null Mon 24 Dec 07:43:34 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-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2okc-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2okc-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2okc-3.8-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-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2okc-3.8-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 07:43:39 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-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2okc-3.8-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 602 and 0 Target number of residues in the AU: 602 Target solvent content: 0.6695 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-3.8-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-3.8-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 3.800 Wilson plot Bfac: 91.87 9104 reflections ( 88.98 % complete ) and 0 restraints for refining 7851 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3400 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2926 (Rfree = 0.000) for 7851 atoms. Found 43 (43 requested) and removed 64 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.79 3.74 Search for helices and strands: 0 residues in 0 chains, 7996 seeds are put forward NCS extension: 0 residues added, 7996 seeds are put forward Round 1: 323 peptides, 66 chains. Longest chain 13 peptides. Score 0.282 Round 2: 395 peptides, 68 chains. Longest chain 14 peptides. Score 0.393 Round 3: 424 peptides, 63 chains. Longest chain 15 peptides. Score 0.473 Round 4: 406 peptides, 60 chains. Longest chain 17 peptides. Score 0.466 Round 5: 413 peptides, 60 chains. Longest chain 21 peptides. Score 0.477 Taking the results from Round 5 Chains 62, Residues 353, Estimated correctness of the model 0.0 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 9104 reflections ( 88.98 % complete ) and 15070 restraints for refining 6439 atoms. 13600 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2472 (Rfree = 0.000) for 6439 atoms. Found 31 (35 requested) and removed 44 (17 requested) atoms. Cycle 2: After refmac, R = 0.2302 (Rfree = 0.000) for 6368 atoms. Found 28 (35 requested) and removed 46 (17 requested) atoms. Cycle 3: After refmac, R = 0.2215 (Rfree = 0.000) for 6312 atoms. Found 34 (34 requested) and removed 40 (17 requested) atoms. Cycle 4: After refmac, R = 0.1817 (Rfree = 0.000) for 6279 atoms. Found 12 (34 requested) and removed 31 (17 requested) atoms. Cycle 5: After refmac, R = 0.1890 (Rfree = 0.000) for 6240 atoms. Found 18 (34 requested) and removed 36 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.74 3.69 Search for helices and strands: 0 residues in 0 chains, 6475 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 6496 seeds are put forward Round 1: 368 peptides, 70 chains. Longest chain 14 peptides. Score 0.333 Round 2: 389 peptides, 65 chains. Longest chain 18 peptides. Score 0.405 Round 3: 422 peptides, 68 chains. Longest chain 16 peptides. Score 0.437 Round 4: 423 peptides, 63 chains. Longest chain 21 peptides. Score 0.472 Round 5: 427 peptides, 66 chains. Longest chain 21 peptides. Score 0.458 Taking the results from Round 4 Chains 67, Residues 360, Estimated correctness of the model 0.0 % 8 chains (55 residues) have been docked in sequence ------------------------------------------------------ 9104 reflections ( 88.98 % complete ) and 14709 restraints for refining 6439 atoms. 13184 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2277 (Rfree = 0.000) for 6439 atoms. Found 26 (35 requested) and removed 43 (17 requested) atoms. Cycle 7: After refmac, R = 0.2079 (Rfree = 0.000) for 6382 atoms. Found 20 (35 requested) and removed 42 (17 requested) atoms. Cycle 8: After refmac, R = 0.1984 (Rfree = 0.000) for 6340 atoms. Found 29 (34 requested) and removed 34 (17 requested) atoms. Cycle 9: After refmac, R = 0.1884 (Rfree = 0.000) for 6321 atoms. Found 17 (34 requested) and removed 36 (17 requested) atoms. Cycle 10: After refmac, R = 0.1944 (Rfree = 0.000) for 6288 atoms. Found 30 (34 requested) and removed 40 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.69 3.64 Search for helices and strands: 0 residues in 0 chains, 6478 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 6499 seeds are put forward Round 1: 358 peptides, 70 chains. Longest chain 10 peptides. Score 0.315 Round 2: 418 peptides, 72 chains. Longest chain 13 peptides. Score 0.403 Round 3: 427 peptides, 69 chains. Longest chain 15 peptides. Score 0.438 Round 4: 410 peptides, 60 chains. Longest chain 16 peptides. Score 0.472 Round 5: 427 peptides, 61 chains. Longest chain 17 peptides. Score 0.491 Taking the results from Round 5 Chains 62, Residues 366, Estimated correctness of the model 0.0 % 7 chains (46 residues) have been docked in sequence ------------------------------------------------------ 9104 reflections ( 88.98 % complete ) and 14766 restraints for refining 6440 atoms. 13222 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2142 (Rfree = 0.000) for 6440 atoms. Found 21 (35 requested) and removed 46 (17 requested) atoms. Cycle 12: After refmac, R = 0.1990 (Rfree = 0.000) for 6373 atoms. Found 13 (35 requested) and removed 33 (17 requested) atoms. Cycle 13: After refmac, R = 0.2010 (Rfree = 0.000) for 6343 atoms. Found 21 (34 requested) and removed 27 (17 requested) atoms. Cycle 14: After refmac, R = 0.1842 (Rfree = 0.000) for 6323 atoms. Found 6 (34 requested) and removed 32 (17 requested) atoms. Cycle 15: After refmac, R = 0.1782 (Rfree = 0.000) for 6286 atoms. Found 5 (34 requested) and removed 24 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.72 3.67 Search for helices and strands: 0 residues in 0 chains, 6471 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 6495 seeds are put forward Round 1: 378 peptides, 74 chains. Longest chain 12 peptides. Score 0.321 Round 2: 400 peptides, 66 chains. Longest chain 16 peptides. Score 0.415 Round 3: 411 peptides, 60 chains. Longest chain 21 peptides. Score 0.474 Round 4: 422 peptides, 64 chains. Longest chain 22 peptides. Score 0.464 Round 5: 421 peptides, 61 chains. Longest chain 21 peptides. Score 0.482 Taking the results from Round 5 Chains 62, Residues 360, Estimated correctness of the model 0.0 % 5 chains (49 residues) have been docked in sequence ------------------------------------------------------ 9104 reflections ( 88.98 % complete ) and 14514 restraints for refining 6440 atoms. 12960 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2254 (Rfree = 0.000) for 6440 atoms. Found 29 (35 requested) and removed 41 (17 requested) atoms. Cycle 17: After refmac, R = 0.2093 (Rfree = 0.000) for 6395 atoms. Found 29 (35 requested) and removed 31 (17 requested) atoms. Cycle 18: After refmac, R = 0.2056 (Rfree = 0.000) for 6376 atoms. Found 26 (35 requested) and removed 30 (17 requested) atoms. Cycle 19: After refmac, R = 0.1730 (Rfree = 0.000) for 6357 atoms. Found 3 (35 requested) and removed 28 (17 requested) atoms. Cycle 20: After refmac, R = 0.1665 (Rfree = 0.000) for 6314 atoms. Found 5 (34 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.72 3.67 Search for helices and strands: 0 residues in 0 chains, 6484 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 6507 seeds are put forward Round 1: 356 peptides, 72 chains. Longest chain 10 peptides. Score 0.297 Round 2: 397 peptides, 66 chains. Longest chain 15 peptides. Score 0.411 Round 3: 414 peptides, 65 chains. Longest chain 15 peptides. Score 0.445 Round 4: 412 peptides, 63 chains. Longest chain 16 peptides. Score 0.455 Round 5: 420 peptides, 66 chains. Longest chain 20 peptides. Score 0.447 Taking the results from Round 4 Chains 63, Residues 349, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 9104 reflections ( 88.98 % complete ) and 15011 restraints for refining 6440 atoms. 13634 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2091 (Rfree = 0.000) for 6440 atoms. Found 18 (35 requested) and removed 33 (17 requested) atoms. Cycle 22: After refmac, R = 0.1992 (Rfree = 0.000) for 6390 atoms. Found 17 (35 requested) and removed 29 (17 requested) atoms. Cycle 23: After refmac, R = 0.1987 (Rfree = 0.000) for 6369 atoms. Found 17 (35 requested) and removed 22 (17 requested) atoms. Cycle 24: After refmac, R = 0.1848 (Rfree = 0.000) for 6356 atoms. Found 12 (34 requested) and removed 23 (17 requested) atoms. Cycle 25: After refmac, R = 0.1915 (Rfree = 0.000) for 6334 atoms. Found 17 (34 requested) and removed 25 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.71 3.66 Search for helices and strands: 0 residues in 0 chains, 6482 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 6502 seeds are put forward Round 1: 290 peptides, 62 chains. Longest chain 11 peptides. Score 0.252 Round 2: 339 peptides, 64 chains. Longest chain 14 peptides. Score 0.327 Round 3: 343 peptides, 59 chains. Longest chain 15 peptides. Score 0.371 Round 4: 355 peptides, 61 chains. Longest chain 17 peptides. Score 0.377 Round 5: 355 peptides, 61 chains. Longest chain 13 peptides. Score 0.377 Taking the results from Round 5 Chains 61, Residues 294, Estimated correctness of the model 0.0 % 6 chains (26 residues) have been docked in sequence ------------------------------------------------------ 9104 reflections ( 88.98 % complete ) and 15265 restraints for refining 6438 atoms. 14100 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2052 (Rfree = 0.000) for 6438 atoms. Found 19 (35 requested) and removed 29 (17 requested) atoms. Cycle 27: After refmac, R = 0.1988 (Rfree = 0.000) for 6404 atoms. Found 33 (35 requested) and removed 23 (17 requested) atoms. Cycle 28: After refmac, R = 0.1874 (Rfree = 0.000) for 6401 atoms. Found 22 (35 requested) and removed 25 (17 requested) atoms. Cycle 29: After refmac, R = 0.1685 (Rfree = 0.000) for 6386 atoms. Found 4 (35 requested) and removed 26 (17 requested) atoms. Cycle 30: After refmac, R = 0.1939 (Rfree = 0.000) for 6359 atoms. Found 34 (34 requested) and removed 25 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.72 3.67 Search for helices and strands: 0 residues in 0 chains, 6564 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 6580 seeds are put forward Round 1: 274 peptides, 60 chains. Longest chain 8 peptides. Score 0.237 Round 2: 312 peptides, 59 chains. Longest chain 10 peptides. Score 0.317 Round 3: 322 peptides, 58 chains. Longest chain 10 peptides. Score 0.342 Round 4: 323 peptides, 60 chains. Longest chain 13 peptides. Score 0.329 Round 5: 341 peptides, 62 chains. Longest chain 15 peptides. Score 0.346 Taking the results from Round 5 Chains 62, Residues 279, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 9104 reflections ( 88.98 % complete ) and 15622 restraints for refining 6439 atoms. 14553 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2077 (Rfree = 0.000) for 6439 atoms. Found 26 (35 requested) and removed 31 (17 requested) atoms. Cycle 32: After refmac, R = 0.1945 (Rfree = 0.000) for 6414 atoms. Found 20 (35 requested) and removed 23 (17 requested) atoms. Cycle 33: After refmac, R = 0.1909 (Rfree = 0.000) for 6400 atoms. Found 31 (35 requested) and removed 26 (17 requested) atoms. Cycle 34: After refmac, R = 0.1622 (Rfree = 0.000) for 6398 atoms. Found 7 (35 requested) and removed 29 (17 requested) atoms. Cycle 35: After refmac, R = 0.1562 (Rfree = 0.000) for 6371 atoms. Found 6 (35 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.67 3.62 Search for helices and strands: 0 residues in 0 chains, 6577 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 6605 seeds are put forward Round 1: 265 peptides, 57 chains. Longest chain 12 peptides. Score 0.244 Round 2: 308 peptides, 60 chains. Longest chain 12 peptides. Score 0.302 Round 3: 310 peptides, 58 chains. Longest chain 12 peptides. Score 0.321 Round 4: 313 peptides, 58 chains. Longest chain 13 peptides. Score 0.326 Round 5: 320 peptides, 54 chains. Longest chain 12 peptides. Score 0.369 Taking the results from Round 5 Chains 54, Residues 266, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 9104 reflections ( 88.98 % complete ) and 15476 restraints for refining 6439 atoms. 14395 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1989 (Rfree = 0.000) for 6439 atoms. Found 11 (35 requested) and removed 29 (17 requested) atoms. Cycle 37: After refmac, R = 0.1858 (Rfree = 0.000) for 6401 atoms. Found 11 (35 requested) and removed 23 (17 requested) atoms. Cycle 38: After refmac, R = 0.1849 (Rfree = 0.000) for 6382 atoms. Found 18 (35 requested) and removed 26 (17 requested) atoms. Cycle 39: After refmac, R = 0.1799 (Rfree = 0.000) for 6369 atoms. Found 10 (35 requested) and removed 21 (17 requested) atoms. Cycle 40: After refmac, R = 0.1746 (Rfree = 0.000) for 6354 atoms. Found 8 (34 requested) and removed 25 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.64 3.59 Search for helices and strands: 0 residues in 0 chains, 6502 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 6517 seeds are put forward Round 1: 253 peptides, 55 chains. Longest chain 9 peptides. Score 0.236 Round 2: 278 peptides, 54 chains. Longest chain 12 peptides. Score 0.293 Round 3: 287 peptides, 53 chains. Longest chain 11 peptides. Score 0.318 Round 4: 270 peptides, 50 chains. Longest chain 11 peptides. Score 0.311 Round 5: 272 peptides, 50 chains. Longest chain 9 peptides. Score 0.315 Taking the results from Round 3 Chains 53, Residues 234, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 9104 reflections ( 88.98 % complete ) and 15689 restraints for refining 6439 atoms. 14797 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1927 (Rfree = 0.000) for 6439 atoms. Found 21 (35 requested) and removed 27 (17 requested) atoms. Cycle 42: After refmac, R = 0.1786 (Rfree = 0.000) for 6417 atoms. Found 18 (35 requested) and removed 25 (17 requested) atoms. Cycle 43: After refmac, R = 0.1772 (Rfree = 0.000) for 6401 atoms. Found 16 (35 requested) and removed 24 (17 requested) atoms. Cycle 44: After refmac, R = 0.1738 (Rfree = 0.000) for 6387 atoms. Found 16 (35 requested) and removed 22 (17 requested) atoms. Cycle 45: After refmac, R = 0.1750 (Rfree = 0.000) for 6373 atoms. Found 30 (35 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 3.63 Search for helices and strands: 0 residues in 0 chains, 6553 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 6567 seeds are put forward Round 1: 238 peptides, 56 chains. Longest chain 6 peptides. Score 0.197 Round 2: 275 peptides, 55 chains. Longest chain 8 peptides. Score 0.280 Round 3: 276 peptides, 53 chains. Longest chain 10 peptides. Score 0.298 Round 4: 288 peptides, 54 chains. Longest chain 10 peptides. Score 0.312 Round 5: 278 peptides, 51 chains. Longest chain 11 peptides. Score 0.318 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 51, Residues 227, 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. 9104 reflections ( 88.98 % complete ) and 15866 restraints for refining 6440 atoms. 15009 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1880 (Rfree = 0.000) for 6440 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.1846 (Rfree = 0.000) for 6416 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 48: After refmac, R = 0.1870 (Rfree = 0.000) for 6394 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.1771 (Rfree = 0.000) for 6370 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:44:35 GMT 2018 Job finished. TimeTaking 61.02 Used memory is bytes: 22650264