585 atoms. Found 54 (54 requested) and removed 37 (34 requested) atoms. Cycle 30: After refmac, R = 0.2250 (Rfree = 0.000) for 7589 atoms. Found 54 (54 requested) and removed 35 (34 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.01 3.26 Search for helices and strands: 0 residues in 0 chains, 7882 seeds are put forward NCS extension: 12 residues added (15 deleted due to clashes), 7894 seeds are put forward Round 1: 552 peptides, 82 chains. Longest chain 21 peptides. Score 0.530 Round 2: 611 peptides, 74 chains. Longest chain 26 peptides. Score 0.643 Round 3: 586 peptides, 74 chains. Longest chain 30 peptides. Score 0.615 Round 4: 626 peptides, 73 chains. Longest chain 30 peptides. Score 0.663 Round 5: 601 peptides, 74 chains. Longest chain 23 peptides. Score 0.632 Taking the results from Round 4 Chains 79, Residues 553, Estimated correctness of the model 56.9 % 9 chains (101 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 99.29 % complete ) and 16120 restraints for refining 7653 atoms. 13559 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2664 (Rfree = 0.000) for 7653 atoms. Found 54 (54 requested) and removed 57 (34 requested) atoms. Cycle 32: After refmac, R = 0.2545 (Rfree = 0.000) for 7623 atoms. Found 54 (54 requested) and removed 42 (34 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2475 (Rfree = 0.000) for 7608 atoms. Found 54 (54 requested) and removed 40 (34 requested) atoms. Cycle 34: After refmac, R = 0.2412 (Rfree = 0.000) for 7617 atoms. Found 54 (54 requested) and removed 41 (34 requested) atoms. Cycle 35: After refmac, R = 0.2365 (Rfree = 0.000) for 7620 atoms. Found 54 (54 requested) and removed 37 (34 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.98 3.23 Search for helices and strands: 0 residues in 0 chains, 7929 seeds are put forward NCS extension: 9 residues added (7 deleted due to clashes), 7938 seeds are put forward Round 1: 510 peptides, 76 chains. Longest chain 14 peptides. Score 0.509 Round 2: 582 peptides, 77 chains. Longest chain 20 peptides. Score 0.595 Round 3: 579 peptides, 77 chains. Longest chain 26 peptides. Score 0.592 Round 4: 602 peptides, 73 chains. Longest chain 26 peptides. Score 0.638 Round 5: 596 peptides, 73 chains. Longest chain 21 peptides. Score 0.632 Taking the results from Round 4 Chains 77, Residues 529, Estimated correctness of the model 50.9 % 9 chains (100 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 99.29 % complete ) and 16202 restraints for refining 7653 atoms. 13737 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2633 (Rfree = 0.000) for 7653 atoms. Found 54 (54 requested) and removed 53 (34 requested) atoms. Cycle 37: After refmac, R = 0.2459 (Rfree = 0.000) for 7621 atoms. Found 54 (54 requested) and removed 38 (34 requested) atoms. Cycle 38: After refmac, R = 0.2383 (Rfree = 0.000) for 7607 atoms. Found 54 (54 requested) and removed 37 (34 requested) atoms. Cycle 39: After refmac, R = 0.2294 (Rfree = 0.000) for 7615 atoms. Found 54 (54 requested) and removed 37 (34 requested) atoms. Cycle 40: After refmac, R = 0.2233 (Rfree = 0.000) for 7628 atoms. Found 54 (54 requested) and removed 40 (34 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.99 3.24 Search for helices and strands: 0 residues in 0 chains, 7896 seeds are put forward NCS extension: 21 residues added (10 deleted due to clashes), 7917 seeds are put forward Round 1: 508 peptides, 74 chains. Longest chain 23 peptides. Score 0.518 Round 2: 577 peptides, 74 chains. Longest chain 19 peptides. Score 0.605 Round 3: 542 peptides, 75 chains. Longest chain 18 peptides. Score 0.557 Round 4: 551 peptides, 75 chains. Longest chain 25 peptides. Score 0.569 Round 5: 550 peptides, 71 chains. Longest chain 25 peptides. Score 0.589 Taking the results from Round 2 Chains 77, Residues 503, Estimated correctness of the model 42.4 % 6 chains (53 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 99.29 % complete ) and 16740 restraints for refining 7652 atoms. 14592 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2510 (Rfree = 0.000) for 7652 atoms. Found 54 (54 requested) and removed 49 (34 requested) atoms. Cycle 42: After refmac, R = 0.2355 (Rfree = 0.000) for 7643 atoms. Found 54 (54 requested) and removed 37 (34 requested) atoms. Cycle 43: After refmac, R = 0.2358 (Rfree = 0.000) for 7647 atoms. Found 54 (54 requested) and removed 40 (34 requested) atoms. Cycle 44: After refmac, R = 0.2305 (Rfree = 0.000) for 7651 atoms. Found 54 (54 requested) and removed 40 (34 requested) atoms. Cycle 45: After refmac, R = 0.2300 (Rfree = 0.000) for 7651 atoms. Found 54 (54 requested) and removed 40 (34 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.00 3.25 Search for helices and strands: 0 residues in 0 chains, 7916 seeds are put forward NCS extension: 15 residues added (8 deleted due to clashes), 7931 seeds are put forward Round 1: 476 peptides, 77 chains. Longest chain 15 peptides. Score 0.454 Round 2: 546 peptides, 72 chains. Longest chain 23 peptides. Score 0.579 Round 3: 538 peptides, 71 chains. Longest chain 19 peptides. Score 0.575 Round 4: 547 peptides, 71 chains. Longest chain 28 peptides. Score 0.586 Round 5: 542 peptides, 75 chains. Longest chain 23 peptides. Score 0.557 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 72, Residues 476, Estimated correctness of the model 37.2 % 5 chains (40 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2pbl-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 165 A and 178 A 71 chains (486 residues) following loop building 4 chains (52 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16523 reflections ( 99.29 % complete ) and 17060 restraints for refining 7654 atoms. 15038 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2606 (Rfree = 0.000) for 7654 atoms. Found 0 (54 requested) and removed 34 (34 requested) atoms. Cycle 47: After refmac, R = 0.2509 (Rfree = 0.000) for 7597 atoms. Found 0 (54 requested) and removed 34 (34 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2395 (Rfree = 0.000) for 7554 atoms. Found 0 (54 requested) and removed 33 (33 requested) atoms. Cycle 49: After refmac, R = 0.2298 (Rfree = 0.000) for 7510 atoms. TimeTaking 72.32