null Sun 23 Dec 22:23:02 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 2hr2-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hr2-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hr2-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hr2-3.6-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/2hr2-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hr2-3.6-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 22:23:12 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/2hr2-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hr2-3.6-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 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-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: 19 Cell parameters: 89.090 91.280 176.170 90.000 90.000 90.000 Input sequence file: 2hr2-3.6-parrot-hancs.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 8464 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3177 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2986 (Rfree = 0.000) for 8464 atoms. Found 54 (54 requested) and removed 37 (27 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.52 2.91 Search for helices and strands: 0 residues in 0 chains, 8766 seeds are put forward NCS extension: 0 residues added, 8766 seeds are put forward Round 1: 508 peptides, 88 chains. Longest chain 16 peptides. Score 0.371 Round 2: 589 peptides, 70 chains. Longest chain 22 peptides. Score 0.543 Round 3: 591 peptides, 67 chains. Longest chain 39 peptides. Score 0.558 Round 4: 592 peptides, 60 chains. Longest chain 26 peptides. Score 0.589 Round 5: 575 peptides, 57 chains. Longest chain 25 peptides. Score 0.586 Taking the results from Round 4 Chains 69, Residues 532, Estimated correctness of the model 10.3 % 10 chains (102 residues) have been docked in sequence ------------------------------------------------------ 16963 reflections ( 98.21 % complete ) and 14252 restraints for refining 6916 atoms. 11843 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2451 (Rfree = 0.000) for 6916 atoms. Found 44 (44 requested) and removed 53 (22 requested) atoms. Cycle 2: After refmac, R = 0.2238 (Rfree = 0.000) for 6791 atoms. Found 34 (44 requested) and removed 41 (22 requested) atoms. Cycle 3: After refmac, R = 0.2154 (Rfree = 0.000) for 6746 atoms. Found 30 (43 requested) and removed 39 (21 requested) atoms. Cycle 4: After refmac, R = 0.2103 (Rfree = 0.000) for 6713 atoms. Found 14 (43 requested) and removed 41 (21 requested) atoms. Cycle 5: After refmac, R = 0.2052 (Rfree = 0.000) for 6672 atoms. Found 15 (42 requested) and removed 32 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.47 2.86 Search for helices and strands: 0 residues in 0 chains, 7061 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 7075 seeds are put forward Round 1: 564 peptides, 73 chains. Longest chain 19 peptides. Score 0.505 Round 2: 587 peptides, 66 chains. Longest chain 20 peptides. Score 0.558 Round 3: 585 peptides, 63 chains. Longest chain 30 peptides. Score 0.570 Round 4: 590 peptides, 61 chains. Longest chain 23 peptides. Score 0.583 Round 5: 604 peptides, 68 chains. Longest chain 21 peptides. Score 0.566 Taking the results from Round 4 Chains 66, Residues 529, Estimated correctness of the model 7.9 % 9 chains (89 residues) have been docked in sequence ------------------------------------------------------ 16963 reflections ( 98.21 % complete ) and 14116 restraints for refining 6918 atoms. 11763 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2358 (Rfree = 0.000) for 6918 atoms. Found 36 (44 requested) and removed 45 (22 requested) atoms. Cycle 7: After refmac, R = 0.2165 (Rfree = 0.000) for 6851 atoms. Found 24 (44 requested) and removed 29 (22 requested) atoms. Cycle 8: After refmac, R = 0.2094 (Rfree = 0.000) for 6812 atoms. Found 24 (43 requested) and removed 26 (21 requested) atoms. Cycle 9: After refmac, R = 0.2036 (Rfree = 0.000) for 6794 atoms. Found 19 (43 requested) and removed 34 (21 requested) atoms. Cycle 10: After refmac, R = 0.1956 (Rfree = 0.000) for 6769 atoms. Found 16 (43 requested) and removed 27 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 2.86 Search for helices and strands: 0 residues in 0 chains, 7140 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 7162 seeds are put forward Round 1: 535 peptides, 80 chains. Longest chain 15 peptides. Score 0.442 Round 2: 577 peptides, 70 chains. Longest chain 25 peptides. Score 0.532 Round 3: 555 peptides, 60 chains. Longest chain 27 peptides. Score 0.555 Round 4: 562 peptides, 66 chains. Longest chain 25 peptides. Score 0.535 Round 5: 578 peptides, 64 chains. Longest chain 27 peptides. Score 0.559 Taking the results from Round 5 Chains 69, Residues 514, Estimated correctness of the model 0.0 % 11 chains (106 residues) have been docked in sequence ------------------------------------------------------ 16963 reflections ( 98.21 % complete ) and 13945 restraints for refining 6918 atoms. 11592 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2436 (Rfree = 0.000) for 6918 atoms. Found 44 (44 requested) and removed 52 (22 requested) atoms. Cycle 12: After refmac, R = 0.2185 (Rfree = 0.000) for 6868 atoms. Found 29 (44 requested) and removed 38 (22 requested) atoms. Cycle 13: After refmac, R = 0.2084 (Rfree = 0.000) for 6829 atoms. Found 23 (44 requested) and removed 29 (22 requested) atoms. Cycle 14: After refmac, R = 0.2053 (Rfree = 0.000) for 6801 atoms. Found 25 (43 requested) and removed 32 (21 requested) atoms. Cycle 15: After refmac, R = 0.2023 (Rfree = 0.000) for 6784 atoms. Found 16 (43 requested) and removed 23 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.50 2.89 Search for helices and strands: 0 residues in 0 chains, 7166 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 7182 seeds are put forward Round 1: 539 peptides, 85 chains. Longest chain 19 peptides. Score 0.422 Round 2: 560 peptides, 64 chains. Longest chain 26 peptides. Score 0.542 Round 3: 559 peptides, 66 chains. Longest chain 29 peptides. Score 0.532 Round 4: 545 peptides, 58 chains. Longest chain 31 peptides. Score 0.555 Round 5: 549 peptides, 61 chains. Longest chain 23 peptides. Score 0.545 Taking the results from Round 4 Chains 63, Residues 487, Estimated correctness of the model 0.0 % 9 chains (104 residues) have been docked in sequence ------------------------------------------------------ 16963 reflections ( 98.21 % complete ) and 14342 restraints for refining 6916 atoms. 12080 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2428 (Rfree = 0.000) for 6916 atoms. Found 44 (44 requested) and removed 47 (22 requested) atoms. Cycle 17: After refmac, R = 0.2173 (Rfree = 0.000) for 6859 atoms. Found 22 (44 requested) and removed 29 (22 requested) atoms. Cycle 18: After refmac, R = 0.2112 (Rfree = 0.000) for 6829 atoms. Found 19 (43 requested) and removed 33 (21 requested) atoms. Cycle 19: After refmac, R = 0.2065 (Rfree = 0.000) for 6803 atoms. Found 14 (43 requested) and removed 28 (21 requested) atoms. Cycle 20: After refmac, R = 0.2032 (Rfree = 0.000) for 6769 atoms. Found 15 (43 requested) and removed 34 (21 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 2.86 Search for helices and strands: 0 residues in 0 chains, 7142 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 7165 seeds are put forward Round 1: 503 peptides, 81 chains. Longest chain 19 peptides. Score 0.401 Round 2: 572 peptides, 71 chains. Longest chain 20 peptides. Score 0.522 Round 3: 542 peptides, 71 chains. Longest chain 24 peptides. Score 0.492 Round 4: 556 peptides, 73 chains. Longest chain 22 peptides. Score 0.497 Round 5: 567 peptides, 69 chains. Longest chain 31 peptides. Score 0.526 Taking the results from Round 5 Chains 77, Residues 498, Estimated correctness of the model 0.0 % 8 chains (83 residues) have been docked in sequence ------------------------------------------------------ 16963 reflections ( 98.21 % complete ) and 14255 restraints for refining 6918 atoms. 12047 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2550 (Rfree = 0.000) for 6918 atoms. Found 44 (44 requested) and removed 38 (22 requested) atoms. Cycle 22: After refmac, R = 0.2297 (Rfree = 0.000) for 6872 atoms. Found 34 (44 requested) and removed 34 (22 requested) atoms. Cycle 23: After refmac, R = 0.2154 (Rfree = 0.000) for 6855 atoms. Found 23 (44 requested) and removed 29 (22 requested) atoms. Cycle 24: After refmac, R = 0.2079 (Rfree = 0.000) for 6837 atoms. Found 21 (43 requested) and removed 26 (21 requested) atoms. Cycle 25: After refmac, R = 0.2005 (Rfree = 0.000) for 6827 atoms. Found 7 (43 requested) and removed 25 (21 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.48 2.87 Search for helices and strands: 0 residues in 0 chains, 7169 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 7187 seeds are put forward Round 1: 502 peptides, 75 chains. Longest chain 15 peptides. Score 0.430 Round 2: 532 peptides, 72 chains. Longest chain 20 peptides. Score 0.477 Round 3: 524 peptides, 66 chains. Longest chain 22 peptides. Score 0.497 Round 4: 531 peptides, 71 chains. Longest chain 19 peptides. Score 0.481 Round 5: 527 peptides, 70 chains. Longest chain 16 peptides. Score 0.481 Taking the results from Round 3 Chains 66, Residues 458, Estimated correctness of the model 0.0 % 3 chains (43 residues) have been docked in sequence ------------------------------------------------------ 16963 reflections ( 98.21 % complete ) and 15019 restraints for refining 6918 atoms. 13091 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2330 (Rfree = 0.000) for 6918 atoms. Found 41 (44 requested) and removed 35 (22 requested) atoms. Cycle 27: After refmac, R = 0.2152 (Rfree = 0.000) for 6895 atoms. Found 33 (44 requested) and removed 31 (22 requested) atoms. Cycle 28: After refmac, R = 0.2080 (Rfree = 0.000) for 6883 atoms. Found 29 (44 requested) and removed 30 (22 requested) atoms. Cycle 29: After refmac, R = 0.1989 (Rfree = 0.000) for 6870 atoms. Found 24 (44 requested) and removed 27 (22 requested) atoms. Cycle 30: After refmac, R = 0.1964 (Rfree = 0.000) for 6855 atoms. Found 12 (44 requested) and removed 25 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.46 2.86 Search for helices and strands: 0 residues in 0 chains, 7237 seeds are put forward NCS extension: 31 residues added (4 deleted due to clashes), 7268 seeds are put forward Round 1: 514 peptides, 88 chains. Longest chain 16 peptides. Score 0.378 Round 2: 557 peptides, 76 chains. Longest chain 23 peptides. Score 0.484 Round 3: 551 peptides, 74 chains. Longest chain 21 peptides. Score 0.487 Round 4: 552 peptides, 77 chains. Longest chain 28 peptides. Score 0.474 Round 5: 550 peptides, 73 chains. Longest chain 20 peptides. Score 0.491 Taking the results from Round 5 Chains 75, Residues 477, Estimated correctness of the model 0.0 % 10 chains (83 residues) have been docked in sequence ------------------------------------------------------ 16963 reflections ( 98.21 % complete ) and 14631 restraints for refining 6918 atoms. 12536 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2284 (Rfree = 0.000) for 6918 atoms. Found 44 (44 requested) and removed 43 (22 requested) atoms. Cycle 32: After refmac, R = 0.2047 (Rfree = 0.000) for 6873 atoms. Found 25 (44 requested) and removed 30 (22 requested) atoms. Cycle 33: After refmac, R = 0.1968 (Rfree = 0.000) for 6839 atoms. Found 17 (44 requested) and removed 30 (22 requested) atoms. Cycle 34: After refmac, R = 0.1919 (Rfree = 0.000) for 6809 atoms. Found 12 (43 requested) and removed 28 (21 requested) atoms. Cycle 35: After refmac, R = 0.1927 (Rfree = 0.000) for 6787 atoms. Found 16 (43 requested) and removed 27 (21 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.52 2.91 Search for helices and strands: 0 residues in 0 chains, 7168 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 7187 seeds are put forward Round 1: 462 peptides, 82 chains. Longest chain 19 peptides. Score 0.347 Round 2: 510 peptides, 72 chains. Longest chain 19 peptides. Score 0.454 Round 3: 491 peptides, 69 chains. Longest chain 26 peptides. Score 0.448 Round 4: 516 peptides, 72 chains. Longest chain 26 peptides. Score 0.460 Round 5: 521 peptides, 75 chains. Longest chain 17 peptides. Score 0.451 Taking the results from Round 4 Chains 74, Residues 444, Estimated correctness of the model 0.0 % 8 chains (80 residues) have been docked in sequence ------------------------------------------------------ 16963 reflections ( 98.21 % complete ) and 14740 restraints for refining 6917 atoms. 12746 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2307 (Rfree = 0.000) for 6917 atoms. Found 44 (44 requested) and removed 36 (22 requested) atoms. Cycle 37: After refmac, R = 0.2175 (Rfree = 0.000) for 6882 atoms. Found 39 (44 requested) and removed 29 (22 requested) atoms. Cycle 38: After refmac, R = 0.2087 (Rfree = 0.000) for 6877 atoms. Found 31 (44 requested) and removed 25 (22 requested) atoms. Cycle 39: After refmac, R = 0.2049 (Rfree = 0.000) for 6875 atoms. Found 23 (44 requested) and removed 25 (22 requested) atoms. Cycle 40: After refmac, R = 0.2017 (Rfree = 0.000) for 6860 atoms. Found 24 (44 requested) and removed 27 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.50 2.89 Search for helices and strands: 0 residues in 0 chains, 7184 seeds are put forward NCS extension: 34 residues added (4 deleted due to clashes), 7218 seeds are put forward Round 1: 471 peptides, 87 chains. Longest chain 15 peptides. Score 0.332 Round 2: 505 peptides, 74 chains. Longest chain 22 peptides. Score 0.438 Round 3: 480 peptides, 77 chains. Longest chain 14 peptides. Score 0.395 Round 4: 492 peptides, 71 chains. Longest chain 18 peptides. Score 0.439 Round 5: 517 peptides, 73 chains. Longest chain 22 peptides. Score 0.456 Taking the results from Round 5 Chains 75, Residues 444, Estimated correctness of the model 0.0 % 7 chains (58 residues) have been docked in sequence ------------------------------------------------------ 16963 reflections ( 98.21 % complete ) and 14939 restraints for refining 6919 atoms. 13050 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2386 (Rfree = 0.000) for 6919 atoms. Found 44 (44 requested) and removed 33 (22 requested) atoms. Cycle 42: After refmac, R = 0.2208 (Rfree = 0.000) for 6906 atoms. Found 31 (44 requested) and removed 28 (22 requested) atoms. Cycle 43: After refmac, R = 0.2122 (Rfree = 0.000) for 6893 atoms. Found 23 (44 requested) and removed 32 (22 requested) atoms. Cycle 44: After refmac, R = 0.2062 (Rfree = 0.000) for 6864 atoms. Found 22 (44 requested) and removed 32 (22 requested) atoms. Cycle 45: After refmac, R = 0.2011 (Rfree = 0.000) for 6843 atoms. Found 27 (43 requested) and removed 26 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.48 2.87 Search for helices and strands: 0 residues in 0 chains, 7229 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 7246 seeds are put forward Round 1: 423 peptides, 79 chains. Longest chain 14 peptides. Score 0.315 Round 2: 475 peptides, 78 chains. Longest chain 15 peptides. Score 0.384 Round 3: 471 peptides, 73 chains. Longest chain 12 peptides. Score 0.405 Round 4: 485 peptides, 71 chains. Longest chain 17 peptides. Score 0.431 Round 5: 485 peptides, 64 chains. Longest chain 21 peptides. Score 0.466 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 66, Residues 421, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2hr2-3_warpNtrace.pdb as input Building loops using Loopy2018 66 chains (421 residues) following loop building 3 chains (19 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16963 reflections ( 98.21 % complete ) and 15573 restraints for refining 6917 atoms. 13897 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2382 (Rfree = 0.000) for 6917 atoms. Found 0 (44 requested) and removed 22 (22 requested) atoms. Cycle 47: After refmac, R = 0.2218 (Rfree = 0.000) for 6862 atoms. Found 0 (44 requested) and removed 22 (22 requested) atoms. Cycle 48: After refmac, R = 0.2194 (Rfree = 0.000) for 6830 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 49: After refmac, R = 0.2138 (Rfree = 0.000) for 6790 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:54:52 GMT 2018 Job finished. TimeTaking 91.84 Used memory is bytes: 17586544