Mon 24 Dec 00:48:53 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 2hr2-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2hr2-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2hr2-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hr2-3.6-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/2hr2-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hr2-3.6-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 00:48:57 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/2hr2-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hr2-3.6-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 927 and 0 Target number of residues in the AU: 927 Target solvent content: 0.6498 Checking the provided sequence file Detected sequence length: 159 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 954 Adjusted target solvent content: 0.64 Input MTZ file: 2hr2-3.6-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: 89.090 91.280 176.170 90.000 90.000 90.000 Input sequence file: 2hr2-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 7632 target number of atoms Had to go as low as 0.80 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: 88.085 3.600 Wilson plot Bfac: 77.86 16963 reflections ( 98.21 % complete ) and 0 restraints for refining 8397 atoms. Observations/parameters ratio is 0.51 ------------------------------------------------------ Starting model: R = 0.3188 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2975 (Rfree = 0.000) for 8397 atoms. Found 53 (53 requested) and removed 38 (26 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.54 2.92 Search for helices and strands: 0 residues in 0 chains, 8691 seeds are put forward NCS extension: 0 residues added, 8691 seeds are put forward Round 1: 483 peptides, 80 chains. Longest chain 18 peptides. Score 0.383 Round 2: 557 peptides, 66 chains. Longest chain 20 peptides. Score 0.530 Round 3: 585 peptides, 63 chains. Longest chain 21 peptides. Score 0.570 Round 4: 585 peptides, 63 chains. Longest chain 27 peptides. Score 0.570 Round 5: 562 peptides, 62 chains. Longest chain 25 peptides. Score 0.553 Taking the results from Round 4 Chains 66, Residues 522, Estimated correctness of the model 2.6 % 5 chains (59 residues) have been docked in sequence ------------------------------------------------------ 16963 reflections ( 98.21 % complete ) and 14695 restraints for refining 6914 atoms. 12479 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2541 (Rfree = 0.000) for 6914 atoms. Found 44 (44 requested) and removed 45 (22 requested) atoms. Cycle 2: After refmac, R = 0.2343 (Rfree = 0.000) for 6789 atoms. Found 41 (44 requested) and removed 43 (22 requested) atoms. Cycle 3: After refmac, R = 0.2256 (Rfree = 0.000) for 6740 atoms. Found 23 (43 requested) and removed 38 (21 requested) atoms. Cycle 4: After refmac, R = 0.2237 (Rfree = 0.000) for 6685 atoms. Found 24 (43 requested) and removed 39 (21 requested) atoms. Cycle 5: After refmac, R = 0.2145 (Rfree = 0.000) for 6644 atoms. Found 22 (42 requested) and removed 38 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.49 2.88 Search for helices and strands: 0 residues in 0 chains, 7021 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 7038 seeds are put forward Round 1: 540 peptides, 73 chains. Longest chain 24 peptides. Score 0.481 Round 2: 583 peptides, 68 chains. Longest chain 23 peptides. Score 0.546 Round 3: 576 peptides, 66 chains. Longest chain 26 peptides. Score 0.548 Round 4: 581 peptides, 66 chains. Longest chain 27 peptides. Score 0.553 Round 5: 585 peptides, 61 chains. Longest chain 31 peptides. Score 0.578 Taking the results from Round 5 Chains 67, Residues 524, Estimated correctness of the model 5.9 % 7 chains (90 residues) have been docked in sequence ------------------------------------------------------ 16963 reflections ( 98.21 % complete ) and 14473 restraints for refining 6919 atoms. 12146 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2592 (Rfree = 0.000) for 6919 atoms. Found 44 (44 requested) and removed 46 (22 requested) atoms. Cycle 7: After refmac, R = 0.2374 (Rfree = 0.000) for 6851 atoms. Found 39 (44 requested) and removed 36 (22 requested) atoms. Cycle 8: After refmac, R = 0.2275 (Rfree = 0.000) for 6824 atoms. Found 31 (43 requested) and removed 29 (21 requested) atoms. Cycle 9: After refmac, R = 0.2186 (Rfree = 0.000) for 6797 atoms. Found 20 (43 requested) and removed 33 (21 requested) atoms. Cycle 10: After refmac, R = 0.2175 (Rfree = 0.000) for 6761 atoms. Found 22 (43 requested) and removed 32 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 2.86 Search for helices and strands: 0 residues in 0 chains, 7102 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 7115 seeds are put forward Round 1: 548 peptides, 76 chains. Longest chain 18 peptides. Score 0.475 Round 2: 601 peptides, 70 chains. Longest chain 24 peptides. Score 0.554 Round 3: 584 peptides, 67 chains. Longest chain 20 peptides. Score 0.551 Round 4: 588 peptides, 69 chains. Longest chain 31 peptides. Score 0.546 Round 5: 572 peptides, 68 chains. Longest chain 20 peptides. Score 0.536 Taking the results from Round 2 Chains 76, Residues 531, Estimated correctness of the model 0.0 % 12 chains (100 residues) have been docked in sequence ------------------------------------------------------ 16963 reflections ( 98.21 % complete ) and 14109 restraints for refining 6917 atoms. 11753 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2405 (Rfree = 0.000) for 6917 atoms. Found 41 (44 requested) and removed 37 (22 requested) atoms. Cycle 12: After refmac, R = 0.2219 (Rfree = 0.000) for 6868 atoms. Found 19 (44 requested) and removed 32 (22 requested) atoms. Cycle 13: After refmac, R = 0.2150 (Rfree = 0.000) for 6831 atoms. Found 25 (43 requested) and removed 39 (21 requested) atoms. Cycle 14: After refmac, R = 0.2126 (Rfree = 0.000) for 6799 atoms. Found 14 (43 requested) and removed 26 (21 requested) atoms. Cycle 15: After refmac, R = 0.2127 (Rfree = 0.000) for 6775 atoms. Found 15 (43 requested) and removed 31 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.48 2.87 Search for helices and strands: 0 residues in 0 chains, 7120 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 7141 seeds are put forward Round 1: 528 peptides, 81 chains. Longest chain 15 peptides. Score 0.429 Round 2: 571 peptides, 68 chains. Longest chain 23 peptides. Score 0.535 Round 3: 562 peptides, 64 chains. Longest chain 27 peptides. Score 0.544 Round 4: 563 peptides, 64 chains. Longest chain 27 peptides. Score 0.545 Round 5: 556 peptides, 67 chains. Longest chain 29 peptides. Score 0.525 Taking the results from Round 4 Chains 69, Residues 499, Estimated correctness of the model 0.0 % 8 chains (64 residues) have been docked in sequence ------------------------------------------------------ 16963 reflections ( 98.21 % complete ) and 14728 restraints for refining 6919 atoms. 12602 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2473 (Rfree = 0.000) for 6919 atoms. Found 44 (44 requested) and removed 51 (22 requested) atoms. Cycle 17: After refmac, R = 0.2232 (Rfree = 0.000) for 6851 atoms. Found 23 (44 requested) and removed 37 (22 requested) atoms. Cycle 18: After refmac, R = 0.2168 (Rfree = 0.000) for 6814 atoms. Found 20 (43 requested) and removed 34 (21 requested) atoms. Cycle 19: After refmac, R = 0.2109 (Rfree = 0.000) for 6780 atoms. Found 23 (43 requested) and removed 26 (21 requested) atoms. Cycle 20: After refmac, R = 0.2078 (Rfree = 0.000) for 6765 atoms. Found 11 (43 requested) and removed 33 (21 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.45 2.85 Search for helices and strands: 0 residues in 0 chains, 7121 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 7136 seeds are put forward Round 1: 502 peptides, 76 chains. Longest chain 14 peptides. Score 0.425 Round 2: 572 peptides, 77 chains. Longest chain 24 peptides. Score 0.495 Round 3: 580 peptides, 71 chains. Longest chain 18 peptides. Score 0.530 Round 4: 568 peptides, 72 chains. Longest chain 30 peptides. Score 0.514 Round 5: 553 peptides, 72 chains. Longest chain 22 peptides. Score 0.499 Taking the results from Round 3 Chains 74, Residues 509, Estimated correctness of the model 0.0 % 7 chains (51 residues) have been docked in sequence ------------------------------------------------------ 16963 reflections ( 98.21 % complete ) and 14436 restraints for refining 6917 atoms. 12282 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2340 (Rfree = 0.000) for 6917 atoms. Found 35 (44 requested) and removed 34 (22 requested) atoms. Cycle 22: After refmac, R = 0.2183 (Rfree = 0.000) for 6865 atoms. Found 23 (44 requested) and removed 39 (22 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2112 (Rfree = 0.000) for 6833 atoms. Found 16 (43 requested) and removed 37 (21 requested) atoms. Cycle 24: After refmac, R = 0.2074 (Rfree = 0.000) for 6805 atoms. Found 20 (43 requested) and removed 27 (21 requested) atoms. Cycle 25: After refmac, R = 0.2054 (Rfree = 0.000) for 6787 atoms. Found 24 (43 requested) and removed 27 (21 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.46 2.86 Search for helices and strands: 0 residues in 0 chains, 7161 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 7174 seeds are put forward Round 1: 506 peptides, 86 chains. Longest chain 14 peptides. Score 0.379 Round 2: 550 peptides, 74 chains. Longest chain 17 peptides. Score 0.486 Round 3: 544 peptides, 68 chains. Longest chain 19 peptides. Score 0.508 Round 4: 548 peptides, 69 chains. Longest chain 31 peptides. Score 0.507 Round 5: 541 peptides, 71 chains. Longest chain 20 peptides. Score 0.491 Taking the results from Round 3 Chains 73, Residues 476, Estimated correctness of the model 0.0 % 8 chains (85 residues) have been docked in sequence ------------------------------------------------------ 16963 reflections ( 98.21 % complete ) and 14543 restraints for refining 6918 atoms. 12437 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2356 (Rfree = 0.000) for 6918 atoms. Found 44 (44 requested) and removed 37 (22 requested) atoms. Cycle 27: After refmac, R = 0.2229 (Rfree = 0.000) for 6866 atoms. Found 21 (44 requested) and removed 35 (22 requested) atoms. Cycle 28: After refmac, R = 0.2144 (Rfree = 0.000) for 6827 atoms. Found 26 (43 requested) and removed 31 (21 requested) atoms. Cycle 29: After refmac, R = 0.2059 (Rfree = 0.000) for 6813 atoms. Found 18 (43 requested) and removed 31 (21 requested) atoms. Cycle 30: After refmac, R = 0.2016 (Rfree = 0.000) for 6788 atoms. Found 18 (43 requested) and removed 25 (21 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.51 2.90 Search for helices and strands: 0 residues in 0 chains, 7173 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 7192 seeds are put forward Round 1: 479 peptides, 80 chains. Longest chain 12 peptides. Score 0.378 Round 2: 531 peptides, 69 chains. Longest chain 19 peptides. Score 0.490 Round 3: 555 peptides, 75 chains. Longest chain 21 peptides. Score 0.487 Round 4: 519 peptides, 68 chains. Longest chain 28 peptides. Score 0.483 Round 5: 551 peptides, 71 chains. Longest chain 23 peptides. Score 0.501 Taking the results from Round 5 Chains 75, Residues 480, Estimated correctness of the model 0.0 % 7 chains (62 residues) have been docked in sequence ------------------------------------------------------ 16963 reflections ( 98.21 % complete ) and 14603 restraints for refining 6918 atoms. 12544 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2453 (Rfree = 0.000) for 6918 atoms. Found 44 (44 requested) and removed 29 (22 requested) atoms. Cycle 32: After refmac, R = 0.2256 (Rfree = 0.000) for 6875 atoms. Found 44 (44 requested) and removed 29 (22 requested) atoms. Cycle 33: After refmac, R = 0.2194 (Rfree = 0.000) for 6850 atoms. Found 32 (44 requested) and removed 24 (22 requested) atoms. Cycle 34: After refmac, R = 0.2158 (Rfree = 0.000) for 6845 atoms. Found 38 (43 requested) and removed 26 (21 requested) atoms. Cycle 35: After refmac, R = 0.2076 (Rfree = 0.000) for 6843 atoms. Found 21 (43 requested) and removed 23 (21 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.52 2.91 Search for helices and strands: 0 residues in 0 chains, 7199 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 7224 seeds are put forward Round 1: 450 peptides, 79 chains. Longest chain 12 peptides. Score 0.349 Round 2: 488 peptides, 68 chains. Longest chain 15 peptides. Score 0.449 Round 3: 505 peptides, 70 chains. Longest chain 16 peptides. Score 0.458 Round 4: 500 peptides, 72 chains. Longest chain 15 peptides. Score 0.443 Round 5: 503 peptides, 74 chains. Longest chain 18 peptides. Score 0.436 Taking the results from Round 3 Chains 71, Residues 435, Estimated correctness of the model 0.0 % 7 chains (40 residues) have been docked in sequence ------------------------------------------------------ 16963 reflections ( 98.21 % complete ) and 15167 restraints for refining 6918 atoms. 13378 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2368 (Rfree = 0.000) for 6918 atoms. Found 44 (44 requested) and removed 39 (22 requested) atoms. Cycle 37: After refmac, R = 0.2249 (Rfree = 0.000) for 6884 atoms. Found 44 (44 requested) and removed 35 (22 requested) atoms. Cycle 38: After refmac, R = 0.2117 (Rfree = 0.000) for 6867 atoms. Found 25 (44 requested) and removed 31 (22 requested) atoms. Cycle 39: After refmac, R = 0.2042 (Rfree = 0.000) for 6840 atoms. Found 21 (44 requested) and removed 27 (22 requested) atoms. Cycle 40: After refmac, R = 0.1987 (Rfree = 0.000) for 6824 atoms. Found 16 (43 requested) and removed 27 (21 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.49 2.88 Search for helices and strands: 0 residues in 0 chains, 7175 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 7189 seeds are put forward Round 1: 442 peptides, 84 chains. Longest chain 10 peptides. Score 0.312 Round 2: 470 peptides, 75 chains. Longest chain 16 peptides. Score 0.394 Round 3: 481 peptides, 68 chains. Longest chain 20 peptides. Score 0.442 Round 4: 500 peptides, 73 chains. Longest chain 17 peptides. Score 0.438 Round 5: 490 peptides, 72 chains. Longest chain 21 peptides. Score 0.432 Taking the results from Round 3 Chains 69, Residues 413, Estimated correctness of the model 0.0 % 3 chains (41 residues) have been docked in sequence ------------------------------------------------------ 16963 reflections ( 98.21 % complete ) and 14989 restraints for refining 6918 atoms. 13218 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2277 (Rfree = 0.000) for 6918 atoms. Found 44 (44 requested) and removed 33 (22 requested) atoms. Cycle 42: After refmac, R = 0.2156 (Rfree = 0.000) for 6894 atoms. Found 37 (44 requested) and removed 32 (22 requested) atoms. Cycle 43: After refmac, R = 0.2048 (Rfree = 0.000) for 6868 atoms. Found 26 (44 requested) and removed 33 (22 requested) atoms. Cycle 44: After refmac, R = 0.2008 (Rfree = 0.000) for 6844 atoms. Found 29 (44 requested) and removed 28 (22 requested) atoms. Cycle 45: After refmac, R = 0.1978 (Rfree = 0.000) for 6831 atoms. Found 30 (43 requested) and removed 29 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 2.86 Search for helices and strands: 0 residues in 0 chains, 7189 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 7215 seeds are put forward Round 1: 429 peptides, 77 chains. Longest chain 12 peptides. Score 0.333 Round 2: 498 peptides, 80 chains. Longest chain 13 peptides. Score 0.400 Round 3: 492 peptides, 73 chains. Longest chain 19 peptides. Score 0.429 Round 4: 510 peptides, 79 chains. Longest chain 19 peptides. Score 0.419 Round 5: 507 peptides, 80 chains. Longest chain 19 peptides. Score 0.411 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 77, Residues 419, Estimated correctness of the model 0.0 % 8 chains (61 residues) have been docked in sequence Sequence coverage is 14 % Consider running further cycles of model building using 2hr2-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 68 B and 80 B 75 chains (426 residues) following loop building 7 chains (72 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16963 reflections ( 98.21 % complete ) and 14645 restraints for refining 6916 atoms. 12804 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2315 (Rfree = 0.000) for 6916 atoms. Found 0 (44 requested) and removed 22 (22 requested) atoms. Cycle 47: After refmac, R = 0.2182 (Rfree = 0.000) for 6864 atoms. Found 0 (44 requested) and removed 22 (22 requested) atoms. Cycle 48: After refmac, R = 0.2169 (Rfree = 0.000) for 6829 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 49: After refmac, R = 0.2091 (Rfree = 0.000) for 6799 atoms. TimeTaking 86.08