Mon 24 Dec 07:53:59 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-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2okc-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2okc-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2okc-4.0-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-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2okc-4.0-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 07:54:04 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-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2okc-4.0-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 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-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-4.0-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 4.000 Wilson plot Bfac: 98.90 7822 reflections ( 88.67 % complete ) and 0 restraints for refining 7876 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3440 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3206 (Rfree = 0.000) for 7876 atoms. Found 37 (37 requested) and removed 52 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.90 3.85 Search for helices and strands: 0 residues in 0 chains, 8016 seeds are put forward NCS extension: 0 residues added, 8016 seeds are put forward Round 1: 281 peptides, 59 chains. Longest chain 10 peptides. Score 0.259 Round 2: 347 peptides, 65 chains. Longest chain 12 peptides. Score 0.333 Round 3: 401 peptides, 70 chains. Longest chain 12 peptides. Score 0.389 Round 4: 415 peptides, 70 chains. Longest chain 13 peptides. Score 0.412 Round 5: 422 peptides, 69 chains. Longest chain 12 peptides. Score 0.430 Taking the results from Round 5 Chains 69, Residues 353, Estimated correctness of the model 0.0 % 5 chains (20 residues) have been docked in sequence ------------------------------------------------------ 7822 reflections ( 88.67 % complete ) and 15444 restraints for refining 6425 atoms. 14056 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2449 (Rfree = 0.000) for 6425 atoms. Found 24 (30 requested) and removed 37 (15 requested) atoms. Cycle 2: After refmac, R = 0.2229 (Rfree = 0.000) for 6299 atoms. Found 23 (30 requested) and removed 39 (15 requested) atoms. Cycle 3: After refmac, R = 0.2200 (Rfree = 0.000) for 6227 atoms. Found 29 (29 requested) and removed 37 (14 requested) atoms. Cycle 4: After refmac, R = 0.1825 (Rfree = 0.000) for 6177 atoms. Found 7 (29 requested) and removed 27 (14 requested) atoms. Cycle 5: After refmac, R = 0.1756 (Rfree = 0.000) for 6135 atoms. Found 6 (29 requested) and removed 25 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.91 3.86 Search for helices and strands: 0 residues in 0 chains, 6332 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 6344 seeds are put forward Round 1: 350 peptides, 69 chains. Longest chain 11 peptides. Score 0.309 Round 2: 386 peptides, 65 chains. Longest chain 13 peptides. Score 0.400 Round 3: 407 peptides, 64 chains. Longest chain 18 peptides. Score 0.440 Round 4: 401 peptides, 63 chains. Longest chain 13 peptides. Score 0.438 Round 5: 414 peptides, 62 chains. Longest chain 19 peptides. Score 0.465 Taking the results from Round 5 Chains 62, Residues 352, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 7822 reflections ( 88.67 % complete ) and 15288 restraints for refining 6429 atoms. 13911 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2197 (Rfree = 0.000) for 6429 atoms. Found 16 (30 requested) and removed 58 (15 requested) atoms. Cycle 7: After refmac, R = 0.2127 (Rfree = 0.000) for 6321 atoms. Found 22 (30 requested) and removed 54 (15 requested) atoms. Cycle 8: After refmac, R = 0.2059 (Rfree = 0.000) for 6256 atoms. Found 22 (29 requested) and removed 36 (14 requested) atoms. Cycle 9: After refmac, R = 0.1679 (Rfree = 0.000) for 6207 atoms. Found 8 (29 requested) and removed 27 (14 requested) atoms. Cycle 10: After refmac, R = 0.1756 (Rfree = 0.000) for 6168 atoms. Found 15 (29 requested) and removed 23 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.85 3.80 Search for helices and strands: 0 residues in 0 chains, 6341 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 6367 seeds are put forward Round 1: 339 peptides, 69 chains. Longest chain 11 peptides. Score 0.289 Round 2: 410 peptides, 68 chains. Longest chain 16 peptides. Score 0.418 Round 3: 417 peptides, 67 chains. Longest chain 15 peptides. Score 0.436 Round 4: 413 peptides, 70 chains. Longest chain 15 peptides. Score 0.408 Round 5: 425 peptides, 64 chains. Longest chain 21 peptides. Score 0.468 Taking the results from Round 5 Chains 65, Residues 361, Estimated correctness of the model 0.0 % 4 chains (33 residues) have been docked in sequence ------------------------------------------------------ 7822 reflections ( 88.67 % complete ) and 14766 restraints for refining 6426 atoms. 13273 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2176 (Rfree = 0.000) for 6426 atoms. Found 24 (30 requested) and removed 68 (15 requested) atoms. Cycle 12: After refmac, R = 0.1993 (Rfree = 0.000) for 6340 atoms. Found 15 (30 requested) and removed 48 (15 requested) atoms. Cycle 13: After refmac, R = 0.1925 (Rfree = 0.000) for 6279 atoms. Found 19 (29 requested) and removed 34 (14 requested) atoms. Cycle 14: After refmac, R = 0.1867 (Rfree = 0.000) for 6237 atoms. Found 19 (29 requested) and removed 38 (14 requested) atoms. Cycle 15: After refmac, R = 0.1485 (Rfree = 0.000) for 6202 atoms. Found 6 (29 requested) and removed 22 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.82 3.77 Search for helices and strands: 0 residues in 0 chains, 6400 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 6425 seeds are put forward Round 1: 370 peptides, 77 chains. Longest chain 13 peptides. Score 0.284 Round 2: 407 peptides, 70 chains. Longest chain 15 peptides. Score 0.399 Round 3: 416 peptides, 68 chains. Longest chain 17 peptides. Score 0.427 Round 4: 422 peptides, 63 chains. Longest chain 16 peptides. Score 0.470 Round 5: 416 peptides, 61 chains. Longest chain 21 peptides. Score 0.475 Taking the results from Round 5 Chains 61, Residues 355, Estimated correctness of the model 0.0 % 7 chains (41 residues) have been docked in sequence ------------------------------------------------------ 7822 reflections ( 88.67 % complete ) and 14855 restraints for refining 6429 atoms. 13404 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2174 (Rfree = 0.000) for 6429 atoms. Found 29 (30 requested) and removed 43 (15 requested) atoms. Cycle 17: After refmac, R = 0.2002 (Rfree = 0.000) for 6370 atoms. Found 30 (30 requested) and removed 33 (15 requested) atoms. Cycle 18: After refmac, R = 0.1952 (Rfree = 0.000) for 6342 atoms. Found 22 (30 requested) and removed 31 (15 requested) atoms. Cycle 19: After refmac, R = 0.1760 (Rfree = 0.000) for 6315 atoms. Found 26 (30 requested) and removed 27 (15 requested) atoms. Cycle 20: After refmac, R = 0.1406 (Rfree = 0.000) for 6290 atoms. Found 5 (30 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.83 3.78 Search for helices and strands: 0 residues in 0 chains, 6450 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 6474 seeds are put forward Round 1: 334 peptides, 67 chains. Longest chain 12 peptides. Score 0.295 Round 2: 385 peptides, 69 chains. Longest chain 12 peptides. Score 0.369 Round 3: 397 peptides, 67 chains. Longest chain 15 peptides. Score 0.404 Round 4: 391 peptides, 66 chains. Longest chain 15 peptides. Score 0.401 Round 5: 397 peptides, 64 chains. Longest chain 15 peptides. Score 0.425 Taking the results from Round 5 Chains 64, Residues 333, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7822 reflections ( 88.67 % complete ) and 15168 restraints for refining 6429 atoms. 13900 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2093 (Rfree = 0.000) for 6429 atoms. Found 21 (30 requested) and removed 40 (15 requested) atoms. Cycle 22: After refmac, R = 0.2049 (Rfree = 0.000) for 6365 atoms. Found 30 (30 requested) and removed 35 (15 requested) atoms. Cycle 23: After refmac, R = 0.1929 (Rfree = 0.000) for 6343 atoms. Found 28 (30 requested) and removed 23 (15 requested) atoms. Cycle 24: After refmac, R = 0.1468 (Rfree = 0.000) for 6320 atoms. Found 6 (30 requested) and removed 23 (15 requested) atoms. Cycle 25: After refmac, R = 0.1343 (Rfree = 0.000) for 6291 atoms. Found 2 (29 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.84 3.79 Search for helices and strands: 0 residues in 0 chains, 6443 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 6464 seeds are put forward Round 1: 299 peptides, 62 chains. Longest chain 9 peptides. Score 0.269 Round 2: 352 peptides, 66 chains. Longest chain 12 peptides. Score 0.335 Round 3: 354 peptides, 61 chains. Longest chain 13 peptides. Score 0.375 Round 4: 332 peptides, 57 chains. Longest chain 17 peptides. Score 0.368 Round 5: 356 peptides, 61 chains. Longest chain 17 peptides. Score 0.379 Taking the results from Round 5 Chains 61, Residues 295, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7822 reflections ( 88.67 % complete ) and 15186 restraints for refining 6430 atoms. 14046 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1894 (Rfree = 0.000) for 6430 atoms. Found 24 (30 requested) and removed 28 (15 requested) atoms. Cycle 27: After refmac, R = 0.1776 (Rfree = 0.000) for 6395 atoms. Found 28 (30 requested) and removed 21 (15 requested) atoms. Cycle 28: After refmac, R = 0.1805 (Rfree = 0.000) for 6387 atoms. Found 30 (30 requested) and removed 36 (15 requested) atoms. Cycle 29: After refmac, R = 0.1667 (Rfree = 0.000) for 6364 atoms. Found 21 (30 requested) and removed 29 (15 requested) atoms. Cycle 30: After refmac, R = 0.1775 (Rfree = 0.000) for 6344 atoms. Found 30 (30 requested) and removed 41 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.81 3.76 Search for helices and strands: 0 residues in 0 chains, 6511 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 6527 seeds are put forward Round 1: 301 peptides, 65 chains. Longest chain 11 peptides. Score 0.249 Round 2: 317 peptides, 60 chains. Longest chain 12 peptides. Score 0.318 Round 3: 351 peptides, 62 chains. Longest chain 10 peptides. Score 0.363 Round 4: 354 peptides, 61 chains. Longest chain 11 peptides. Score 0.375 Round 5: 344 peptides, 57 chains. Longest chain 13 peptides. Score 0.388 Taking the results from Round 5 Chains 59, Residues 287, Estimated correctness of the model 0.0 % 6 chains (35 residues) have been docked in sequence ------------------------------------------------------ 7822 reflections ( 88.67 % complete ) and 14916 restraints for refining 6428 atoms. 13728 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1972 (Rfree = 0.000) for 6428 atoms. Found 20 (30 requested) and removed 34 (15 requested) atoms. Cycle 32: After refmac, R = 0.1994 (Rfree = 0.000) for 6377 atoms. Found 30 (30 requested) and removed 37 (15 requested) atoms. Cycle 33: After refmac, R = 0.1923 (Rfree = 0.000) for 6342 atoms. Found 30 (30 requested) and removed 30 (15 requested) atoms. Cycle 34: After refmac, R = 0.1933 (Rfree = 0.000) for 6314 atoms. Found 30 (30 requested) and removed 23 (15 requested) atoms. Cycle 35: After refmac, R = 0.1938 (Rfree = 0.000) for 6301 atoms. Found 30 (30 requested) and removed 31 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.87 3.82 Search for helices and strands: 0 residues in 0 chains, 6505 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 6520 seeds are put forward Round 1: 246 peptides, 55 chains. Longest chain 8 peptides. Score 0.222 Round 2: 287 peptides, 58 chains. Longest chain 8 peptides. Score 0.278 Round 3: 308 peptides, 58 chains. Longest chain 10 peptides. Score 0.317 Round 4: 287 peptides, 54 chains. Longest chain 11 peptides. Score 0.310 Round 5: 279 peptides, 55 chains. Longest chain 11 peptides. Score 0.287 Taking the results from Round 3 Chains 58, Residues 250, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 7822 reflections ( 88.67 % complete ) and 15041 restraints for refining 6386 atoms. 14068 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1866 (Rfree = 0.000) for 6386 atoms. Found 27 (30 requested) and removed 46 (15 requested) atoms. Cycle 37: After refmac, R = 0.1886 (Rfree = 0.000) for 6338 atoms. Found 30 (30 requested) and removed 38 (15 requested) atoms. Cycle 38: After refmac, R = 0.1710 (Rfree = 0.000) for 6304 atoms. Found 28 (30 requested) and removed 27 (15 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1714 (Rfree = 0.000) for 6280 atoms. Found 29 (29 requested) and removed 23 (14 requested) atoms. Cycle 40: After refmac, R = 0.1688 (Rfree = 0.000) for 6269 atoms. Found 29 (29 requested) and removed 24 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.85 3.80 Search for helices and strands: 0 residues in 0 chains, 6470 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 6481 seeds are put forward Round 1: 222 peptides, 52 chains. Longest chain 7 peptides. Score 0.198 Round 2: 273 peptides, 57 chains. Longest chain 9 peptides. Score 0.259 Round 3: 257 peptides, 53 chains. Longest chain 8 peptides. Score 0.261 Round 4: 263 peptides, 54 chains. Longest chain 8 peptides. Score 0.265 Round 5: 261 peptides, 48 chains. Longest chain 12 peptides. Score 0.310 Taking the results from Round 5 Chains 48, Residues 213, Estimated correctness of the model 0.0 % 6 chains (30 residues) have been docked in sequence ------------------------------------------------------ 7822 reflections ( 88.67 % complete ) and 15415 restraints for refining 6430 atoms. 14531 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1781 (Rfree = 0.000) for 6430 atoms. Found 17 (30 requested) and removed 35 (15 requested) atoms. Cycle 42: After refmac, R = 0.1726 (Rfree = 0.000) for 6382 atoms. Found 30 (30 requested) and removed 26 (15 requested) atoms. Cycle 43: After refmac, R = 0.1789 (Rfree = 0.000) for 6376 atoms. Found 30 (30 requested) and removed 35 (15 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1315 (Rfree = 0.000) for 6360 atoms. Found 5 (30 requested) and removed 24 (15 requested) atoms. Cycle 45: After refmac, R = 0.1142 (Rfree = 0.000) for 6336 atoms. Found 8 (30 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.83 3.78 Search for helices and strands: 0 residues in 0 chains, 6469 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 6487 seeds are put forward Round 1: 239 peptides, 55 chains. Longest chain 8 peptides. Score 0.207 Round 2: 255 peptides, 54 chains. Longest chain 10 peptides. Score 0.249 Round 3: 263 peptides, 53 chains. Longest chain 8 peptides. Score 0.273 Round 4: 263 peptides, 54 chains. Longest chain 10 peptides. Score 0.265 Round 5: 268 peptides, 51 chains. Longest chain 11 peptides. Score 0.299 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 51, Residues 217, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2okc-4_warpNtrace.pdb as input Building loops using Loopy2018 51 chains (217 residues) following loop building 2 chains (15 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7822 reflections ( 88.67 % complete ) and 15531 restraints for refining 6430 atoms. 14658 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1834 (Rfree = 0.000) for 6430 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2009 (Rfree = 0.000) for 6391 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.1752 (Rfree = 0.000) for 6364 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.1827 (Rfree = 0.000) for 6334 atoms. TimeTaking 71.43