Mon 24 Dec 00:11:40 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-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pbl-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pbl-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pbl-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/2pbl-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pbl-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 00:11:45 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/mrncs/ArpWArp/wArpResults/WorkingDir/2pbl-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pbl-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 721 and 0 Target number of residues in the AU: 721 Target solvent content: 0.6136 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-3.4-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: 4 Cell parameters: 77.197 74.438 95.727 90.000 113.394 90.000 Input sequence file: 2pbl-3.4-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 3.400 Wilson plot Bfac: 58.38 13810 reflections ( 99.18 % complete ) and 0 restraints for refining 9263 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3464 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4212 (Rfree = 0.000) for 9263 atoms. Found 69 (69 requested) and removed 145 (34 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.06 3.32 Search for helices and strands: 0 residues in 0 chains, 9437 seeds are put forward NCS extension: 0 residues added, 9437 seeds are put forward Round 1: 373 peptides, 78 chains. Longest chain 9 peptides. Score 0.280 Round 2: 517 peptides, 92 chains. Longest chain 14 peptides. Score 0.419 Round 3: 537 peptides, 89 chains. Longest chain 15 peptides. Score 0.468 Round 4: 556 peptides, 83 chains. Longest chain 16 peptides. Score 0.530 Round 5: 552 peptides, 80 chains. Longest chain 18 peptides. Score 0.542 Taking the results from Round 5 Chains 84, Residues 472, Estimated correctness of the model 8.6 % 13 chains (103 residues) have been docked in sequence ------------------------------------------------------ 13810 reflections ( 99.18 % complete ) and 16139 restraints for refining 7619 atoms. 14006 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3370 (Rfree = 0.000) for 7619 atoms. Found 57 (57 requested) and removed 98 (28 requested) atoms. Cycle 2: After refmac, R = 0.3217 (Rfree = 0.000) for 7435 atoms. Found 57 (57 requested) and removed 53 (28 requested) atoms. Cycle 3: After refmac, R = 0.3175 (Rfree = 0.000) for 7352 atoms. Found 56 (56 requested) and removed 50 (28 requested) atoms. Cycle 4: After refmac, R = 0.3099 (Rfree = 0.000) for 7295 atoms. Found 55 (55 requested) and removed 45 (27 requested) atoms. Cycle 5: After refmac, R = 0.3010 (Rfree = 0.000) for 7270 atoms. Found 55 (55 requested) and removed 42 (27 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.08 3.34 Search for helices and strands: 0 residues in 0 chains, 7581 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 7594 seeds are put forward Round 1: 542 peptides, 95 chains. Longest chain 15 peptides. Score 0.438 Round 2: 615 peptides, 91 chains. Longest chain 20 peptides. Score 0.561 Round 3: 637 peptides, 86 chains. Longest chain 20 peptides. Score 0.613 Round 4: 639 peptides, 90 chains. Longest chain 20 peptides. Score 0.595 Round 5: 617 peptides, 77 chains. Longest chain 25 peptides. Score 0.635 Taking the results from Round 5 Chains 80, Residues 540, Estimated correctness of the model 39.7 % 9 chains (88 residues) have been docked in sequence ------------------------------------------------------ 13810 reflections ( 99.18 % complete ) and 16250 restraints for refining 7573 atoms. 13890 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3154 (Rfree = 0.000) for 7573 atoms. Found 57 (57 requested) and removed 107 (28 requested) atoms. Cycle 7: After refmac, R = 0.3010 (Rfree = 0.000) for 7407 atoms. Found 56 (56 requested) and removed 47 (28 requested) atoms. Cycle 8: After refmac, R = 0.2930 (Rfree = 0.000) for 7354 atoms. Found 55 (55 requested) and removed 40 (27 requested) atoms. Cycle 9: After refmac, R = 0.2763 (Rfree = 0.000) for 7341 atoms. Found 55 (55 requested) and removed 38 (27 requested) atoms. Cycle 10: After refmac, R = 0.2678 (Rfree = 0.000) for 7333 atoms. Found 55 (55 requested) and removed 35 (27 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.12 3.38 Search for helices and strands: 0 residues in 0 chains, 7646 seeds are put forward NCS extension: 24 residues added (7 deleted due to clashes), 7670 seeds are put forward Round 1: 545 peptides, 89 chains. Longest chain 15 peptides. Score 0.479 Round 2: 624 peptides, 86 chains. Longest chain 22 peptides. Score 0.598 Round 3: 653 peptides, 83 chains. Longest chain 22 peptides. Score 0.645 Round 4: 646 peptides, 78 chains. Longest chain 26 peptides. Score 0.661 Round 5: 633 peptides, 84 chains. Longest chain 27 peptides. Score 0.618 Taking the results from Round 4 Chains 83, Residues 568, Estimated correctness of the model 47.3 % 9 chains (84 residues) have been docked in sequence ------------------------------------------------------ 13810 reflections ( 99.18 % complete ) and 15958 restraints for refining 7589 atoms. 13488 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2971 (Rfree = 0.000) for 7589 atoms. Found 57 (57 requested) and removed 80 (28 requested) atoms. Cycle 12: After refmac, R = 0.2804 (Rfree = 0.000) for 7514 atoms. Found 57 (57 requested) and removed 51 (28 requested) atoms. Cycle 13: After refmac, R = 0.2732 (Rfree = 0.000) for 7486 atoms. Found 56 (56 requested) and removed 37 (28 requested) atoms. Cycle 14: After refmac, R = 0.2695 (Rfree = 0.000) for 7483 atoms. Found 56 (56 requested) and removed 44 (28 requested) atoms. Cycle 15: After refmac, R = 0.2643 (Rfree = 0.000) for 7473 atoms. Found 56 (56 requested) and removed 42 (28 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.15 3.41 Search for helices and strands: 0 residues in 0 chains, 7800 seeds are put forward NCS extension: 14 residues added (7 deleted due to clashes), 7814 seeds are put forward Round 1: 548 peptides, 87 chains. Longest chain 22 peptides. Score 0.495 Round 2: 622 peptides, 83 chains. Longest chain 26 peptides. Score 0.611 Round 3: 617 peptides, 79 chains. Longest chain 26 peptides. Score 0.625 Round 4: 634 peptides, 80 chains. Longest chain 33 peptides. Score 0.639 Round 5: 636 peptides, 81 chains. Longest chain 24 peptides. Score 0.636 Taking the results from Round 4 Chains 86, Residues 554, Estimated correctness of the model 40.9 % 7 chains (62 residues) have been docked in sequence ------------------------------------------------------ 13810 reflections ( 99.18 % complete ) and 16472 restraints for refining 7621 atoms. 14133 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3085 (Rfree = 0.000) for 7621 atoms. Found 57 (57 requested) and removed 78 (28 requested) atoms. Cycle 17: After refmac, R = 0.2815 (Rfree = 0.000) for 7546 atoms. Found 57 (57 requested) and removed 53 (28 requested) atoms. Cycle 18: After refmac, R = 0.2604 (Rfree = 0.000) for 7511 atoms. Found 57 (57 requested) and removed 43 (28 requested) atoms. Cycle 19: After refmac, R = 0.2540 (Rfree = 0.000) for 7506 atoms. Found 56 (56 requested) and removed 31 (28 requested) atoms. Cycle 20: After refmac, R = 0.2465 (Rfree = 0.000) for 7517 atoms. Found 56 (56 requested) and removed 40 (28 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.15 3.41 Search for helices and strands: 0 residues in 0 chains, 7796 seeds are put forward NCS extension: 9 residues added (21 deleted due to clashes), 7805 seeds are put forward Round 1: 555 peptides, 90 chains. Longest chain 18 peptides. Score 0.487 Round 2: 598 peptides, 75 chains. Longest chain 31 peptides. Score 0.624 Round 3: 615 peptides, 87 chains. Longest chain 17 peptides. Score 0.582 Round 4: 626 peptides, 81 chains. Longest chain 35 peptides. Score 0.625 Round 5: 621 peptides, 82 chains. Longest chain 25 peptides. Score 0.615 Taking the results from Round 4 Chains 86, Residues 545, Estimated correctness of the model 36.6 % 9 chains (86 residues) have been docked in sequence ------------------------------------------------------ 13810 reflections ( 99.18 % complete ) and 16208 restraints for refining 7622 atoms. 13812 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2828 (Rfree = 0.000) for 7622 atoms. Found 57 (57 requested) and removed 71 (28 requested) atoms. Cycle 22: After refmac, R = 0.2747 (Rfree = 0.000) for 7558 atoms. Found 57 (57 requested) and removed 38 (28 requested) atoms. Cycle 23: After refmac, R = 0.2736 (Rfree = 0.000) for 7547 atoms. Found 57 (57 requested) and removed 41 (28 requested) atoms. Cycle 24: After refmac, R = 0.2667 (Rfree = 0.000) for 7546 atoms. Found 57 (57 requested) and removed 36 (28 requested) atoms. Cycle 25: After refmac, R = 0.2585 (Rfree = 0.000) for 7552 atoms. Found 57 (57 requested) and removed 34 (28 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.17 3.44 Search for helices and strands: 0 residues in 0 chains, 7837 seeds are put forward NCS extension: 4 residues added (19 deleted due to clashes), 7841 seeds are put forward Round 1: 509 peptides, 84 chains. Longest chain 21 peptides. Score 0.458 Round 2: 577 peptides, 82 chains. Longest chain 23 peptides. Score 0.562 Round 3: 588 peptides, 84 chains. Longest chain 18 peptides. Score 0.565 Round 4: 573 peptides, 75 chains. Longest chain 30 peptides. Score 0.595 Round 5: 586 peptides, 77 chains. Longest chain 25 peptides. Score 0.600 Taking the results from Round 5 Chains 83, Residues 509, Estimated correctness of the model 28.7 % 6 chains (49 residues) have been docked in sequence ------------------------------------------------------ 13810 reflections ( 99.18 % complete ) and 16946 restraints for refining 7621 atoms. 14847 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2995 (Rfree = 0.000) for 7621 atoms. Found 57 (57 requested) and removed 57 (28 requested) atoms. Cycle 27: After refmac, R = 0.2965 (Rfree = 0.000) for 7571 atoms. Found 57 (57 requested) and removed 36 (28 requested) atoms. Cycle 28: After refmac, R = 0.2749 (Rfree = 0.000) for 7564 atoms. Found 57 (57 requested) and removed 38 (28 requested) atoms. Cycle 29: After refmac, R = 0.2706 (Rfree = 0.000) for 7569 atoms. Found 57 (57 requested) and removed 37 (28 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2719 (Rfree = 0.000) for 7571 atoms. Found 57 (57 requested) and removed 37 (28 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.12 3.38 Search for helices and strands: 0 residues in 0 chains, 7826 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 7843 seeds are put forward Round 1: 430 peptides, 69 chains. Longest chain 25 peptides. Score 0.438 Round 2: 497 peptides, 72 chains. Longest chain 25 peptides. Score 0.515 Round 3: 507 peptides, 73 chains. Longest chain 27 peptides. Score 0.523 Round 4: 520 peptides, 71 chains. Longest chain 21 peptides. Score 0.552 Round 5: 514 peptides, 71 chains. Longest chain 21 peptides. Score 0.544 Taking the results from Round 4 Chains 73, Residues 449, Estimated correctness of the model 12.2 % 9 chains (63 residues) have been docked in sequence ------------------------------------------------------ 13810 reflections ( 99.18 % complete ) and 16848 restraints for refining 7603 atoms. 14905 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3004 (Rfree = 0.000) for 7603 atoms. Found 57 (57 requested) and removed 66 (28 requested) atoms. Cycle 32: After refmac, R = 0.2845 (Rfree = 0.000) for 7552 atoms. Found 57 (57 requested) and removed 36 (28 requested) atoms. Cycle 33: After refmac, R = 0.2728 (Rfree = 0.000) for 7536 atoms. Found 57 (57 requested) and removed 36 (28 requested) atoms. Cycle 34: After refmac, R = 0.2685 (Rfree = 0.000) for 7544 atoms. Found 57 (57 requested) and removed 35 (28 requested) atoms. Cycle 35: After refmac, R = 0.2584 (Rfree = 0.000) for 7548 atoms. Found 57 (57 requested) and removed 35 (28 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.13 3.39 Search for helices and strands: 0 residues in 0 chains, 7797 seeds are put forward NCS extension: 7 residues added (9 deleted due to clashes), 7804 seeds are put forward Round 1: 438 peptides, 82 chains. Longest chain 15 peptides. Score 0.362 Round 2: 524 peptides, 84 chains. Longest chain 15 peptides. Score 0.480 Round 3: 532 peptides, 87 chains. Longest chain 15 peptides. Score 0.473 Round 4: 523 peptides, 77 chains. Longest chain 19 peptides. Score 0.521 Round 5: 511 peptides, 78 chains. Longest chain 18 peptides. Score 0.498 Taking the results from Round 4 Chains 77, Residues 446, Estimated correctness of the model 0.8 % 5 chains (29 residues) have been docked in sequence ------------------------------------------------------ 13810 reflections ( 99.18 % complete ) and 17308 restraints for refining 7622 atoms. 15515 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2849 (Rfree = 0.000) for 7622 atoms. Found 57 (57 requested) and removed 58 (28 requested) atoms. Cycle 37: After refmac, R = 0.2695 (Rfree = 0.000) for 7580 atoms. Found 57 (57 requested) and removed 42 (28 requested) atoms. Cycle 38: After refmac, R = 0.2639 (Rfree = 0.000) for 7580 atoms. Found 57 (57 requested) and removed 33 (28 requested) atoms. Cycle 39: After refmac, R = 0.2540 (Rfree = 0.000) for 7588 atoms. Found 57 (57 requested) and removed 38 (28 requested) atoms. Cycle 40: After refmac, R = 0.2465 (Rfree = 0.000) for 7597 atoms. Found 57 (57 requested) and removed 35 (28 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.12 3.38 Search for helices and strands: 0 residues in 0 chains, 7840 seeds are put forward NCS extension: 19 residues added (6 deleted due to clashes), 7859 seeds are put forward Round 1: 419 peptides, 80 chains. Longest chain 16 peptides. Score 0.345 Round 2: 458 peptides, 72 chains. Longest chain 21 peptides. Score 0.460 Round 3: 437 peptides, 65 chains. Longest chain 18 peptides. Score 0.474 Round 4: 453 peptides, 64 chains. Longest chain 19 peptides. Score 0.504 Round 5: 447 peptides, 66 chains. Longest chain 15 peptides. Score 0.482 Taking the results from Round 4 Chains 65, Residues 389, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 13810 reflections ( 99.18 % complete ) and 17635 restraints for refining 7599 atoms. 16111 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2660 (Rfree = 0.000) for 7599 atoms. Found 57 (57 requested) and removed 49 (28 requested) atoms. Cycle 42: After refmac, R = 0.2651 (Rfree = 0.000) for 7577 atoms. Found 57 (57 requested) and removed 51 (28 requested) atoms. Cycle 43: After refmac, R = 0.2672 (Rfree = 0.000) for 7577 atoms. Found 57 (57 requested) and removed 40 (28 requested) atoms. Cycle 44: After refmac, R = 0.2679 (Rfree = 0.000) for 7583 atoms. Found 57 (57 requested) and removed 36 (28 requested) atoms. Cycle 45: After refmac, R = 0.2540 (Rfree = 0.000) for 7600 atoms. Found 57 (57 requested) and removed 34 (28 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.13 3.39 Search for helices and strands: 0 residues in 0 chains, 7876 seeds are put forward NCS extension: 10 residues added (5 deleted due to clashes), 7886 seeds are put forward Round 1: 371 peptides, 71 chains. Longest chain 11 peptides. Score 0.328 Round 2: 421 peptides, 70 chains. Longest chain 20 peptides. Score 0.417 Round 3: 431 peptides, 68 chains. Longest chain 16 peptides. Score 0.446 Round 4: 413 peptides, 58 chains. Longest chain 19 peptides. Score 0.485 Round 5: 393 peptides, 62 chains. Longest chain 15 peptides. Score 0.428 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 60, Residues 355, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2pbl-3_warpNtrace.pdb as input Building loops using Loopy2018 60 chains (355 residues) following loop building 3 chains (18 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13810 reflections ( 99.18 % complete ) and 17610 restraints for refining 7555 atoms. 16207 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2776 (Rfree = 0.000) for 7555 atoms. Found 0 (57 requested) and removed 28 (28 requested) atoms. Cycle 47: After refmac, R = 0.2660 (Rfree = 0.000) for 7512 atoms. Found 0 (56 requested) and removed 28 (28 requested) atoms. Cycle 48: After refmac, R = 0.2687 (Rfree = 0.000) for 7475 atoms. Found 0 (56 requested) and removed 28 (28 requested) atoms. Cycle 49: After refmac, R = 0.2579 (Rfree = 0.000) for 7436 atoms. Found 0 (56 requested) and removed 28 (28 requested) atoms. Writing output files ... TimeTaking 90.1