Sun 23 Dec 22:23:01 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vl5-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vl5-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vl5-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl5-3.2-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/1vl5-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl5-3.2-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:23:11 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/hancs/ArpWArp/wArpResults/WorkingDir/1vl5-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl5-3.2-parrot-hancs/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 835 and 0 Target number of residues in the AU: 835 Target solvent content: 0.6099 Checking the provided sequence file Detected sequence length: 260 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1040 Adjusted target solvent content: 0.51 Input MTZ file: 1vl5-3.2-parrot-hancs.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: 64.006 87.475 105.236 90.000 100.573 90.000 Input sequence file: 1vl5-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 8320 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: 49.849 3.200 Wilson plot Bfac: 56.78 19002 reflections ( 99.93 % complete ) and 0 restraints for refining 9172 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.2988 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2300 (Rfree = 0.000) for 9172 atoms. Found 56 (82 requested) and removed 80 (41 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.05 3.01 Search for helices and strands: 0 residues in 0 chains, 9317 seeds are put forward NCS extension: 0 residues added, 9317 seeds are put forward Round 1: 571 peptides, 89 chains. Longest chain 24 peptides. Score 0.482 Round 2: 668 peptides, 76 chains. Longest chain 30 peptides. Score 0.650 Round 3: 679 peptides, 75 chains. Longest chain 25 peptides. Score 0.664 Round 4: 706 peptides, 70 chains. Longest chain 31 peptides. Score 0.707 Round 5: 710 peptides, 65 chains. Longest chain 31 peptides. Score 0.728 Taking the results from Round 5 Chains 70, Residues 645, Estimated correctness of the model 70.9 % 12 chains (206 residues) have been docked in sequence Building loops using Loopy2018 70 chains (645 residues) following loop building 12 chains (206 residues) in sequence following loop building ------------------------------------------------------ 19002 reflections ( 99.93 % complete ) and 14338 restraints for refining 7593 atoms. 10983 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2431 (Rfree = 0.000) for 7593 atoms. Found 68 (68 requested) and removed 59 (34 requested) atoms. Cycle 2: After refmac, R = 0.2230 (Rfree = 0.000) for 7467 atoms. Found 36 (67 requested) and removed 45 (34 requested) atoms. Cycle 3: After refmac, R = 0.2145 (Rfree = 0.000) for 7390 atoms. Found 34 (63 requested) and removed 43 (33 requested) atoms. Cycle 4: After refmac, R = 0.2085 (Rfree = 0.000) for 7358 atoms. Found 27 (62 requested) and removed 33 (33 requested) atoms. Cycle 5: After refmac, R = 0.2044 (Rfree = 0.000) for 7346 atoms. Found 14 (60 requested) and removed 32 (32 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.07 3.03 Search for helices and strands: 0 residues in 0 chains, 7571 seeds are put forward NCS extension: 11 residues added (14 deleted due to clashes), 7582 seeds are put forward Round 1: 677 peptides, 73 chains. Longest chain 44 peptides. Score 0.671 Round 2: 689 peptides, 64 chains. Longest chain 30 peptides. Score 0.716 Round 3: 729 peptides, 57 chains. Longest chain 45 peptides. Score 0.768 Round 4: 723 peptides, 64 chains. Longest chain 36 peptides. Score 0.741 Round 5: 698 peptides, 62 chains. Longest chain 40 peptides. Score 0.730 Taking the results from Round 3 Chains 68, Residues 672, Estimated correctness of the model 78.2 % 15 chains (287 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 145 C and 153 C 66 chains (672 residues) following loop building 14 chains (294 residues) in sequence following loop building ------------------------------------------------------ 19002 reflections ( 99.93 % complete ) and 13221 restraints for refining 7595 atoms. 9366 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2496 (Rfree = 0.000) for 7595 atoms. Found 61 (61 requested) and removed 59 (34 requested) atoms. Cycle 7: After refmac, R = 0.2326 (Rfree = 0.000) for 7519 atoms. Found 29 (60 requested) and removed 44 (34 requested) atoms. Cycle 8: After refmac, R = 0.2264 (Rfree = 0.000) for 7480 atoms. Found 15 (58 requested) and removed 33 (33 requested) atoms. Cycle 9: After refmac, R = 0.2216 (Rfree = 0.000) for 7453 atoms. Found 16 (55 requested) and removed 33 (33 requested) atoms. Cycle 10: After refmac, R = 0.2184 (Rfree = 0.000) for 7425 atoms. Found 15 (54 requested) and removed 33 (33 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.07 3.03 Search for helices and strands: 0 residues in 0 chains, 7666 seeds are put forward NCS extension: 70 residues added (96 deleted due to clashes), 7736 seeds are put forward Round 1: 644 peptides, 69 chains. Longest chain 29 peptides. Score 0.658 Round 2: 691 peptides, 65 chains. Longest chain 33 peptides. Score 0.713 Round 3: 695 peptides, 60 chains. Longest chain 45 peptides. Score 0.735 Round 4: 698 peptides, 62 chains. Longest chain 37 peptides. Score 0.730 Round 5: 694 peptides, 66 chains. Longest chain 41 peptides. Score 0.712 Taking the results from Round 3 Chains 69, Residues 635, Estimated correctness of the model 72.3 % 12 chains (260 residues) have been docked in sequence Building loops using Loopy2018 69 chains (635 residues) following loop building 12 chains (260 residues) in sequence following loop building ------------------------------------------------------ 19002 reflections ( 99.93 % complete ) and 13954 restraints for refining 7595 atoms. 10345 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2446 (Rfree = 0.000) for 7595 atoms. Found 54 (54 requested) and removed 54 (34 requested) atoms. Cycle 12: After refmac, R = 0.2319 (Rfree = 0.000) for 7569 atoms. Found 27 (53 requested) and removed 37 (34 requested) atoms. Cycle 13: After refmac, R = 0.2248 (Rfree = 0.000) for 7538 atoms. Found 16 (51 requested) and removed 33 (33 requested) atoms. Cycle 14: After refmac, R = 0.2203 (Rfree = 0.000) for 7506 atoms. Found 15 (50 requested) and removed 33 (33 requested) atoms. Cycle 15: After refmac, R = 0.2183 (Rfree = 0.000) for 7471 atoms. Found 14 (48 requested) and removed 33 (33 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.08 3.04 Search for helices and strands: 0 residues in 0 chains, 7667 seeds are put forward NCS extension: 7 residues added (23 deleted due to clashes), 7674 seeds are put forward Round 1: 670 peptides, 74 chains. Longest chain 32 peptides. Score 0.660 Round 2: 729 peptides, 64 chains. Longest chain 33 peptides. Score 0.745 Round 3: 707 peptides, 71 chains. Longest chain 40 peptides. Score 0.704 Round 4: 732 peptides, 69 chains. Longest chain 39 peptides. Score 0.730 Round 5: 726 peptides, 67 chains. Longest chain 46 peptides. Score 0.733 Taking the results from Round 2 Chains 70, Residues 665, Estimated correctness of the model 74.1 % 15 chains (287 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 145 C and 155 C Built loop between residues 233 C and 236 C Built loop between residues 110 B and 121 B 65 chains (669 residues) following loop building 12 chains (308 residues) in sequence following loop building ------------------------------------------------------ 19002 reflections ( 99.93 % complete ) and 13074 restraints for refining 7596 atoms. 9183 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2453 (Rfree = 0.000) for 7596 atoms. Found 48 (48 requested) and removed 63 (34 requested) atoms. Cycle 17: After refmac, R = 0.2302 (Rfree = 0.000) for 7544 atoms. Found 22 (46 requested) and removed 37 (34 requested) atoms. Cycle 18: After refmac, R = 0.2271 (Rfree = 0.000) for 7508 atoms. Found 24 (44 requested) and removed 34 (33 requested) atoms. Cycle 19: After refmac, R = 0.2195 (Rfree = 0.000) for 7484 atoms. Found 10 (43 requested) and removed 33 (33 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2178 (Rfree = 0.000) for 7446 atoms. Found 12 (41 requested) and removed 33 (33 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.09 3.05 Search for helices and strands: 0 residues in 0 chains, 7657 seeds are put forward NCS extension: 24 residues added (13 deleted due to clashes), 7681 seeds are put forward Round 1: 635 peptides, 73 chains. Longest chain 30 peptides. Score 0.632 Round 2: 666 peptides, 69 chains. Longest chain 33 peptides. Score 0.677 Round 3: 685 peptides, 69 chains. Longest chain 30 peptides. Score 0.693 Round 4: 683 peptides, 67 chains. Longest chain 30 peptides. Score 0.699 Round 5: 674 peptides, 67 chains. Longest chain 47 peptides. Score 0.692 Taking the results from Round 4 Chains 74, Residues 616, Estimated correctness of the model 65.0 % 12 chains (220 residues) have been docked in sequence ------------------------------------------------------ 19002 reflections ( 99.93 % complete ) and 14188 restraints for refining 7595 atoms. 10810 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2409 (Rfree = 0.000) for 7595 atoms. Found 41 (41 requested) and removed 49 (34 requested) atoms. Cycle 22: After refmac, R = 0.2282 (Rfree = 0.000) for 7561 atoms. Found 26 (41 requested) and removed 37 (34 requested) atoms. Cycle 23: After refmac, R = 0.2219 (Rfree = 0.000) for 7539 atoms. Found 12 (40 requested) and removed 34 (33 requested) atoms. Cycle 24: After refmac, R = 0.2151 (Rfree = 0.000) for 7505 atoms. Found 19 (40 requested) and removed 33 (33 requested) atoms. Cycle 25: After refmac, R = 0.2130 (Rfree = 0.000) for 7479 atoms. Found 14 (40 requested) and removed 33 (33 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.08 3.04 Search for helices and strands: 0 residues in 0 chains, 7691 seeds are put forward NCS extension: 6 residues added (19 deleted due to clashes), 7697 seeds are put forward Round 1: 612 peptides, 68 chains. Longest chain 26 peptides. Score 0.632 Round 2: 669 peptides, 66 chains. Longest chain 38 peptides. Score 0.692 Round 3: 682 peptides, 63 chains. Longest chain 37 peptides. Score 0.714 Round 4: 672 peptides, 67 chains. Longest chain 32 peptides. Score 0.690 Round 5: 669 peptides, 66 chains. Longest chain 32 peptides. Score 0.692 Taking the results from Round 3 Chains 70, Residues 619, Estimated correctness of the model 68.1 % 14 chains (256 residues) have been docked in sequence Building loops using Loopy2018 70 chains (619 residues) following loop building 14 chains (256 residues) in sequence following loop building ------------------------------------------------------ 19002 reflections ( 99.93 % complete ) and 13821 restraints for refining 7595 atoms. 10282 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2339 (Rfree = 0.000) for 7595 atoms. Found 41 (41 requested) and removed 55 (34 requested) atoms. Cycle 27: After refmac, R = 0.2222 (Rfree = 0.000) for 7554 atoms. Found 26 (39 requested) and removed 44 (34 requested) atoms. Cycle 28: After refmac, R = 0.2160 (Rfree = 0.000) for 7519 atoms. Found 13 (38 requested) and removed 33 (33 requested) atoms. Cycle 29: After refmac, R = 0.2125 (Rfree = 0.000) for 7493 atoms. Found 12 (36 requested) and removed 34 (33 requested) atoms. Cycle 30: After refmac, R = 0.2077 (Rfree = 0.000) for 7461 atoms. Found 14 (35 requested) and removed 33 (33 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.11 3.07 Search for helices and strands: 0 residues in 0 chains, 7634 seeds are put forward NCS extension: 10 residues added (23 deleted due to clashes), 7644 seeds are put forward Round 1: 583 peptides, 73 chains. Longest chain 30 peptides. Score 0.579 Round 2: 636 peptides, 65 chains. Longest chain 32 peptides. Score 0.667 Round 3: 659 peptides, 71 chains. Longest chain 35 peptides. Score 0.663 Round 4: 650 peptides, 70 chains. Longest chain 31 peptides. Score 0.659 Round 5: 649 peptides, 71 chains. Longest chain 21 peptides. Score 0.654 Taking the results from Round 2 Chains 68, Residues 571, Estimated correctness of the model 57.9 % 14 chains (198 residues) have been docked in sequence ------------------------------------------------------ 19002 reflections ( 99.93 % complete ) and 14793 restraints for refining 7595 atoms. 11703 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2292 (Rfree = 0.000) for 7595 atoms. Found 34 (34 requested) and removed 48 (34 requested) atoms. Cycle 32: After refmac, R = 0.2183 (Rfree = 0.000) for 7560 atoms. Found 19 (34 requested) and removed 34 (34 requested) atoms. Cycle 33: After refmac, R = 0.2139 (Rfree = 0.000) for 7542 atoms. Found 13 (33 requested) and removed 33 (33 requested) atoms. Cycle 34: After refmac, R = 0.2076 (Rfree = 0.000) for 7514 atoms. Found 9 (33 requested) and removed 33 (33 requested) atoms. Cycle 35: After refmac, R = 0.2018 (Rfree = 0.000) for 7478 atoms. Found 17 (33 requested) and removed 33 (33 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.09 3.05 Search for helices and strands: 0 residues in 0 chains, 7655 seeds are put forward NCS extension: 22 residues added (6 deleted due to clashes), 7677 seeds are put forward Round 1: 553 peptides, 75 chains. Longest chain 20 peptides. Score 0.535 Round 2: 602 peptides, 64 chains. Longest chain 31 peptides. Score 0.640 Round 3: 621 peptides, 66 chains. Longest chain 32 peptides. Score 0.649 Round 4: 623 peptides, 69 chains. Longest chain 44 peptides. Score 0.638 Round 5: 635 peptides, 71 chains. Longest chain 24 peptides. Score 0.641 Taking the results from Round 3 Chains 69, Residues 555, Estimated correctness of the model 53.6 % 9 chains (171 residues) have been docked in sequence ------------------------------------------------------ 19002 reflections ( 99.93 % complete ) and 15013 restraints for refining 7593 atoms. 12076 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2250 (Rfree = 0.000) for 7593 atoms. Found 34 (34 requested) and removed 49 (34 requested) atoms. Cycle 37: After refmac, R = 0.2125 (Rfree = 0.000) for 7553 atoms. Found 25 (34 requested) and removed 34 (34 requested) atoms. Cycle 38: After refmac, R = 0.2066 (Rfree = 0.000) for 7527 atoms. Found 20 (33 requested) and removed 33 (33 requested) atoms. Cycle 39: After refmac, R = 0.2039 (Rfree = 0.000) for 7508 atoms. Found 8 (33 requested) and removed 33 (33 requested) atoms. Cycle 40: After refmac, R = 0.2010 (Rfree = 0.000) for 7478 atoms. Found 9 (33 requested) and removed 33 (33 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.09 3.05 Search for helices and strands: 0 residues in 0 chains, 7665 seeds are put forward NCS extension: 18 residues added (9 deleted due to clashes), 7683 seeds are put forward Round 1: 534 peptides, 72 chains. Longest chain 22 peptides. Score 0.528 Round 2: 581 peptides, 68 chains. Longest chain 34 peptides. Score 0.601 Round 3: 582 peptides, 65 chains. Longest chain 27 peptides. Score 0.616 Round 4: 585 peptides, 72 chains. Longest chain 30 peptides. Score 0.586 Round 5: 593 peptides, 65 chains. Longest chain 36 peptides. Score 0.627 Taking the results from Round 5 Chains 69, Residues 528, Estimated correctness of the model 48.1 % 9 chains (138 residues) have been docked in sequence ------------------------------------------------------ 19002 reflections ( 99.93 % complete ) and 15565 restraints for refining 7595 atoms. 12903 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2184 (Rfree = 0.000) for 7595 atoms. Found 34 (34 requested) and removed 47 (34 requested) atoms. Cycle 42: After refmac, R = 0.2060 (Rfree = 0.000) for 7560 atoms. Found 24 (34 requested) and removed 34 (34 requested) atoms. Cycle 43: After refmac, R = 0.1991 (Rfree = 0.000) for 7542 atoms. Found 12 (33 requested) and removed 33 (33 requested) atoms. Cycle 44: After refmac, R = 0.1954 (Rfree = 0.000) for 7513 atoms. Found 7 (33 requested) and removed 34 (33 requested) atoms. Cycle 45: After refmac, R = 0.1929 (Rfree = 0.000) for 7477 atoms. Found 11 (33 requested) and removed 34 (33 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.08 3.04 Search for helices and strands: 0 residues in 0 chains, 7656 seeds are put forward NCS extension: 18 residues added (11 deleted due to clashes), 7674 seeds are put forward Round 1: 528 peptides, 73 chains. Longest chain 21 peptides. Score 0.516 Round 2: 586 peptides, 74 chains. Longest chain 23 peptides. Score 0.577 Round 3: 569 peptides, 72 chains. Longest chain 30 peptides. Score 0.568 Round 4: 576 peptides, 73 chains. Longest chain 23 peptides. Score 0.571 Round 5: 567 peptides, 75 chains. Longest chain 21 peptides. Score 0.551 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 80, Residues 512, Estimated correctness of the model 34.7 % 9 chains (131 residues) have been docked in sequence Sequence coverage is 25 % Consider running further cycles of model building using 1vl5-3_warpNtrace.pdb as input Building loops using Loopy2018 80 chains (512 residues) following loop building 9 chains (131 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 19002 reflections ( 99.93 % complete ) and 15859 restraints for refining 7590 atoms. 13343 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2103 (Rfree = 0.000) for 7590 atoms. Found 0 (34 requested) and removed 16 (34 requested) atoms. Cycle 47: After refmac, R = 0.2025 (Rfree = 0.000) for 7561 atoms. Found 0 (33 requested) and removed 11 (33 requested) atoms. Cycle 48: After refmac, R = 0.2016 (Rfree = 0.000) for 7543 atoms. Found 0 (33 requested) and removed 5 (33 requested) atoms. Cycle 49: After refmac, R = 0.1994 (Rfree = 0.000) for 7534 atoms. TimeTaking 99.33