null Sun 23 Dec 22:22:52 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 1vm8-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vm8-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vm8-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vm8-3.8-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/1vm8-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vm8-3.8-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 22:23:02 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/1vm8-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vm8-3.8-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 793 and 0 Target number of residues in the AU: 793 Target solvent content: 0.6542 Checking the provided sequence file Detected sequence length: 534 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 1068 Adjusted target solvent content: 0.53 Input MTZ file: 1vm8-3.8-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: 80.094 73.402 107.132 90.000 99.827 90.000 Input sequence file: 1vm8-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 8544 target number of atoms Had to go as low as 0.65 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: 105.560 3.800 Wilson plot Bfac: 80.80 12194 reflections ( 98.99 % complete ) and 0 restraints for refining 9484 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3278 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3172 (Rfree = 0.000) for 9484 atoms. Found 52 (52 requested) and removed 78 (26 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.62 3.48 Search for helices and strands: 0 residues in 0 chains, 9638 seeds are put forward NCS extension: 0 residues added, 9638 seeds are put forward Round 1: 376 peptides, 78 chains. Longest chain 12 peptides. Score 0.269 Round 2: 457 peptides, 77 chains. Longest chain 15 peptides. Score 0.389 Round 3: 505 peptides, 83 chains. Longest chain 16 peptides. Score 0.418 Round 4: 534 peptides, 82 chains. Longest chain 20 peptides. Score 0.459 Round 5: 551 peptides, 79 chains. Longest chain 21 peptides. Score 0.495 Taking the results from Round 5 Chains 82, Residues 472, Estimated correctness of the model 0.0 % 6 chains (37 residues) have been docked in sequence ------------------------------------------------------ 12194 reflections ( 98.99 % complete ) and 18214 restraints for refining 7723 atoms. 16302 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2531 (Rfree = 0.000) for 7723 atoms. Found 33 (42 requested) and removed 70 (21 requested) atoms. Cycle 2: After refmac, R = 0.2408 (Rfree = 0.000) for 7584 atoms. Found 28 (42 requested) and removed 62 (21 requested) atoms. Cycle 3: After refmac, R = 0.2326 (Rfree = 0.000) for 7499 atoms. Found 24 (41 requested) and removed 60 (20 requested) atoms. Cycle 4: After refmac, R = 0.2235 (Rfree = 0.000) for 7436 atoms. Found 19 (41 requested) and removed 39 (20 requested) atoms. Cycle 5: After refmac, R = 0.1937 (Rfree = 0.000) for 7395 atoms. Found 8 (40 requested) and removed 32 (20 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.64 3.50 Search for helices and strands: 0 residues in 0 chains, 7656 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 7678 seeds are put forward Round 1: 471 peptides, 85 chains. Longest chain 16 peptides. Score 0.362 Round 2: 522 peptides, 81 chains. Longest chain 24 peptides. Score 0.450 Round 3: 526 peptides, 79 chains. Longest chain 17 peptides. Score 0.466 Round 4: 540 peptides, 70 chains. Longest chain 23 peptides. Score 0.529 Round 5: 551 peptides, 76 chains. Longest chain 21 peptides. Score 0.510 Taking the results from Round 4 Chains 70, Residues 470, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12194 reflections ( 98.99 % complete ) and 18071 restraints for refining 7689 atoms. 16261 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2215 (Rfree = 0.000) for 7689 atoms. Found 29 (42 requested) and removed 79 (21 requested) atoms. Cycle 7: After refmac, R = 0.2236 (Rfree = 0.000) for 7573 atoms. Found 42 (42 requested) and removed 72 (21 requested) atoms. Cycle 8: After refmac, R = 0.1855 (Rfree = 0.000) for 7512 atoms. Found 7 (41 requested) and removed 45 (20 requested) atoms. Cycle 9: After refmac, R = 0.2005 (Rfree = 0.000) for 7449 atoms. Found 29 (41 requested) and removed 38 (20 requested) atoms. Cycle 10: After refmac, R = 0.2111 (Rfree = 0.000) for 7428 atoms. Found 40 (40 requested) and removed 41 (20 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.60 3.46 Search for helices and strands: 0 residues in 0 chains, 7671 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 7705 seeds are put forward Round 1: 449 peptides, 84 chains. Longest chain 17 peptides. Score 0.338 Round 2: 478 peptides, 76 chains. Longest chain 18 peptides. Score 0.422 Round 3: 482 peptides, 76 chains. Longest chain 19 peptides. Score 0.428 Round 4: 497 peptides, 76 chains. Longest chain 21 peptides. Score 0.446 Round 5: 513 peptides, 72 chains. Longest chain 19 peptides. Score 0.487 Taking the results from Round 5 Chains 73, Residues 441, Estimated correctness of the model 0.0 % 6 chains (44 residues) have been docked in sequence ------------------------------------------------------ 12194 reflections ( 98.99 % complete ) and 17555 restraints for refining 7726 atoms. 15723 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2218 (Rfree = 0.000) for 7726 atoms. Found 33 (42 requested) and removed 90 (21 requested) atoms. Cycle 12: After refmac, R = 0.2177 (Rfree = 0.000) for 7617 atoms. Found 36 (42 requested) and removed 51 (21 requested) atoms. Cycle 13: After refmac, R = 0.2175 (Rfree = 0.000) for 7568 atoms. Found 41 (41 requested) and removed 47 (20 requested) atoms. Cycle 14: After refmac, R = 0.2188 (Rfree = 0.000) for 7529 atoms. Found 41 (41 requested) and removed 53 (20 requested) atoms. Cycle 15: After refmac, R = 0.2037 (Rfree = 0.000) for 7483 atoms. Found 41 (41 requested) and removed 37 (20 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.63 3.49 Search for helices and strands: 0 residues in 0 chains, 7763 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 7780 seeds are put forward Round 1: 428 peptides, 79 chains. Longest chain 13 peptides. Score 0.338 Round 2: 485 peptides, 74 chains. Longest chain 14 peptides. Score 0.442 Round 3: 468 peptides, 72 chains. Longest chain 21 peptides. Score 0.432 Round 4: 491 peptides, 73 chains. Longest chain 17 peptides. Score 0.455 Round 5: 491 peptides, 75 chains. Longest chain 16 peptides. Score 0.444 Taking the results from Round 4 Chains 73, Residues 418, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 12194 reflections ( 98.99 % complete ) and 18227 restraints for refining 7726 atoms. 16563 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2145 (Rfree = 0.000) for 7726 atoms. Found 34 (42 requested) and removed 56 (21 requested) atoms. Cycle 17: After refmac, R = 0.2027 (Rfree = 0.000) for 7645 atoms. Found 36 (42 requested) and removed 42 (21 requested) atoms. Cycle 18: After refmac, R = 0.2025 (Rfree = 0.000) for 7594 atoms. Found 42 (42 requested) and removed 47 (21 requested) atoms. Cycle 19: After refmac, R = 0.1938 (Rfree = 0.000) for 7554 atoms. Found 36 (41 requested) and removed 41 (20 requested) atoms. Cycle 20: After refmac, R = 0.1950 (Rfree = 0.000) for 7519 atoms. Found 39 (41 requested) and removed 45 (20 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.59 3.45 Search for helices and strands: 0 residues in 0 chains, 7727 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 7746 seeds are put forward Round 1: 405 peptides, 79 chains. Longest chain 13 peptides. Score 0.305 Round 2: 447 peptides, 74 chains. Longest chain 16 peptides. Score 0.394 Round 3: 476 peptides, 74 chains. Longest chain 19 peptides. Score 0.431 Round 4: 471 peptides, 74 chains. Longest chain 16 peptides. Score 0.425 Round 5: 472 peptides, 73 chains. Longest chain 15 peptides. Score 0.432 Taking the results from Round 5 Chains 73, Residues 399, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 12194 reflections ( 98.99 % complete ) and 18154 restraints for refining 7728 atoms. 16573 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2051 (Rfree = 0.000) for 7728 atoms. Found 42 (42 requested) and removed 67 (21 requested) atoms. Cycle 22: After refmac, R = 0.1990 (Rfree = 0.000) for 7652 atoms. Found 42 (42 requested) and removed 50 (21 requested) atoms. Cycle 23: After refmac, R = 0.1959 (Rfree = 0.000) for 7613 atoms. Found 42 (42 requested) and removed 36 (21 requested) atoms. Cycle 24: After refmac, R = 0.1890 (Rfree = 0.000) for 7595 atoms. Found 41 (41 requested) and removed 34 (20 requested) atoms. Cycle 25: After refmac, R = 0.1487 (Rfree = 0.000) for 7582 atoms. Found 7 (41 requested) and removed 27 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.65 3.51 Search for helices and strands: 0 residues in 0 chains, 7801 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 7817 seeds are put forward Round 1: 412 peptides, 84 chains. Longest chain 12 peptides. Score 0.285 Round 2: 467 peptides, 84 chains. Longest chain 17 peptides. Score 0.362 Round 3: 487 peptides, 87 chains. Longest chain 15 peptides. Score 0.372 Round 4: 487 peptides, 77 chains. Longest chain 14 peptides. Score 0.428 Round 5: 481 peptides, 75 chains. Longest chain 16 peptides. Score 0.432 Taking the results from Round 5 Chains 75, Residues 406, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 12194 reflections ( 98.99 % complete ) and 18127 restraints for refining 7726 atoms. 16504 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1943 (Rfree = 0.000) for 7726 atoms. Found 37 (42 requested) and removed 56 (21 requested) atoms. Cycle 27: After refmac, R = 0.1859 (Rfree = 0.000) for 7672 atoms. Found 35 (42 requested) and removed 36 (21 requested) atoms. Cycle 28: After refmac, R = 0.1790 (Rfree = 0.000) for 7653 atoms. Found 38 (42 requested) and removed 37 (21 requested) atoms. Cycle 29: After refmac, R = 0.1748 (Rfree = 0.000) for 7635 atoms. Found 42 (42 requested) and removed 37 (21 requested) atoms. Cycle 30: After refmac, R = 0.1686 (Rfree = 0.000) for 7620 atoms. Found 32 (42 requested) and removed 32 (21 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 3.45 Search for helices and strands: 0 residues in 0 chains, 7855 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 7881 seeds are put forward Round 1: 375 peptides, 78 chains. Longest chain 11 peptides. Score 0.267 Round 2: 456 peptides, 80 chains. Longest chain 14 peptides. Score 0.371 Round 3: 453 peptides, 78 chains. Longest chain 17 peptides. Score 0.378 Round 4: 453 peptides, 77 chains. Longest chain 14 peptides. Score 0.384 Round 5: 478 peptides, 76 chains. Longest chain 15 peptides. Score 0.422 Taking the results from Round 5 Chains 78, Residues 402, Estimated correctness of the model 0.0 % 9 chains (59 residues) have been docked in sequence ------------------------------------------------------ 12194 reflections ( 98.99 % complete ) and 17746 restraints for refining 7725 atoms. 16006 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1889 (Rfree = 0.000) for 7725 atoms. Found 36 (42 requested) and removed 54 (21 requested) atoms. Cycle 32: After refmac, R = 0.1733 (Rfree = 0.000) for 7673 atoms. Found 16 (42 requested) and removed 32 (21 requested) atoms. Cycle 33: After refmac, R = 0.1694 (Rfree = 0.000) for 7645 atoms. Found 12 (42 requested) and removed 35 (21 requested) atoms. Cycle 34: After refmac, R = 0.1684 (Rfree = 0.000) for 7614 atoms. Found 13 (41 requested) and removed 33 (20 requested) atoms. Cycle 35: After refmac, R = 0.1692 (Rfree = 0.000) for 7585 atoms. Found 22 (41 requested) and removed 33 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.61 3.47 Search for helices and strands: 0 residues in 0 chains, 7780 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 7800 seeds are put forward Round 1: 378 peptides, 81 chains. Longest chain 9 peptides. Score 0.253 Round 2: 473 peptides, 82 chains. Longest chain 17 peptides. Score 0.382 Round 3: 493 peptides, 79 chains. Longest chain 16 peptides. Score 0.425 Round 4: 478 peptides, 81 chains. Longest chain 17 peptides. Score 0.394 Round 5: 466 peptides, 73 chains. Longest chain 21 peptides. Score 0.424 Taking the results from Round 3 Chains 79, Residues 414, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 12194 reflections ( 98.99 % complete ) and 18086 restraints for refining 7726 atoms. 16466 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1943 (Rfree = 0.000) for 7726 atoms. Found 42 (42 requested) and removed 65 (21 requested) atoms. Cycle 37: After refmac, R = 0.1898 (Rfree = 0.000) for 7657 atoms. Found 42 (42 requested) and removed 50 (21 requested) atoms. Cycle 38: After refmac, R = 0.1831 (Rfree = 0.000) for 7628 atoms. Found 42 (42 requested) and removed 45 (21 requested) atoms. Cycle 39: After refmac, R = 0.1580 (Rfree = 0.000) for 7606 atoms. Found 14 (41 requested) and removed 26 (20 requested) atoms. Cycle 40: After refmac, R = 0.1658 (Rfree = 0.000) for 7580 atoms. Found 6 (41 requested) and removed 29 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.64 3.50 Search for helices and strands: 0 residues in 0 chains, 7802 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 7820 seeds are put forward Round 1: 357 peptides, 75 chains. Longest chain 10 peptides. Score 0.259 Round 2: 405 peptides, 72 chains. Longest chain 17 peptides. Score 0.348 Round 3: 416 peptides, 75 chains. Longest chain 12 peptides. Score 0.345 Round 4: 427 peptides, 73 chains. Longest chain 11 peptides. Score 0.373 Round 5: 411 peptides, 75 chains. Longest chain 13 peptides. Score 0.338 Taking the results from Round 4 Chains 73, Residues 354, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 12194 reflections ( 98.99 % complete ) and 18203 restraints for refining 7728 atoms. 16773 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1928 (Rfree = 0.000) for 7728 atoms. Found 41 (42 requested) and removed 39 (21 requested) atoms. Cycle 42: After refmac, R = 0.1930 (Rfree = 0.000) for 7688 atoms. Found 42 (42 requested) and removed 38 (21 requested) atoms. Cycle 43: After refmac, R = 0.1955 (Rfree = 0.000) for 7673 atoms. Found 42 (42 requested) and removed 39 (21 requested) atoms. Cycle 44: After refmac, R = 0.1934 (Rfree = 0.000) for 7656 atoms. Found 42 (42 requested) and removed 28 (21 requested) atoms. Cycle 45: After refmac, R = 0.1622 (Rfree = 0.000) for 7652 atoms. Found 12 (42 requested) and removed 27 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.64 3.50 Search for helices and strands: 0 residues in 0 chains, 7806 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 7818 seeds are put forward Round 1: 299 peptides, 63 chains. Longest chain 10 peptides. Score 0.247 Round 2: 352 peptides, 68 chains. Longest chain 13 peptides. Score 0.296 Round 3: 361 peptides, 61 chains. Longest chain 14 peptides. Score 0.354 Round 4: 358 peptides, 65 chains. Longest chain 14 peptides. Score 0.324 Round 5: 358 peptides, 59 chains. Longest chain 14 peptides. Score 0.362 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 59, Residues 299, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 1vm8-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12194 reflections ( 98.99 % complete ) and 18586 restraints for refining 7727 atoms. 17418 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1923 (Rfree = 0.000) for 7727 atoms. Found 0 (42 requested) and removed 21 (21 requested) atoms. Cycle 47: After refmac, R = 0.2074 (Rfree = 0.000) for 7686 atoms. Found 0 (42 requested) and removed 21 (21 requested) atoms. Cycle 48: After refmac, R = 0.2029 (Rfree = 0.000) for 7652 atoms. Found 0 (42 requested) and removed 21 (21 requested) atoms. Cycle 49: After refmac, R = 0.1608 (Rfree = 0.000) for 7613 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:53:45 GMT 2018 Job finished. TimeTaking 90.88 Used memory is bytes: 22236888