Mon 24 Dec 07:29:46 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2okc-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2okc-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2okc-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2okc-3.6-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2okc-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2okc-3.6-parrot-noncs ############### 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 07:29:50 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/noncs/ArpWArp/wArpResults/WorkingDir/2okc-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2okc-3.6-parrot-noncs/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 620 and 0 Target number of residues in the AU: 620 Target solvent content: 0.6596 Checking the provided sequence file Detected sequence length: 445 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 890 Adjusted target solvent content: 0.51 Input MTZ file: 2okc-3.6-parrot-noncs.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: 75.340 85.750 152.600 90.000 90.000 90.000 Input sequence file: 2okc-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 7120 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: 28.546 3.600 Wilson plot Bfac: 84.60 10697 reflections ( 89.31 % complete ) and 0 restraints for refining 7907 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3349 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3091 (Rfree = 0.000) for 7907 atoms. Found 50 (50 requested) and removed 69 (25 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.65 3.60 Search for helices and strands: 0 residues in 0 chains, 8038 seeds are put forward NCS extension: 0 residues added, 8038 seeds are put forward Round 1: 337 peptides, 69 chains. Longest chain 10 peptides. Score 0.285 Round 2: 407 peptides, 72 chains. Longest chain 12 peptides. Score 0.385 Round 3: 443 peptides, 74 chains. Longest chain 16 peptides. Score 0.429 Round 4: 457 peptides, 73 chains. Longest chain 15 peptides. Score 0.457 Round 5: 466 peptides, 72 chains. Longest chain 16 peptides. Score 0.477 Taking the results from Round 5 Chains 73, Residues 394, Estimated correctness of the model 0.0 % 5 chains (35 residues) have been docked in sequence ------------------------------------------------------ 10697 reflections ( 89.31 % complete ) and 14806 restraints for refining 6450 atoms. 13197 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2589 (Rfree = 0.000) for 6450 atoms. Found 31 (41 requested) and removed 46 (20 requested) atoms. Cycle 2: After refmac, R = 0.2314 (Rfree = 0.000) for 6330 atoms. Found 31 (41 requested) and removed 42 (20 requested) atoms. Cycle 3: After refmac, R = 0.2146 (Rfree = 0.000) for 6283 atoms. Found 22 (40 requested) and removed 34 (20 requested) atoms. Cycle 4: After refmac, R = 0.2089 (Rfree = 0.000) for 6257 atoms. Found 24 (40 requested) and removed 36 (20 requested) atoms. Cycle 5: After refmac, R = 0.1991 (Rfree = 0.000) for 6229 atoms. Found 24 (40 requested) and removed 34 (20 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.56 3.51 Search for helices and strands: 0 residues in 0 chains, 6429 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 6448 seeds are put forward Round 1: 403 peptides, 78 chains. Longest chain 10 peptides. Score 0.335 Round 2: 455 peptides, 71 chains. Longest chain 19 peptides. Score 0.467 Round 3: 471 peptides, 75 chains. Longest chain 13 peptides. Score 0.465 Round 4: 448 peptides, 67 chains. Longest chain 20 peptides. Score 0.483 Round 5: 449 peptides, 62 chains. Longest chain 16 peptides. Score 0.516 Taking the results from Round 5 Chains 62, Residues 387, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 10697 reflections ( 89.31 % complete ) and 15210 restraints for refining 6453 atoms. 13704 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2200 (Rfree = 0.000) for 6453 atoms. Found 26 (41 requested) and removed 40 (20 requested) atoms. Cycle 7: After refmac, R = 0.2129 (Rfree = 0.000) for 6389 atoms. Found 30 (41 requested) and removed 37 (20 requested) atoms. Cycle 8: After refmac, R = 0.2050 (Rfree = 0.000) for 6353 atoms. Found 21 (40 requested) and removed 34 (20 requested) atoms. Cycle 9: After refmac, R = 0.1752 (Rfree = 0.000) for 6320 atoms. Found 8 (40 requested) and removed 22 (20 requested) atoms. Cycle 10: After refmac, R = 0.1708 (Rfree = 0.000) for 6293 atoms. Found 9 (40 requested) and removed 23 (20 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.55 3.50 Search for helices and strands: 0 residues in 0 chains, 6495 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 6511 seeds are put forward Round 1: 362 peptides, 69 chains. Longest chain 10 peptides. Score 0.330 Round 2: 400 peptides, 64 chains. Longest chain 14 peptides. Score 0.429 Round 3: 427 peptides, 65 chains. Longest chain 14 peptides. Score 0.464 Round 4: 429 peptides, 63 chains. Longest chain 17 peptides. Score 0.481 Round 5: 416 peptides, 62 chains. Longest chain 17 peptides. Score 0.468 Taking the results from Round 4 Chains 63, Residues 366, Estimated correctness of the model 0.0 % 6 chains (30 residues) have been docked in sequence ------------------------------------------------------ 10697 reflections ( 89.31 % complete ) and 15046 restraints for refining 6453 atoms. 13567 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2104 (Rfree = 0.000) for 6453 atoms. Found 32 (41 requested) and removed 40 (20 requested) atoms. Cycle 12: After refmac, R = 0.2010 (Rfree = 0.000) for 6408 atoms. Found 28 (41 requested) and removed 27 (20 requested) atoms. Cycle 13: After refmac, R = 0.1971 (Rfree = 0.000) for 6385 atoms. Found 25 (41 requested) and removed 35 (20 requested) atoms. Cycle 14: After refmac, R = 0.1849 (Rfree = 0.000) for 6362 atoms. Found 24 (40 requested) and removed 28 (20 requested) atoms. Cycle 15: After refmac, R = 0.1902 (Rfree = 0.000) for 6350 atoms. Found 26 (40 requested) and removed 29 (20 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.51 3.46 Search for helices and strands: 0 residues in 0 chains, 6596 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 6621 seeds are put forward Round 1: 391 peptides, 75 chains. Longest chain 10 peptides. Score 0.336 Round 2: 444 peptides, 73 chains. Longest chain 20 peptides. Score 0.437 Round 3: 439 peptides, 76 chains. Longest chain 12 peptides. Score 0.409 Round 4: 437 peptides, 71 chains. Longest chain 15 peptides. Score 0.440 Round 5: 446 peptides, 72 chains. Longest chain 15 peptides. Score 0.447 Taking the results from Round 5 Chains 74, Residues 374, Estimated correctness of the model 0.0 % 8 chains (52 residues) have been docked in sequence ------------------------------------------------------ 10697 reflections ( 89.31 % complete ) and 14517 restraints for refining 6453 atoms. 12947 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2220 (Rfree = 0.000) for 6453 atoms. Found 35 (41 requested) and removed 41 (20 requested) atoms. Cycle 17: After refmac, R = 0.2093 (Rfree = 0.000) for 6424 atoms. Found 34 (41 requested) and removed 30 (20 requested) atoms. Cycle 18: After refmac, R = 0.2017 (Rfree = 0.000) for 6415 atoms. Found 27 (41 requested) and removed 31 (20 requested) atoms. Cycle 19: After refmac, R = 0.1992 (Rfree = 0.000) for 6398 atoms. Found 24 (41 requested) and removed 30 (20 requested) atoms. Cycle 20: After refmac, R = 0.1959 (Rfree = 0.000) for 6377 atoms. Found 18 (41 requested) and removed 32 (20 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.57 3.52 Search for helices and strands: 0 residues in 0 chains, 6556 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 6569 seeds are put forward Round 1: 366 peptides, 72 chains. Longest chain 12 peptides. Score 0.315 Round 2: 397 peptides, 65 chains. Longest chain 14 peptides. Score 0.418 Round 3: 409 peptides, 70 chains. Longest chain 15 peptides. Score 0.402 Round 4: 414 peptides, 65 chains. Longest chain 16 peptides. Score 0.445 Round 5: 395 peptides, 69 chains. Longest chain 17 peptides. Score 0.386 Taking the results from Round 4 Chains 65, Residues 349, Estimated correctness of the model 0.0 % 8 chains (38 residues) have been docked in sequence ------------------------------------------------------ 10697 reflections ( 89.31 % complete ) and 14835 restraints for refining 6453 atoms. 13406 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2195 (Rfree = 0.000) for 6453 atoms. Found 31 (41 requested) and removed 33 (20 requested) atoms. Cycle 22: After refmac, R = 0.2053 (Rfree = 0.000) for 6427 atoms. Found 20 (41 requested) and removed 35 (20 requested) atoms. Cycle 23: After refmac, R = 0.1991 (Rfree = 0.000) for 6398 atoms. Found 22 (41 requested) and removed 30 (20 requested) atoms. Cycle 24: After refmac, R = 0.1958 (Rfree = 0.000) for 6379 atoms. Found 22 (40 requested) and removed 24 (20 requested) atoms. Cycle 25: After refmac, R = 0.1686 (Rfree = 0.000) for 6368 atoms. Found 7 (40 requested) and removed 22 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.54 3.49 Search for helices and strands: 0 residues in 0 chains, 6522 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 6543 seeds are put forward Round 1: 350 peptides, 72 chains. Longest chain 9 peptides. Score 0.286 Round 2: 376 peptides, 64 chains. Longest chain 11 peptides. Score 0.390 Round 3: 381 peptides, 63 chains. Longest chain 13 peptides. Score 0.406 Round 4: 383 peptides, 62 chains. Longest chain 14 peptides. Score 0.416 Round 5: 374 peptides, 63 chains. Longest chain 12 peptides. Score 0.394 Taking the results from Round 4 Chains 63, Residues 321, Estimated correctness of the model 0.0 % 4 chains (28 residues) have been docked in sequence ------------------------------------------------------ 10697 reflections ( 89.31 % complete ) and 15229 restraints for refining 6454 atoms. 13940 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2228 (Rfree = 0.000) for 6454 atoms. Found 32 (41 requested) and removed 36 (20 requested) atoms. Cycle 27: After refmac, R = 0.2136 (Rfree = 0.000) for 6423 atoms. Found 40 (41 requested) and removed 24 (20 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2068 (Rfree = 0.000) for 6426 atoms. Found 41 (41 requested) and removed 33 (20 requested) atoms. Cycle 29: After refmac, R = 0.1956 (Rfree = 0.000) for 6416 atoms. Found 38 (41 requested) and removed 25 (20 requested) atoms. Cycle 30: After refmac, R = 0.1887 (Rfree = 0.000) for 6417 atoms. Found 33 (41 requested) and removed 25 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.54 3.49 Search for helices and strands: 0 residues in 0 chains, 6613 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 6631 seeds are put forward Round 1: 289 peptides, 62 chains. Longest chain 8 peptides. Score 0.250 Round 2: 327 peptides, 64 chains. Longest chain 12 peptides. Score 0.305 Round 3: 335 peptides, 58 chains. Longest chain 13 peptides. Score 0.365 Round 4: 329 peptides, 57 chains. Longest chain 16 peptides. Score 0.362 Round 5: 331 peptides, 59 chains. Longest chain 11 peptides. Score 0.351 Taking the results from Round 3 Chains 58, Residues 277, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 10697 reflections ( 89.31 % complete ) and 15209 restraints for refining 6453 atoms. 14084 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2020 (Rfree = 0.000) for 6453 atoms. Found 41 (41 requested) and removed 38 (20 requested) atoms. Cycle 32: After refmac, R = 0.1978 (Rfree = 0.000) for 6436 atoms. Found 41 (41 requested) and removed 27 (20 requested) atoms. Cycle 33: After refmac, R = 0.1904 (Rfree = 0.000) for 6442 atoms. Found 38 (41 requested) and removed 33 (20 requested) atoms. Cycle 34: After refmac, R = 0.1880 (Rfree = 0.000) for 6432 atoms. Found 29 (41 requested) and removed 28 (20 requested) atoms. Cycle 35: After refmac, R = 0.1625 (Rfree = 0.000) for 6425 atoms. Found 5 (41 requested) and removed 22 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 3.49 Search for helices and strands: 0 residues in 0 chains, 6566 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 6581 seeds are put forward Round 1: 304 peptides, 64 chains. Longest chain 10 peptides. Score 0.263 Round 2: 336 peptides, 66 chains. Longest chain 11 peptides. Score 0.306 Round 3: 335 peptides, 58 chains. Longest chain 12 peptides. Score 0.365 Round 4: 334 peptides, 61 chains. Longest chain 11 peptides. Score 0.341 Round 5: 344 peptides, 58 chains. Longest chain 11 peptides. Score 0.381 Taking the results from Round 5 Chains 59, Residues 286, Estimated correctness of the model 0.0 % 6 chains (29 residues) have been docked in sequence ------------------------------------------------------ 10697 reflections ( 89.31 % complete ) and 15065 restraints for refining 6452 atoms. 13881 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2080 (Rfree = 0.000) for 6452 atoms. Found 33 (41 requested) and removed 32 (20 requested) atoms. Cycle 37: After refmac, R = 0.1982 (Rfree = 0.000) for 6432 atoms. Found 22 (41 requested) and removed 29 (20 requested) atoms. Cycle 38: After refmac, R = 0.1902 (Rfree = 0.000) for 6412 atoms. Found 24 (41 requested) and removed 24 (20 requested) atoms. Cycle 39: After refmac, R = 0.1901 (Rfree = 0.000) for 6401 atoms. Found 26 (41 requested) and removed 25 (20 requested) atoms. Cycle 40: After refmac, R = 0.1884 (Rfree = 0.000) for 6391 atoms. Found 23 (41 requested) and removed 27 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.56 3.51 Search for helices and strands: 0 residues in 0 chains, 6547 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 6558 seeds are put forward Round 1: 293 peptides, 60 chains. Longest chain 10 peptides. Score 0.274 Round 2: 339 peptides, 60 chains. Longest chain 16 peptides. Score 0.357 Round 3: 332 peptides, 57 chains. Longest chain 17 peptides. Score 0.368 Round 4: 342 peptides, 57 chains. Longest chain 14 peptides. Score 0.385 Round 5: 331 peptides, 56 chains. Longest chain 13 peptides. Score 0.373 Taking the results from Round 4 Chains 57, Residues 285, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10697 reflections ( 89.31 % complete ) and 15568 restraints for refining 6454 atoms. 14485 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2102 (Rfree = 0.000) for 6454 atoms. Found 37 (41 requested) and removed 29 (20 requested) atoms. Cycle 42: After refmac, R = 0.2006 (Rfree = 0.000) for 6446 atoms. Found 24 (41 requested) and removed 24 (20 requested) atoms. Cycle 43: After refmac, R = 0.1954 (Rfree = 0.000) for 6438 atoms. Found 29 (41 requested) and removed 26 (20 requested) atoms. Cycle 44: After refmac, R = 0.1723 (Rfree = 0.000) for 6433 atoms. Found 4 (41 requested) and removed 24 (20 requested) atoms. Cycle 45: After refmac, R = 0.1717 (Rfree = 0.000) for 6412 atoms. Found 7 (41 requested) and removed 20 (20 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.50 3.45 Search for helices and strands: 0 residues in 0 chains, 6538 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 6556 seeds are put forward Round 1: 287 peptides, 62 chains. Longest chain 9 peptides. Score 0.246 Round 2: 320 peptides, 60 chains. Longest chain 10 peptides. Score 0.323 Round 3: 328 peptides, 57 chains. Longest chain 13 peptides. Score 0.361 Round 4: 336 peptides, 57 chains. Longest chain 15 peptides. Score 0.374 Round 5: 314 peptides, 54 chains. Longest chain 14 peptides. Score 0.359 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 57, Residues 279, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2okc-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10697 reflections ( 89.31 % complete ) and 15394 restraints for refining 6454 atoms. 14335 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1876 (Rfree = 0.000) for 6454 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 47: After refmac, R = 0.1844 (Rfree = 0.000) for 6422 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 48: After refmac, R = 0.1868 (Rfree = 0.000) for 6393 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 49: After refmac, R = 0.1817 (Rfree = 0.000) for 6360 atoms. TimeTaking 63.38