Mon 24 Dec 00:40:41 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2okc-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2okc-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2okc-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2okc-4.0-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2okc-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2okc-4.0-parrot-mrncs ############### 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 00:40:46 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/mrncs/ArpWArp/wArpResults/WorkingDir/2okc-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2okc-4.0-parrot-mrncs/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 587 and 0 Target number of residues in the AU: 587 Target solvent content: 0.6778 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-4.0-parrot-mrncs.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-4.0-parrot-mrncs.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 4.000 Wilson plot Bfac: 98.90 7822 reflections ( 88.67 % complete ) and 0 restraints for refining 7866 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3410 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3232 (Rfree = 0.000) for 7866 atoms. Found 37 (37 requested) and removed 56 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.92 3.87 Search for helices and strands: 0 residues in 0 chains, 7992 seeds are put forward NCS extension: 0 residues added, 7992 seeds are put forward Round 1: 291 peptides, 60 chains. Longest chain 8 peptides. Score 0.270 Round 2: 366 peptides, 62 chains. Longest chain 13 peptides. Score 0.388 Round 3: 389 peptides, 62 chains. Longest chain 20 peptides. Score 0.426 Round 4: 401 peptides, 62 chains. Longest chain 13 peptides. Score 0.445 Round 5: 395 peptides, 60 chains. Longest chain 14 peptides. Score 0.449 Taking the results from Round 5 Chains 60, Residues 335, Estimated correctness of the model 0.0 % 4 chains (22 residues) have been docked in sequence ------------------------------------------------------ 7822 reflections ( 88.67 % complete ) and 15522 restraints for refining 6429 atoms. 14190 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2387 (Rfree = 0.000) for 6429 atoms. Found 27 (30 requested) and removed 52 (15 requested) atoms. Cycle 2: After refmac, R = 0.2294 (Rfree = 0.000) for 6311 atoms. Found 26 (30 requested) and removed 42 (15 requested) atoms. Cycle 3: After refmac, R = 0.1920 (Rfree = 0.000) for 6243 atoms. Found 10 (29 requested) and removed 27 (14 requested) atoms. Cycle 4: After refmac, R = 0.1827 (Rfree = 0.000) for 6198 atoms. Found 5 (29 requested) and removed 18 (14 requested) atoms. Cycle 5: After refmac, R = 0.1758 (Rfree = 0.000) for 6170 atoms. Found 3 (29 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.87 3.82 Search for helices and strands: 0 residues in 0 chains, 6390 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 6408 seeds are put forward Round 1: 336 peptides, 62 chains. Longest chain 14 peptides. Score 0.337 Round 2: 368 peptides, 62 chains. Longest chain 14 peptides. Score 0.392 Round 3: 394 peptides, 63 chains. Longest chain 18 peptides. Score 0.427 Round 4: 386 peptides, 58 chains. Longest chain 15 peptides. Score 0.449 Round 5: 383 peptides, 62 chains. Longest chain 16 peptides. Score 0.416 Taking the results from Round 4 Chains 58, Residues 328, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 7822 reflections ( 88.67 % complete ) and 14913 restraints for refining 6263 atoms. 13641 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2214 (Rfree = 0.000) for 6263 atoms. Found 28 (29 requested) and removed 55 (14 requested) atoms. Cycle 7: After refmac, R = 0.2090 (Rfree = 0.000) for 6191 atoms. Found 29 (29 requested) and removed 49 (14 requested) atoms. Cycle 8: After refmac, R = 0.1681 (Rfree = 0.000) for 6132 atoms. Found 12 (29 requested) and removed 23 (14 requested) atoms. Cycle 9: After refmac, R = 0.1625 (Rfree = 0.000) for 6105 atoms. Found 8 (29 requested) and removed 19 (14 requested) atoms. Cycle 10: After refmac, R = 0.1590 (Rfree = 0.000) for 6078 atoms. Found 2 (28 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.88 3.83 Search for helices and strands: 0 residues in 0 chains, 6281 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 6296 seeds are put forward Round 1: 334 peptides, 66 chains. Longest chain 9 peptides. Score 0.303 Round 2: 395 peptides, 67 chains. Longest chain 12 peptides. Score 0.400 Round 3: 405 peptides, 68 chains. Longest chain 14 peptides. Score 0.410 Round 4: 401 peptides, 61 chains. Longest chain 15 peptides. Score 0.452 Round 5: 390 peptides, 60 chains. Longest chain 15 peptides. Score 0.441 Taking the results from Round 4 Chains 63, Residues 340, Estimated correctness of the model 0.0 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 7822 reflections ( 88.67 % complete ) and 14640 restraints for refining 6333 atoms. 13249 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2282 (Rfree = 0.000) for 6333 atoms. Found 29 (30 requested) and removed 63 (15 requested) atoms. Cycle 12: After refmac, R = 0.2070 (Rfree = 0.000) for 6259 atoms. Found 28 (29 requested) and removed 45 (14 requested) atoms. Cycle 13: After refmac, R = 0.1934 (Rfree = 0.000) for 6223 atoms. Found 23 (29 requested) and removed 31 (14 requested) atoms. Cycle 14: After refmac, R = 0.1883 (Rfree = 0.000) for 6202 atoms. Found 23 (29 requested) and removed 34 (14 requested) atoms. Cycle 15: After refmac, R = 0.1923 (Rfree = 0.000) for 6170 atoms. Found 24 (29 requested) and removed 23 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.89 3.84 Search for helices and strands: 0 residues in 0 chains, 6377 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 6397 seeds are put forward Round 1: 314 peptides, 64 chains. Longest chain 10 peptides. Score 0.281 Round 2: 379 peptides, 67 chains. Longest chain 12 peptides. Score 0.374 Round 3: 385 peptides, 62 chains. Longest chain 15 peptides. Score 0.419 Round 4: 411 peptides, 64 chains. Longest chain 15 peptides. Score 0.447 Round 5: 427 peptides, 71 chains. Longest chain 16 peptides. Score 0.424 Taking the results from Round 4 Chains 64, Residues 347, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7822 reflections ( 88.67 % complete ) and 14991 restraints for refining 6428 atoms. 13641 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2168 (Rfree = 0.000) for 6428 atoms. Found 30 (30 requested) and removed 80 (15 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.1896 (Rfree = 0.000) for 6341 atoms. Found 30 (30 requested) and removed 36 (15 requested) atoms. Cycle 18: After refmac, R = 0.1830 (Rfree = 0.000) for 6313 atoms. Found 27 (30 requested) and removed 32 (15 requested) atoms. Cycle 19: After refmac, R = 0.1883 (Rfree = 0.000) for 6292 atoms. Found 29 (29 requested) and removed 27 (14 requested) atoms. Cycle 20: After refmac, R = 0.1781 (Rfree = 0.000) for 6277 atoms. Found 29 (29 requested) and removed 28 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.87 3.82 Search for helices and strands: 0 residues in 0 chains, 6471 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 6493 seeds are put forward Round 1: 313 peptides, 63 chains. Longest chain 12 peptides. Score 0.287 Round 2: 343 peptides, 62 chains. Longest chain 12 peptides. Score 0.349 Round 3: 337 peptides, 54 chains. Longest chain 14 peptides. Score 0.398 Round 4: 349 peptides, 58 chains. Longest chain 16 peptides. Score 0.389 Round 5: 359 peptides, 54 chains. Longest chain 20 peptides. Score 0.435 Taking the results from Round 5 Chains 54, Residues 305, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7822 reflections ( 88.67 % complete ) and 15530 restraints for refining 6429 atoms. 14346 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1938 (Rfree = 0.000) for 6429 atoms. Found 19 (30 requested) and removed 53 (15 requested) atoms. Cycle 22: After refmac, R = 0.1918 (Rfree = 0.000) for 6356 atoms. Found 30 (30 requested) and removed 36 (15 requested) atoms. Cycle 23: After refmac, R = 0.1831 (Rfree = 0.000) for 6319 atoms. Found 30 (30 requested) and removed 27 (15 requested) atoms. Cycle 24: After refmac, R = 0.1413 (Rfree = 0.000) for 6296 atoms. Found 11 (30 requested) and removed 21 (15 requested) atoms. Cycle 25: After refmac, R = 0.1343 (Rfree = 0.000) for 6273 atoms. Found 8 (29 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.87 3.82 Search for helices and strands: 0 residues in 0 chains, 6459 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 6487 seeds are put forward Round 1: 321 peptides, 67 chains. Longest chain 15 peptides. Score 0.271 Round 2: 361 peptides, 64 chains. Longest chain 14 peptides. Score 0.365 Round 3: 373 peptides, 61 chains. Longest chain 15 peptides. Score 0.407 Round 4: 379 peptides, 63 chains. Longest chain 15 peptides. Score 0.403 Round 5: 358 peptides, 56 chains. Longest chain 15 peptides. Score 0.419 Taking the results from Round 5 Chains 56, Residues 302, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7822 reflections ( 88.67 % complete ) and 15313 restraints for refining 6425 atoms. 14161 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2122 (Rfree = 0.000) for 6425 atoms. Found 30 (30 requested) and removed 42 (15 requested) atoms. Cycle 27: After refmac, R = 0.2006 (Rfree = 0.000) for 6385 atoms. Found 30 (30 requested) and removed 33 (15 requested) atoms. Cycle 28: After refmac, R = 0.1886 (Rfree = 0.000) for 6344 atoms. Found 30 (30 requested) and removed 35 (15 requested) atoms. Cycle 29: After refmac, R = 0.1824 (Rfree = 0.000) for 6318 atoms. Found 30 (30 requested) and removed 24 (15 requested) atoms. Cycle 30: After refmac, R = 0.1890 (Rfree = 0.000) for 6306 atoms. Found 30 (30 requested) and removed 25 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.83 3.78 Search for helices and strands: 0 residues in 0 chains, 6475 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 6493 seeds are put forward Round 1: 278 peptides, 58 chains. Longest chain 9 peptides. Score 0.261 Round 2: 309 peptides, 59 chains. Longest chain 11 peptides. Score 0.311 Round 3: 345 peptides, 65 chains. Longest chain 12 peptides. Score 0.330 Round 4: 339 peptides, 59 chains. Longest chain 12 peptides. Score 0.365 Round 5: 342 peptides, 59 chains. Longest chain 13 peptides. Score 0.370 Taking the results from Round 5 Chains 59, Residues 283, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 7822 reflections ( 88.67 % complete ) and 15411 restraints for refining 6430 atoms. 14298 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1999 (Rfree = 0.000) for 6430 atoms. Found 30 (30 requested) and removed 43 (15 requested) atoms. Cycle 32: After refmac, R = 0.1914 (Rfree = 0.000) for 6378 atoms. Found 27 (30 requested) and removed 30 (15 requested) atoms. Cycle 33: After refmac, R = 0.1763 (Rfree = 0.000) for 6353 atoms. Found 23 (30 requested) and removed 28 (15 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1406 (Rfree = 0.000) for 6332 atoms. Found 6 (30 requested) and removed 21 (15 requested) atoms. Cycle 35: After refmac, R = 0.1312 (Rfree = 0.000) for 6303 atoms. Found 4 (30 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.84 3.79 Search for helices and strands: 0 residues in 0 chains, 6469 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 6489 seeds are put forward Round 1: 262 peptides, 57 chains. Longest chain 11 peptides. Score 0.238 Round 2: 305 peptides, 59 chains. Longest chain 9 peptides. Score 0.304 Round 3: 310 peptides, 56 chains. Longest chain 11 peptides. Score 0.337 Round 4: 299 peptides, 52 chains. Longest chain 10 peptides. Score 0.348 Round 5: 290 peptides, 50 chains. Longest chain 11 peptides. Score 0.348 Taking the results from Round 5 Chains 50, Residues 240, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7822 reflections ( 88.67 % complete ) and 15498 restraints for refining 6430 atoms. 14579 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2103 (Rfree = 0.000) for 6430 atoms. Found 30 (30 requested) and removed 38 (15 requested) atoms. Cycle 37: After refmac, R = 0.1919 (Rfree = 0.000) for 6404 atoms. Found 30 (30 requested) and removed 31 (15 requested) atoms. Cycle 38: After refmac, R = 0.1481 (Rfree = 0.000) for 6390 atoms. Found 6 (30 requested) and removed 25 (15 requested) atoms. Cycle 39: After refmac, R = 0.1607 (Rfree = 0.000) for 6359 atoms. Found 21 (30 requested) and removed 23 (15 requested) atoms. Cycle 40: After refmac, R = 0.1436 (Rfree = 0.000) for 6349 atoms. Found 4 (30 requested) and removed 25 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.86 3.81 Search for helices and strands: 0 residues in 0 chains, 6493 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 6505 seeds are put forward Round 1: 250 peptides, 54 chains. Longest chain 8 peptides. Score 0.239 Round 2: 267 peptides, 47 chains. Longest chain 11 peptides. Score 0.330 Round 3: 263 peptides, 47 chains. Longest chain 11 peptides. Score 0.322 Round 4: 266 peptides, 46 chains. Longest chain 12 peptides. Score 0.336 Round 5: 291 peptides, 53 chains. Longest chain 10 peptides. Score 0.326 Taking the results from Round 4 Chains 46, Residues 220, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 7822 reflections ( 88.67 % complete ) and 15396 restraints for refining 6388 atoms. 14551 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1882 (Rfree = 0.000) for 6388 atoms. Found 24 (30 requested) and removed 35 (15 requested) atoms. Cycle 42: After refmac, R = 0.1875 (Rfree = 0.000) for 6361 atoms. Found 26 (30 requested) and removed 107 (15 requested) atoms. Cycle 43: After refmac, R = 0.1989 (Rfree = 0.000) for 6269 atoms. Found 29 (29 requested) and removed 35 (14 requested) atoms. Cycle 44: After refmac, R = 0.1496 (Rfree = 0.000) for 6253 atoms. Found 5 (29 requested) and removed 17 (14 requested) atoms. Cycle 45: After refmac, R = 0.1520 (Rfree = 0.000) for 6234 atoms. Found 8 (29 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.88 3.83 Search for helices and strands: 0 residues in 0 chains, 6388 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 6403 seeds are put forward Round 1: 216 peptides, 46 chains. Longest chain 8 peptides. Score 0.238 Round 2: 244 peptides, 45 chains. Longest chain 10 peptides. Score 0.303 Round 3: 254 peptides, 49 chains. Longest chain 9 peptides. Score 0.289 Round 4: 259 peptides, 48 chains. Longest chain 9 peptides. Score 0.306 Round 5: 248 peptides, 45 chains. Longest chain 11 peptides. Score 0.310 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 45, Residues 203, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2okc-4_warpNtrace.pdb as input Building loops using Loopy2018 45 chains (203 residues) following loop building 3 chains (15 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7822 reflections ( 88.67 % complete ) and 15505 restraints for refining 6388 atoms. 14693 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1936 (Rfree = 0.000) for 6388 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2073 (Rfree = 0.000) for 6352 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.1931 (Rfree = 0.000) for 6322 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.1875 (Rfree = 0.000) for 6301 atoms. TimeTaking 70.15