null Sun 23 Dec 22:23:05 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 2okc-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2okc-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2okc-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okc-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/2okc-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okc-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 22:23:12 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/2okc-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okc-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 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-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: 75.340 85.750 152.600 90.000 90.000 90.000 Input sequence file: 2okc-3.8-parrot-hancs.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 7939 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3359 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2903 (Rfree = 0.000) for 7939 atoms. Found 43 (43 requested) and removed 65 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.82 3.77 Search for helices and strands: 0 residues in 0 chains, 8087 seeds are put forward NCS extension: 0 residues added, 8087 seeds are put forward Round 1: 296 peptides, 59 chains. Longest chain 10 peptides. Score 0.287 Round 2: 387 peptides, 64 chains. Longest chain 17 peptides. Score 0.409 Round 3: 391 peptides, 64 chains. Longest chain 19 peptides. Score 0.415 Round 4: 413 peptides, 65 chains. Longest chain 17 peptides. Score 0.443 Round 5: 426 peptides, 65 chains. Longest chain 20 peptides. Score 0.463 Taking the results from Round 5 Chains 66, Residues 361, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 9104 reflections ( 88.98 % complete ) and 15295 restraints for refining 6438 atoms. 13833 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2500 (Rfree = 0.000) for 6438 atoms. Found 27 (35 requested) and removed 43 (17 requested) atoms. Cycle 2: After refmac, R = 0.2350 (Rfree = 0.000) for 6361 atoms. Found 31 (35 requested) and removed 31 (17 requested) atoms. Cycle 3: After refmac, R = 0.2287 (Rfree = 0.000) for 6329 atoms. Found 27 (34 requested) and removed 42 (17 requested) atoms. Cycle 4: After refmac, R = 0.1963 (Rfree = 0.000) for 6283 atoms. Found 12 (34 requested) and removed 33 (17 requested) atoms. Cycle 5: After refmac, R = 0.1876 (Rfree = 0.000) for 6252 atoms. Found 5 (34 requested) and removed 34 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.73 3.68 Search for helices and strands: 0 residues in 0 chains, 6453 seeds are put forward NCS extension: 23 residues added (4 deleted due to clashes), 6476 seeds are put forward Round 1: 363 peptides, 67 chains. Longest chain 14 peptides. Score 0.347 Round 2: 433 peptides, 68 chains. Longest chain 25 peptides. Score 0.454 Round 3: 439 peptides, 65 chains. Longest chain 17 peptides. Score 0.482 Round 4: 453 peptides, 65 chains. Longest chain 19 peptides. Score 0.503 Round 5: 437 peptides, 63 chains. Longest chain 22 peptides. Score 0.492 Taking the results from Round 4 Chains 68, Residues 388, Estimated correctness of the model 0.0 % 7 chains (36 residues) have been docked in sequence ------------------------------------------------------ 9104 reflections ( 88.98 % complete ) and 14858 restraints for refining 6438 atoms. 13294 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2156 (Rfree = 0.000) for 6438 atoms. Found 23 (35 requested) and removed 43 (17 requested) atoms. Cycle 7: After refmac, R = 0.2104 (Rfree = 0.000) for 6379 atoms. Found 16 (35 requested) and removed 38 (17 requested) atoms. Cycle 8: After refmac, R = 0.2179 (Rfree = 0.000) for 6337 atoms. Found 23 (34 requested) and removed 37 (17 requested) atoms. Cycle 9: After refmac, R = 0.2090 (Rfree = 0.000) for 6315 atoms. Found 18 (34 requested) and removed 41 (17 requested) atoms. Cycle 10: After refmac, R = 0.2119 (Rfree = 0.000) for 6282 atoms. Found 31 (34 requested) and removed 38 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.73 3.68 Search for helices and strands: 0 residues in 0 chains, 6492 seeds are put forward NCS extension: 31 residues added (0 deleted due to clashes), 6523 seeds are put forward Round 1: 386 peptides, 72 chains. Longest chain 15 peptides. Score 0.349 Round 2: 436 peptides, 71 chains. Longest chain 13 peptides. Score 0.438 Round 3: 443 peptides, 70 chains. Longest chain 13 peptides. Score 0.456 Round 4: 428 peptides, 64 chains. Longest chain 20 peptides. Score 0.473 Round 5: 427 peptides, 62 chains. Longest chain 14 peptides. Score 0.484 Taking the results from Round 5 Chains 64, Residues 365, Estimated correctness of the model 0.0 % 5 chains (33 residues) have been docked in sequence ------------------------------------------------------ 9104 reflections ( 88.98 % complete ) and 14976 restraints for refining 6440 atoms. 13491 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2272 (Rfree = 0.000) for 6440 atoms. Found 27 (35 requested) and removed 37 (17 requested) atoms. Cycle 12: After refmac, R = 0.2177 (Rfree = 0.000) for 6383 atoms. Found 35 (35 requested) and removed 44 (17 requested) atoms. Cycle 13: After refmac, R = 0.2024 (Rfree = 0.000) for 6352 atoms. Found 31 (35 requested) and removed 32 (17 requested) atoms. Cycle 14: After refmac, R = 0.1707 (Rfree = 0.000) for 6328 atoms. Found 9 (34 requested) and removed 25 (17 requested) atoms. Cycle 15: After refmac, R = 0.1838 (Rfree = 0.000) for 6292 atoms. Found 31 (34 requested) and removed 28 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.67 3.62 Search for helices and strands: 0 residues in 0 chains, 6511 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 6527 seeds are put forward Round 1: 362 peptides, 71 chains. Longest chain 10 peptides. Score 0.315 Round 2: 421 peptides, 70 chains. Longest chain 16 peptides. Score 0.421 Round 3: 411 peptides, 64 chains. Longest chain 17 peptides. Score 0.447 Round 4: 409 peptides, 62 chains. Longest chain 16 peptides. Score 0.457 Round 5: 404 peptides, 60 chains. Longest chain 17 peptides. Score 0.463 Taking the results from Round 5 Chains 60, Residues 344, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9104 reflections ( 88.98 % complete ) and 15456 restraints for refining 6439 atoms. 14140 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2121 (Rfree = 0.000) for 6439 atoms. Found 26 (35 requested) and removed 29 (17 requested) atoms. Cycle 17: After refmac, R = 0.2049 (Rfree = 0.000) for 6418 atoms. Found 23 (35 requested) and removed 34 (17 requested) atoms. Cycle 18: After refmac, R = 0.1738 (Rfree = 0.000) for 6386 atoms. Found 5 (35 requested) and removed 32 (17 requested) atoms. Cycle 19: After refmac, R = 0.1676 (Rfree = 0.000) for 6348 atoms. Found 7 (34 requested) and removed 22 (17 requested) atoms. Cycle 20: After refmac, R = 0.1662 (Rfree = 0.000) for 6331 atoms. Found 4 (34 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.69 3.64 Search for helices and strands: 0 residues in 0 chains, 6524 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 6553 seeds are put forward Round 1: 319 peptides, 62 chains. Longest chain 12 peptides. Score 0.306 Round 2: 364 peptides, 57 chains. Longest chain 14 peptides. Score 0.421 Round 3: 370 peptides, 62 chains. Longest chain 13 peptides. Score 0.395 Round 4: 368 peptides, 57 chains. Longest chain 13 peptides. Score 0.428 Round 5: 371 peptides, 62 chains. Longest chain 18 peptides. Score 0.397 Taking the results from Round 4 Chains 57, Residues 311, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 9104 reflections ( 88.98 % complete ) and 15396 restraints for refining 6440 atoms. 14159 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2001 (Rfree = 0.000) for 6440 atoms. Found 27 (35 requested) and removed 36 (17 requested) atoms. Cycle 22: After refmac, R = 0.1901 (Rfree = 0.000) for 6415 atoms. Found 29 (35 requested) and removed 29 (17 requested) atoms. Cycle 23: After refmac, R = 0.1937 (Rfree = 0.000) for 6403 atoms. Found 35 (35 requested) and removed 26 (17 requested) atoms. Cycle 24: After refmac, R = 0.1832 (Rfree = 0.000) for 6408 atoms. Found 24 (35 requested) and removed 26 (17 requested) atoms. Cycle 25: After refmac, R = 0.1836 (Rfree = 0.000) for 6399 atoms. Found 25 (35 requested) and removed 26 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.68 3.63 Search for helices and strands: 0 residues in 0 chains, 6573 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 6586 seeds are put forward Round 1: 322 peptides, 65 chains. Longest chain 10 peptides. Score 0.288 Round 2: 378 peptides, 66 chains. Longest chain 13 peptides. Score 0.379 Round 3: 385 peptides, 65 chains. Longest chain 17 peptides. Score 0.398 Round 4: 373 peptides, 62 chains. Longest chain 15 peptides. Score 0.400 Round 5: 388 peptides, 57 chains. Longest chain 17 peptides. Score 0.459 Taking the results from Round 5 Chains 59, Residues 331, Estimated correctness of the model 0.0 % 5 chains (37 residues) have been docked in sequence ------------------------------------------------------ 9104 reflections ( 88.98 % complete ) and 14854 restraints for refining 6440 atoms. 13472 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2010 (Rfree = 0.000) for 6440 atoms. Found 23 (35 requested) and removed 27 (17 requested) atoms. Cycle 27: After refmac, R = 0.1884 (Rfree = 0.000) for 6406 atoms. Found 17 (35 requested) and removed 25 (17 requested) atoms. Cycle 28: After refmac, R = 0.1890 (Rfree = 0.000) for 6374 atoms. Found 34 (35 requested) and removed 25 (17 requested) atoms. Cycle 29: After refmac, R = 0.1591 (Rfree = 0.000) for 6368 atoms. Found 4 (35 requested) and removed 26 (17 requested) atoms. Cycle 30: After refmac, R = 0.1627 (Rfree = 0.000) for 6338 atoms. Found 4 (34 requested) and removed 24 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.68 3.63 Search for helices and strands: 0 residues in 0 chains, 6484 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 6506 seeds are put forward Round 1: 315 peptides, 66 chains. Longest chain 11 peptides. Score 0.268 Round 2: 349 peptides, 58 chains. Longest chain 18 peptides. Score 0.389 Round 3: 347 peptides, 60 chains. Longest chain 17 peptides. Score 0.371 Round 4: 350 peptides, 58 chains. Longest chain 18 peptides. Score 0.391 Round 5: 355 peptides, 60 chains. Longest chain 18 peptides. Score 0.384 Taking the results from Round 4 Chains 59, Residues 292, Estimated correctness of the model 0.0 % 5 chains (38 residues) have been docked in sequence ------------------------------------------------------ 9104 reflections ( 88.98 % complete ) and 14884 restraints for refining 6440 atoms. 13665 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2090 (Rfree = 0.000) for 6440 atoms. Found 35 (35 requested) and removed 38 (17 requested) atoms. Cycle 32: After refmac, R = 0.2044 (Rfree = 0.000) for 6416 atoms. Found 35 (35 requested) and removed 29 (17 requested) atoms. Cycle 33: After refmac, R = 0.1901 (Rfree = 0.000) for 6407 atoms. Found 35 (35 requested) and removed 24 (17 requested) atoms. Cycle 34: After refmac, R = 0.1526 (Rfree = 0.000) for 6401 atoms. Found 4 (35 requested) and removed 21 (17 requested) atoms. Cycle 35: After refmac, R = 0.1542 (Rfree = 0.000) for 6378 atoms. Found 13 (35 requested) and removed 21 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.72 3.67 Search for helices and strands: 0 residues in 0 chains, 6536 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 6550 seeds are put forward Round 1: 257 peptides, 54 chains. Longest chain 9 peptides. Score 0.253 Round 2: 287 peptides, 54 chains. Longest chain 14 peptides. Score 0.310 Round 3: 291 peptides, 54 chains. Longest chain 11 peptides. Score 0.318 Round 4: 327 peptides, 56 chains. Longest chain 16 peptides. Score 0.366 Round 5: 321 peptides, 57 chains. Longest chain 13 peptides. Score 0.348 Taking the results from Round 4 Chains 57, Residues 271, Estimated correctness of the model 0.0 % 5 chains (28 residues) have been docked in sequence ------------------------------------------------------ 9104 reflections ( 88.98 % complete ) and 15388 restraints for refining 6440 atoms. 14294 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2014 (Rfree = 0.000) for 6440 atoms. Found 29 (35 requested) and removed 31 (17 requested) atoms. Cycle 37: After refmac, R = 0.1829 (Rfree = 0.000) for 6408 atoms. Found 29 (35 requested) and removed 28 (17 requested) atoms. Cycle 38: After refmac, R = 0.1776 (Rfree = 0.000) for 6395 atoms. Found 27 (35 requested) and removed 27 (17 requested) atoms. Cycle 39: After refmac, R = 0.1686 (Rfree = 0.000) for 6378 atoms. Found 20 (35 requested) and removed 24 (17 requested) atoms. Cycle 40: After refmac, R = 0.1597 (Rfree = 0.000) for 6365 atoms. Found 16 (35 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.64 3.59 Search for helices and strands: 0 residues in 0 chains, 6498 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 6523 seeds are put forward Round 1: 231 peptides, 50 chains. Longest chain 8 peptides. Score 0.234 Round 2: 305 peptides, 61 chains. Longest chain 9 peptides. Score 0.288 Round 3: 300 peptides, 54 chains. Longest chain 11 peptides. Score 0.334 Round 4: 315 peptides, 57 chains. Longest chain 11 peptides. Score 0.338 Round 5: 321 peptides, 61 chains. Longest chain 9 peptides. Score 0.318 Taking the results from Round 4 Chains 57, Residues 258, Estimated correctness of the model 0.0 % 4 chains (23 residues) have been docked in sequence ------------------------------------------------------ 9104 reflections ( 88.98 % complete ) and 15388 restraints for refining 6439 atoms. 14363 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1806 (Rfree = 0.000) for 6439 atoms. Found 35 (35 requested) and removed 31 (17 requested) atoms. Cycle 42: After refmac, R = 0.1711 (Rfree = 0.000) for 6424 atoms. Found 35 (35 requested) and removed 38 (17 requested) atoms. Cycle 43: After refmac, R = 0.1703 (Rfree = 0.000) for 6408 atoms. Found 35 (35 requested) and removed 19 (17 requested) atoms. Cycle 44: After refmac, R = 0.1635 (Rfree = 0.000) for 6415 atoms. Found 32 (35 requested) and removed 25 (17 requested) atoms. Cycle 45: After refmac, R = 0.1659 (Rfree = 0.000) for 6418 atoms. Found 24 (35 requested) and removed 25 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.64 3.59 Search for helices and strands: 0 residues in 0 chains, 6537 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 6549 seeds are put forward Round 1: 269 peptides, 59 chains. Longest chain 9 peptides. Score 0.235 Round 2: 302 peptides, 56 chains. Longest chain 11 peptides. Score 0.322 Round 3: 305 peptides, 57 chains. Longest chain 12 peptides. Score 0.320 Round 4: 293 peptides, 58 chains. Longest chain 9 peptides. Score 0.290 Round 5: 310 peptides, 56 chains. Longest chain 11 peptides. Score 0.337 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 56, Residues 254, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2okc-3_warpNtrace.pdb as input Building loops using Loopy2018 56 chains (254 residues) following loop building 3 chains (14 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9104 reflections ( 88.98 % complete ) and 15534 restraints for refining 6440 atoms. 14542 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2001 (Rfree = 0.000) for 6440 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.1990 (Rfree = 0.000) for 6403 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 48: After refmac, R = 0.1893 (Rfree = 0.000) for 6372 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.1811 (Rfree = 0.000) for 6345 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:45:31 GMT 2018 Job finished. TimeTaking 82.45 Used memory is bytes: 7383024