Mon 24 Dec 00:38:34 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 1ztc-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1ztc-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1ztc-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1ztc-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/1ztc-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1ztc-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 00:38:39 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/1ztc-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1ztc-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 1182 and 0 Target number of residues in the AU: 1182 Target solvent content: 0.6324 Checking the provided sequence file Detected sequence length: 221 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 884 Adjusted target solvent content: 0.73 Input MTZ file: 1ztc-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: 19 Cell parameters: 89.783 127.343 152.224 90.000 90.000 90.000 Input sequence file: 1ztc-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 7072 target number of atoms Had to go as low as 1.05 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: 97.673 3.200 Wilson plot Bfac: 67.79 29180 reflections ( 98.97 % complete ) and 0 restraints for refining 7860 atoms. Observations/parameters ratio is 0.93 ------------------------------------------------------ Starting model: R = 0.3174 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3068 (Rfree = 0.000) for 7860 atoms. Found 70 (70 requested) and removed 49 (35 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 2.36 Search for helices and strands: 0 residues in 0 chains, 8009 seeds are put forward NCS extension: 0 residues added, 8009 seeds are put forward Round 1: 619 peptides, 77 chains. Longest chain 29 peptides. Score 0.495 Round 2: 701 peptides, 56 chains. Longest chain 41 peptides. Score 0.633 Round 3: 694 peptides, 58 chains. Longest chain 43 peptides. Score 0.622 Round 4: 705 peptides, 58 chains. Longest chain 51 peptides. Score 0.629 Round 5: 708 peptides, 56 chains. Longest chain 51 peptides. Score 0.638 Taking the results from Round 5 Chains 57, Residues 652, Estimated correctness of the model 50.9 % 7 chains (228 residues) have been docked in sequence ------------------------------------------------------ 29180 reflections ( 98.97 % complete ) and 11920 restraints for refining 6795 atoms. 8372 conditional restraints added. Observations/parameters ratio is 1.07 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2744 (Rfree = 0.000) for 6795 atoms. Found 61 (61 requested) and removed 88 (30 requested) atoms. Cycle 2: After refmac, R = 0.2509 (Rfree = 0.000) for 6657 atoms. Found 60 (60 requested) and removed 48 (30 requested) atoms. Cycle 3: After refmac, R = 0.2389 (Rfree = 0.000) for 6637 atoms. Found 57 (59 requested) and removed 36 (29 requested) atoms. Cycle 4: After refmac, R = 0.2383 (Rfree = 0.000) for 6645 atoms. Found 54 (59 requested) and removed 44 (29 requested) atoms. Cycle 5: After refmac, R = 0.2202 (Rfree = 0.000) for 6633 atoms. Found 33 (59 requested) and removed 38 (29 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.21 2.30 Search for helices and strands: 0 residues in 0 chains, 6853 seeds are put forward NCS extension: 34 residues added (40 deleted due to clashes), 6887 seeds are put forward Round 1: 706 peptides, 60 chains. Longest chain 40 peptides. Score 0.623 Round 2: 722 peptides, 48 chains. Longest chain 54 peptides. Score 0.672 Round 3: 709 peptides, 50 chains. Longest chain 48 peptides. Score 0.658 Round 4: 712 peptides, 46 chains. Longest chain 63 peptides. Score 0.672 Round 5: 712 peptides, 44 chains. Longest chain 98 peptides. Score 0.679 Taking the results from Round 5 Chains 53, Residues 668, Estimated correctness of the model 60.6 % 12 chains (324 residues) have been docked in sequence ------------------------------------------------------ 29180 reflections ( 98.97 % complete ) and 10811 restraints for refining 6731 atoms. 6738 conditional restraints added. Observations/parameters ratio is 1.08 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2439 (Rfree = 0.000) for 6731 atoms. Found 60 (60 requested) and removed 59 (30 requested) atoms. Cycle 7: After refmac, R = 0.2461 (Rfree = 0.000) for 6684 atoms. Found 60 (60 requested) and removed 41 (30 requested) atoms. Cycle 8: After refmac, R = 0.2522 (Rfree = 0.000) for 6656 atoms. Found 60 (60 requested) and removed 56 (30 requested) atoms. Cycle 9: After refmac, R = 0.2437 (Rfree = 0.000) for 6622 atoms. Found 59 (59 requested) and removed 45 (29 requested) atoms. Cycle 10: After refmac, R = 0.2129 (Rfree = 0.000) for 6609 atoms. Found 59 (59 requested) and removed 38 (29 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 2.30 Search for helices and strands: 0 residues in 0 chains, 6864 seeds are put forward NCS extension: 16 residues added (25 deleted due to clashes), 6880 seeds are put forward Round 1: 705 peptides, 54 chains. Longest chain 44 peptides. Score 0.642 Round 2: 722 peptides, 52 chains. Longest chain 55 peptides. Score 0.660 Round 3: 719 peptides, 47 chains. Longest chain 46 peptides. Score 0.674 Round 4: 729 peptides, 49 chains. Longest chain 41 peptides. Score 0.673 Round 5: 725 peptides, 52 chains. Longest chain 49 peptides. Score 0.662 Taking the results from Round 3 Chains 54, Residues 672, Estimated correctness of the model 59.5 % 14 chains (334 residues) have been docked in sequence ------------------------------------------------------ 29180 reflections ( 98.97 % complete ) and 10642 restraints for refining 6673 atoms. 6509 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2469 (Rfree = 0.000) for 6673 atoms. Found 59 (59 requested) and removed 68 (29 requested) atoms. Cycle 12: After refmac, R = 0.2479 (Rfree = 0.000) for 6615 atoms. Found 59 (59 requested) and removed 48 (29 requested) atoms. Cycle 13: After refmac, R = 0.2546 (Rfree = 0.000) for 6599 atoms. Found 59 (59 requested) and removed 65 (29 requested) atoms. Cycle 14: After refmac, R = 0.2412 (Rfree = 0.000) for 6577 atoms. Found 59 (59 requested) and removed 54 (29 requested) atoms. Cycle 15: After refmac, R = 0.2404 (Rfree = 0.000) for 6559 atoms. Found 59 (59 requested) and removed 46 (29 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.21 2.30 Search for helices and strands: 0 residues in 0 chains, 6834 seeds are put forward NCS extension: 21 residues added (34 deleted due to clashes), 6855 seeds are put forward Round 1: 729 peptides, 56 chains. Longest chain 45 peptides. Score 0.651 Round 2: 728 peptides, 48 chains. Longest chain 55 peptides. Score 0.676 Round 3: 711 peptides, 46 chains. Longest chain 51 peptides. Score 0.672 Round 4: 695 peptides, 53 chains. Longest chain 51 peptides. Score 0.639 Round 5: 721 peptides, 52 chains. Longest chain 48 peptides. Score 0.659 Taking the results from Round 2 Chains 53, Residues 680, Estimated correctness of the model 59.9 % 13 chains (388 residues) have been docked in sequence ------------------------------------------------------ 29180 reflections ( 98.97 % complete ) and 10161 restraints for refining 6687 atoms. 5758 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2557 (Rfree = 0.000) for 6687 atoms. Found 60 (60 requested) and removed 67 (30 requested) atoms. Cycle 17: After refmac, R = 0.2458 (Rfree = 0.000) for 6626 atoms. Found 59 (59 requested) and removed 57 (29 requested) atoms. Cycle 18: After refmac, R = 0.2449 (Rfree = 0.000) for 6604 atoms. Found 59 (59 requested) and removed 46 (29 requested) atoms. Cycle 19: After refmac, R = 0.2364 (Rfree = 0.000) for 6591 atoms. Found 59 (59 requested) and removed 49 (29 requested) atoms. Cycle 20: After refmac, R = 0.2110 (Rfree = 0.000) for 6582 atoms. Found 49 (59 requested) and removed 35 (29 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.22 2.31 Search for helices and strands: 0 residues in 0 chains, 6784 seeds are put forward NCS extension: 3 residues added (32 deleted due to clashes), 6787 seeds are put forward Round 1: 710 peptides, 55 chains. Longest chain 44 peptides. Score 0.642 Round 2: 719 peptides, 43 chains. Longest chain 64 peptides. Score 0.686 Round 3: 715 peptides, 47 chains. Longest chain 46 peptides. Score 0.671 Round 4: 727 peptides, 51 chains. Longest chain 46 peptides. Score 0.666 Round 5: 723 peptides, 42 chains. Longest chain 62 peptides. Score 0.691 Taking the results from Round 5 Chains 49, Residues 681, Estimated correctness of the model 63.2 % 14 chains (323 residues) have been docked in sequence ------------------------------------------------------ 29180 reflections ( 98.97 % complete ) and 10676 restraints for refining 6572 atoms. 6590 conditional restraints added. Observations/parameters ratio is 1.11 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2582 (Rfree = 0.000) for 6572 atoms. Found 58 (58 requested) and removed 57 (29 requested) atoms. Cycle 22: After refmac, R = 0.2516 (Rfree = 0.000) for 6539 atoms. Found 58 (58 requested) and removed 47 (29 requested) atoms. Cycle 23: After refmac, R = 0.2552 (Rfree = 0.000) for 6537 atoms. Found 58 (58 requested) and removed 41 (29 requested) atoms. Cycle 24: After refmac, R = 0.2212 (Rfree = 0.000) for 6529 atoms. Found 58 (58 requested) and removed 44 (29 requested) atoms. Cycle 25: After refmac, R = 0.2131 (Rfree = 0.000) for 6533 atoms. Found 41 (58 requested) and removed 33 (29 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.22 2.31 Search for helices and strands: 0 residues in 0 chains, 6714 seeds are put forward NCS extension: 2 residues added (36 deleted due to clashes), 6716 seeds are put forward Round 1: 727 peptides, 58 chains. Longest chain 54 peptides. Score 0.644 Round 2: 722 peptides, 52 chains. Longest chain 50 peptides. Score 0.660 Round 3: 715 peptides, 51 chains. Longest chain 43 peptides. Score 0.658 Round 4: 724 peptides, 48 chains. Longest chain 48 peptides. Score 0.673 Round 5: 700 peptides, 53 chains. Longest chain 45 peptides. Score 0.642 Taking the results from Round 4 Chains 57, Residues 676, Estimated correctness of the model 59.2 % 16 chains (368 residues) have been docked in sequence ------------------------------------------------------ 29180 reflections ( 98.97 % complete ) and 10446 restraints for refining 6668 atoms. 6130 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2571 (Rfree = 0.000) for 6668 atoms. Found 59 (59 requested) and removed 78 (29 requested) atoms. Cycle 27: After refmac, R = 0.2602 (Rfree = 0.000) for 6625 atoms. Found 59 (59 requested) and removed 48 (29 requested) atoms. Cycle 28: After refmac, R = 0.2529 (Rfree = 0.000) for 6616 atoms. Found 59 (59 requested) and removed 44 (29 requested) atoms. Cycle 29: After refmac, R = 0.2546 (Rfree = 0.000) for 6597 atoms. Found 59 (59 requested) and removed 41 (29 requested) atoms. Cycle 30: After refmac, R = 0.2523 (Rfree = 0.000) for 6595 atoms. Found 59 (59 requested) and removed 47 (29 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.21 2.30 Search for helices and strands: 0 residues in 0 chains, 6821 seeds are put forward NCS extension: 6 residues added (49 deleted due to clashes), 6827 seeds are put forward Round 1: 712 peptides, 54 chains. Longest chain 44 peptides. Score 0.647 Round 2: 724 peptides, 44 chains. Longest chain 41 peptides. Score 0.686 Round 3: 728 peptides, 45 chains. Longest chain 58 peptides. Score 0.685 Round 4: 722 peptides, 50 chains. Longest chain 42 peptides. Score 0.666 Round 5: 725 peptides, 46 chains. Longest chain 46 peptides. Score 0.680 Taking the results from Round 2 Chains 52, Residues 680, Estimated correctness of the model 62.2 % 17 chains (433 residues) have been docked in sequence ------------------------------------------------------ 29180 reflections ( 98.97 % complete ) and 10116 restraints for refining 6720 atoms. 5503 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2443 (Rfree = 0.000) for 6720 atoms. Found 60 (60 requested) and removed 49 (30 requested) atoms. Cycle 32: After refmac, R = 0.2405 (Rfree = 0.000) for 6700 atoms. Found 60 (60 requested) and removed 36 (30 requested) atoms. Cycle 33: After refmac, R = 0.2382 (Rfree = 0.000) for 6696 atoms. Found 60 (60 requested) and removed 41 (30 requested) atoms. Cycle 34: After refmac, R = 0.2319 (Rfree = 0.000) for 6687 atoms. Found 60 (60 requested) and removed 70 (30 requested) atoms. Cycle 35: After refmac, R = 0.2288 (Rfree = 0.000) for 6657 atoms. Found 59 (59 requested) and removed 42 (29 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.20 2.30 Search for helices and strands: 0 residues in 0 chains, 6869 seeds are put forward NCS extension: 11 residues added (38 deleted due to clashes), 6880 seeds are put forward Round 1: 700 peptides, 47 chains. Longest chain 45 peptides. Score 0.662 Round 2: 724 peptides, 42 chains. Longest chain 49 peptides. Score 0.692 Round 3: 724 peptides, 46 chains. Longest chain 61 peptides. Score 0.680 Round 4: 734 peptides, 52 chains. Longest chain 51 peptides. Score 0.667 Round 5: 736 peptides, 53 chains. Longest chain 49 peptides. Score 0.665 Taking the results from Round 2 Chains 46, Residues 682, Estimated correctness of the model 63.5 % 15 chains (451 residues) have been docked in sequence ------------------------------------------------------ 29180 reflections ( 98.97 % complete ) and 10213 restraints for refining 6785 atoms. 5553 conditional restraints added. Observations/parameters ratio is 1.08 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2485 (Rfree = 0.000) for 6785 atoms. Found 60 (60 requested) and removed 85 (30 requested) atoms. Cycle 37: After refmac, R = 0.2363 (Rfree = 0.000) for 6720 atoms. Found 60 (60 requested) and removed 53 (30 requested) atoms. Cycle 38: After refmac, R = 0.2283 (Rfree = 0.000) for 6696 atoms. Found 60 (60 requested) and removed 40 (30 requested) atoms. Cycle 39: After refmac, R = 0.2023 (Rfree = 0.000) for 6703 atoms. Found 54 (60 requested) and removed 50 (30 requested) atoms. Cycle 40: After refmac, R = 0.1911 (Rfree = 0.000) for 6692 atoms. Found 41 (60 requested) and removed 50 (30 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.21 2.30 Search for helices and strands: 0 residues in 0 chains, 6865 seeds are put forward NCS extension: 10 residues added (27 deleted due to clashes), 6875 seeds are put forward Round 1: 713 peptides, 52 chains. Longest chain 55 peptides. Score 0.654 Round 2: 721 peptides, 47 chains. Longest chain 64 peptides. Score 0.675 Round 3: 736 peptides, 50 chains. Longest chain 44 peptides. Score 0.675 Round 4: 735 peptides, 48 chains. Longest chain 49 peptides. Score 0.680 Round 5: 726 peptides, 51 chains. Longest chain 41 peptides. Score 0.665 Taking the results from Round 4 Chains 53, Residues 687, Estimated correctness of the model 60.8 % 17 chains (402 residues) have been docked in sequence ------------------------------------------------------ 29180 reflections ( 98.97 % complete ) and 10225 restraints for refining 6662 atoms. 5763 conditional restraints added. Observations/parameters ratio is 1.10 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2512 (Rfree = 0.000) for 6662 atoms. Found 59 (59 requested) and removed 60 (29 requested) atoms. Cycle 42: After refmac, R = 0.2437 (Rfree = 0.000) for 6616 atoms. Found 59 (59 requested) and removed 49 (29 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2391 (Rfree = 0.000) for 6589 atoms. Found 59 (59 requested) and removed 45 (29 requested) atoms. Cycle 44: After refmac, R = 0.2349 (Rfree = 0.000) for 6578 atoms. Found 59 (59 requested) and removed 41 (29 requested) atoms. Cycle 45: After refmac, R = 0.2325 (Rfree = 0.000) for 6573 atoms. Found 59 (59 requested) and removed 40 (29 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.22 2.31 Search for helices and strands: 0 residues in 0 chains, 6789 seeds are put forward NCS extension: 7 residues added (17 deleted due to clashes), 6796 seeds are put forward Round 1: 721 peptides, 50 chains. Longest chain 50 peptides. Score 0.665 Round 2: 732 peptides, 49 chains. Longest chain 61 peptides. Score 0.675 Round 3: 724 peptides, 42 chains. Longest chain 67 peptides. Score 0.692 Round 4: 726 peptides, 48 chains. Longest chain 47 peptides. Score 0.675 Round 5: 735 peptides, 43 chains. Longest chain 61 peptides. Score 0.695 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 52, Residues 692, Estimated correctness of the model 64.1 % 15 chains (362 residues) have been docked in sequence Sequence coverage is 52 % Consider running further cycles of model building using 1ztc-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 64 A and 70 A Built loop between residues 135 C and 142 C Built loop between residues 43 D and 55 D 47 chains (705 residues) following loop building 12 chains (384 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 29180 reflections ( 98.97 % complete ) and 9839 restraints for refining 6468 atoms. 5489 conditional restraints added. Observations/parameters ratio is 1.13 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2628 (Rfree = 0.000) for 6468 atoms. Found 0 (58 requested) and removed 29 (29 requested) atoms. Cycle 47: After refmac, R = 0.2424 (Rfree = 0.000) for 6402 atoms. Found 0 (57 requested) and removed 7 (28 requested) atoms. Cycle 48: After refmac, R = 0.2365 (Rfree = 0.000) for 6384 atoms. Found 0 (57 requested) and removed 8 (28 requested) atoms. Cycle 49: After refmac, R = 0.2495 (Rfree = 0.000) for 6364 atoms. TimeTaking 100.8