null Tue 25 Dec 19:27:57 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-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2okc-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2okc-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okc-4.0-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-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okc-4.0-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 ============================================================ Tue 25 Dec 19:28:07 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-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okc-4.0-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 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-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-4.0-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 4.000 Wilson plot Bfac: 98.90 7822 reflections ( 88.67 % complete ) and 0 restraints for refining 7916 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3402 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3237 (Rfree = 0.000) for 7916 atoms. Found 37 (37 requested) and removed 55 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.88 3.83 Search for helices and strands: 0 residues in 0 chains, 8049 seeds are put forward NCS extension: 0 residues added, 8049 seeds are put forward Round 1: 288 peptides, 61 chains. Longest chain 9 peptides. Score 0.256 Round 2: 369 peptides, 64 chains. Longest chain 13 peptides. Score 0.379 Round 3: 384 peptides, 65 chains. Longest chain 14 peptides. Score 0.397 Round 4: 388 peptides, 62 chains. Longest chain 17 peptides. Score 0.424 Round 5: 392 peptides, 62 chains. Longest chain 16 peptides. Score 0.431 Taking the results from Round 5 Chains 62, Residues 330, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 7822 reflections ( 88.67 % complete ) and 15581 restraints for refining 6428 atoms. 14316 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2420 (Rfree = 0.000) for 6428 atoms. Found 21 (30 requested) and removed 37 (15 requested) atoms. Cycle 2: After refmac, R = 0.2289 (Rfree = 0.000) for 6329 atoms. Found 26 (30 requested) and removed 42 (15 requested) atoms. Cycle 3: After refmac, R = 0.2167 (Rfree = 0.000) for 6271 atoms. Found 28 (29 requested) and removed 31 (14 requested) atoms. Cycle 4: After refmac, R = 0.1814 (Rfree = 0.000) for 6236 atoms. Found 8 (29 requested) and removed 26 (14 requested) atoms. Cycle 5: After refmac, R = 0.1765 (Rfree = 0.000) for 6197 atoms. Found 8 (29 requested) and removed 23 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.89 3.84 Search for helices and strands: 0 residues in 0 chains, 6395 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 6408 seeds are put forward Round 1: 360 peptides, 71 chains. Longest chain 9 peptides. Score 0.311 Round 2: 401 peptides, 61 chains. Longest chain 16 peptides. Score 0.452 Round 3: 402 peptides, 63 chains. Longest chain 18 peptides. Score 0.440 Round 4: 403 peptides, 62 chains. Longest chain 17 peptides. Score 0.448 Round 5: 411 peptides, 67 chains. Longest chain 13 peptides. Score 0.426 Taking the results from Round 2 Chains 61, Residues 340, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 7822 reflections ( 88.67 % complete ) and 14729 restraints for refining 6234 atoms. 13408 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2136 (Rfree = 0.000) for 6234 atoms. Found 17 (29 requested) and removed 45 (14 requested) atoms. Cycle 7: After refmac, R = 0.1966 (Rfree = 0.000) for 6158 atoms. Found 22 (29 requested) and removed 33 (14 requested) atoms. Cycle 8: After refmac, R = 0.1943 (Rfree = 0.000) for 6110 atoms. Found 21 (29 requested) and removed 32 (14 requested) atoms. Cycle 9: After refmac, R = 0.1591 (Rfree = 0.000) for 6078 atoms. Found 4 (28 requested) and removed 21 (14 requested) atoms. Cycle 10: After refmac, R = 0.1587 (Rfree = 0.000) for 6033 atoms. Found 7 (28 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.87 3.82 Search for helices and strands: 0 residues in 0 chains, 6238 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 6257 seeds are put forward Round 1: 355 peptides, 70 chains. Longest chain 16 peptides. Score 0.310 Round 2: 400 peptides, 67 chains. Longest chain 18 peptides. Score 0.408 Round 3: 404 peptides, 61 chains. Longest chain 17 peptides. Score 0.456 Round 4: 380 peptides, 61 chains. Longest chain 16 peptides. Score 0.418 Round 5: 407 peptides, 62 chains. Longest chain 17 peptides. Score 0.454 Taking the results from Round 3 Chains 61, Residues 343, Estimated correctness of the model 0.0 % 4 chains (38 residues) have been docked in sequence ------------------------------------------------------ 7822 reflections ( 88.67 % complete ) and 14515 restraints for refining 6304 atoms. 13064 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2003 (Rfree = 0.000) for 6304 atoms. Found 16 (29 requested) and removed 58 (14 requested) atoms. Cycle 12: After refmac, R = 0.2012 (Rfree = 0.000) for 6216 atoms. Found 25 (29 requested) and removed 38 (14 requested) atoms. Cycle 13: After refmac, R = 0.1853 (Rfree = 0.000) for 6179 atoms. Found 13 (29 requested) and removed 27 (14 requested) atoms. Cycle 14: After refmac, R = 0.1634 (Rfree = 0.000) for 6149 atoms. Found 2 (29 requested) and removed 22 (14 requested) atoms. Cycle 15: After refmac, R = 0.1597 (Rfree = 0.000) for 6119 atoms. Found 2 (29 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.90 3.85 Search for helices and strands: 0 residues in 0 chains, 6294 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 6307 seeds are put forward Round 1: 323 peptides, 64 chains. Longest chain 11 peptides. Score 0.298 Round 2: 371 peptides, 63 chains. Longest chain 13 peptides. Score 0.389 Round 3: 387 peptides, 61 chains. Longest chain 22 peptides. Score 0.430 Round 4: 396 peptides, 64 chains. Longest chain 17 peptides. Score 0.423 Round 5: 401 peptides, 59 chains. Longest chain 16 peptides. Score 0.465 Taking the results from Round 5 Chains 59, Residues 342, Estimated correctness of the model 0.0 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 7822 reflections ( 88.67 % complete ) and 14812 restraints for refining 6429 atoms. 13408 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2233 (Rfree = 0.000) for 6429 atoms. Found 30 (30 requested) and removed 97 (15 requested) atoms. Cycle 17: After refmac, R = 0.2000 (Rfree = 0.000) for 6319 atoms. Found 19 (30 requested) and removed 51 (15 requested) atoms. Cycle 18: After refmac, R = 0.1873 (Rfree = 0.000) for 6265 atoms. Found 24 (29 requested) and removed 30 (14 requested) atoms. Cycle 19: After refmac, R = 0.1574 (Rfree = 0.000) for 6246 atoms. Found 5 (29 requested) and removed 25 (14 requested) atoms. Cycle 20: After refmac, R = 0.1529 (Rfree = 0.000) for 6216 atoms. Found 5 (29 requested) and removed 22 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.90 3.85 Search for helices and strands: 0 residues in 0 chains, 6399 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 6417 seeds are put forward Round 1: 336 peptides, 71 chains. Longest chain 11 peptides. Score 0.268 Round 2: 356 peptides, 61 chains. Longest chain 19 peptides. Score 0.379 Round 3: 374 peptides, 63 chains. Longest chain 15 peptides. Score 0.394 Round 4: 379 peptides, 57 chains. Longest chain 17 peptides. Score 0.445 Round 5: 387 peptides, 61 chains. Longest chain 16 peptides. Score 0.430 Taking the results from Round 4 Chains 57, Residues 322, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 7822 reflections ( 88.67 % complete ) and 15043 restraints for refining 6430 atoms. 13750 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2008 (Rfree = 0.000) for 6430 atoms. Found 9 (30 requested) and removed 42 (15 requested) atoms. Cycle 22: After refmac, R = 0.1848 (Rfree = 0.000) for 6368 atoms. Found 20 (30 requested) and removed 29 (15 requested) atoms. Cycle 23: After refmac, R = 0.1781 (Rfree = 0.000) for 6336 atoms. Found 10 (30 requested) and removed 28 (15 requested) atoms. Cycle 24: After refmac, R = 0.1814 (Rfree = 0.000) for 6303 atoms. Found 16 (30 requested) and removed 25 (15 requested) atoms. Cycle 25: After refmac, R = 0.1774 (Rfree = 0.000) for 6284 atoms. Found 12 (29 requested) and removed 24 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.84 3.79 Search for helices and strands: 0 residues in 0 chains, 6429 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 6444 seeds are put forward Round 1: 305 peptides, 64 chains. Longest chain 10 peptides. Score 0.264 Round 2: 344 peptides, 63 chains. Longest chain 12 peptides. Score 0.343 Round 3: 339 peptides, 58 chains. Longest chain 11 peptides. Score 0.372 Round 4: 341 peptides, 58 chains. Longest chain 15 peptides. Score 0.376 Round 5: 349 peptides, 58 chains. Longest chain 15 peptides. Score 0.389 Taking the results from Round 5 Chains 58, Residues 291, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 7822 reflections ( 88.67 % complete ) and 15300 restraints for refining 6430 atoms. 14134 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2101 (Rfree = 0.000) for 6430 atoms. Found 28 (30 requested) and removed 23 (15 requested) atoms. Cycle 27: After refmac, R = 0.1985 (Rfree = 0.000) for 6411 atoms. Found 30 (30 requested) and removed 23 (15 requested) atoms. Cycle 28: After refmac, R = 0.1719 (Rfree = 0.000) for 6393 atoms. Found 8 (30 requested) and removed 25 (15 requested) atoms. Cycle 29: After refmac, R = 0.1714 (Rfree = 0.000) for 6361 atoms. Found 15 (30 requested) and removed 24 (15 requested) atoms. Cycle 30: After refmac, R = 0.1600 (Rfree = 0.000) for 6341 atoms. Found 4 (30 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.89 3.84 Search for helices and strands: 0 residues in 0 chains, 6488 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 6503 seeds are put forward Round 1: 256 peptides, 54 chains. Longest chain 10 peptides. Score 0.251 Round 2: 299 peptides, 55 chains. Longest chain 12 peptides. Score 0.324 Round 3: 303 peptides, 55 chains. Longest chain 12 peptides. Score 0.332 Round 4: 316 peptides, 56 chains. Longest chain 13 peptides. Score 0.347 Round 5: 315 peptides, 51 chains. Longest chain 15 peptides. Score 0.384 Taking the results from Round 5 Chains 52, Residues 264, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 7822 reflections ( 88.67 % complete ) and 15319 restraints for refining 6429 atoms. 14239 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2199 (Rfree = 0.000) for 6429 atoms. Found 30 (30 requested) and removed 77 (15 requested) atoms. Cycle 32: After refmac, R = 0.1994 (Rfree = 0.000) for 6363 atoms. Found 30 (30 requested) and removed 34 (15 requested) atoms. Cycle 33: After refmac, R = 0.1680 (Rfree = 0.000) for 6347 atoms. Found 6 (30 requested) and removed 30 (15 requested) atoms. Cycle 34: After refmac, R = 0.1620 (Rfree = 0.000) for 6304 atoms. Found 7 (30 requested) and removed 16 (15 requested) atoms. Cycle 35: After refmac, R = 0.1593 (Rfree = 0.000) for 6292 atoms. Found 10 (29 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.89 3.84 Search for helices and strands: 0 residues in 0 chains, 6456 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 6479 seeds are put forward Round 1: 262 peptides, 57 chains. Longest chain 9 peptides. Score 0.238 Round 2: 295 peptides, 57 chains. Longest chain 10 peptides. Score 0.301 Round 3: 294 peptides, 53 chains. Longest chain 11 peptides. Score 0.331 Round 4: 273 peptides, 48 chains. Longest chain 12 peptides. Score 0.333 Round 5: 287 peptides, 48 chains. Longest chain 12 peptides. Score 0.358 Taking the results from Round 5 Chains 48, Residues 239, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 7822 reflections ( 88.67 % complete ) and 15663 restraints for refining 6430 atoms. 14720 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1956 (Rfree = 0.000) for 6430 atoms. Found 26 (30 requested) and removed 33 (15 requested) atoms. Cycle 37: After refmac, R = 0.2066 (Rfree = 0.000) for 6403 atoms. Found 30 (30 requested) and removed 36 (15 requested) atoms. Cycle 38: After refmac, R = 0.1957 (Rfree = 0.000) for 6385 atoms. Found 30 (30 requested) and removed 35 (15 requested) atoms. Cycle 39: After refmac, R = 0.1479 (Rfree = 0.000) for 6360 atoms. Found 5 (30 requested) and removed 28 (15 requested) atoms. Cycle 40: After refmac, R = 0.1432 (Rfree = 0.000) for 6324 atoms. Found 12 (30 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.91 3.86 Search for helices and strands: 0 residues in 0 chains, 6463 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 6479 seeds are put forward Round 1: 265 peptides, 58 chains. Longest chain 7 peptides. Score 0.235 Round 2: 286 peptides, 48 chains. Longest chain 13 peptides. Score 0.356 Round 3: 282 peptides, 51 chains. Longest chain 12 peptides. Score 0.325 Round 4: 273 peptides, 48 chains. Longest chain 12 peptides. Score 0.333 Round 5: 280 peptides, 50 chains. Longest chain 12 peptides. Score 0.329 Taking the results from Round 2 Chains 49, Residues 238, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 7822 reflections ( 88.67 % complete ) and 15343 restraints for refining 6389 atoms. 14386 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1799 (Rfree = 0.000) for 6389 atoms. Found 30 (30 requested) and removed 49 (15 requested) atoms. Cycle 42: After refmac, R = 0.1783 (Rfree = 0.000) for 6354 atoms. Found 30 (30 requested) and removed 34 (15 requested) atoms. Cycle 43: After refmac, R = 0.1805 (Rfree = 0.000) for 6341 atoms. Found 30 (30 requested) and removed 31 (15 requested) atoms. Cycle 44: After refmac, R = 0.1828 (Rfree = 0.000) for 6333 atoms. Found 30 (30 requested) and removed 26 (15 requested) atoms. Cycle 45: After refmac, R = 0.1356 (Rfree = 0.000) for 6327 atoms. Found 6 (30 requested) and removed 26 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.85 3.80 Search for helices and strands: 0 residues in 0 chains, 6462 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 6475 seeds are put forward Round 1: 244 peptides, 51 chains. Longest chain 8 peptides. Score 0.252 Round 2: 283 peptides, 52 chains. Longest chain 14 peptides. Score 0.319 Round 3: 281 peptides, 52 chains. Longest chain 11 peptides. Score 0.315 Round 4: 266 peptides, 47 chains. Longest chain 14 peptides. Score 0.328 Round 5: 248 peptides, 45 chains. Longest chain 11 peptides. Score 0.310 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 47, Residues 219, 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-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7822 reflections ( 88.67 % complete ) and 15676 restraints for refining 6430 atoms. 14847 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1719 (Rfree = 0.000) for 6430 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.1922 (Rfree = 0.000) for 6393 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.1911 (Rfree = 0.000) for 6355 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.1873 (Rfree = 0.000) for 6318 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:55:11 GMT 2018 Job finished. TimeTaking 87.23 Used memory is bytes: 3749776