null Sun 23 Dec 22:23:10 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 2oh1-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2oh1-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2oh1-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh1-3.8-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/2oh1-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh1-3.8-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 22:23:18 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/2oh1-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh1-3.8-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 501 and 0 Target number of residues in the AU: 501 Target solvent content: 0.6635 Checking the provided sequence file Detected sequence length: 179 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 716 Adjusted target solvent content: 0.52 Input MTZ file: 2oh1-3.8-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: 65.646 99.855 122.905 90.000 90.000 90.000 Input sequence file: 2oh1-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 5728 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: 77.501 3.800 Wilson plot Bfac: 87.48 8322 reflections ( 99.07 % complete ) and 0 restraints for refining 6379 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3365 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3075 (Rfree = 0.000) for 6379 atoms. Found 18 (35 requested) and removed 45 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.71 3.61 Search for helices and strands: 0 residues in 0 chains, 6478 seeds are put forward NCS extension: 0 residues added, 6478 seeds are put forward Round 1: 311 peptides, 56 chains. Longest chain 17 peptides. Score 0.365 Round 2: 384 peptides, 57 chains. Longest chain 23 peptides. Score 0.497 Round 3: 393 peptides, 56 chains. Longest chain 23 peptides. Score 0.520 Round 4: 392 peptides, 52 chains. Longest chain 17 peptides. Score 0.548 Round 5: 418 peptides, 53 chains. Longest chain 21 peptides. Score 0.583 Taking the results from Round 5 Chains 53, Residues 365, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 8322 reflections ( 99.07 % complete ) and 11610 restraints for refining 5176 atoms. 10173 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2743 (Rfree = 0.000) for 5176 atoms. Found 28 (28 requested) and removed 27 (14 requested) atoms. Cycle 2: After refmac, R = 0.2520 (Rfree = 0.000) for 5138 atoms. Found 5 (28 requested) and removed 26 (14 requested) atoms. Cycle 3: After refmac, R = 0.2448 (Rfree = 0.000) for 5101 atoms. Found 3 (28 requested) and removed 20 (14 requested) atoms. Cycle 4: After refmac, R = 0.2402 (Rfree = 0.000) for 5078 atoms. Found 2 (27 requested) and removed 16 (13 requested) atoms. Cycle 5: After refmac, R = 0.2387 (Rfree = 0.000) for 5063 atoms. Found 1 (27 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.78 3.68 Search for helices and strands: 0 residues in 0 chains, 5227 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 5243 seeds are put forward Round 1: 378 peptides, 60 chains. Longest chain 23 peptides. Score 0.463 Round 2: 392 peptides, 49 chains. Longest chain 21 peptides. Score 0.570 Round 3: 388 peptides, 49 chains. Longest chain 19 peptides. Score 0.564 Round 4: 399 peptides, 51 chains. Longest chain 15 peptides. Score 0.567 Round 5: 396 peptides, 47 chains. Longest chain 19 peptides. Score 0.591 Taking the results from Round 5 Chains 48, Residues 349, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 8322 reflections ( 99.07 % complete ) and 11726 restraints for refining 5178 atoms. 10349 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2468 (Rfree = 0.000) for 5178 atoms. Found 13 (28 requested) and removed 26 (14 requested) atoms. Cycle 7: After refmac, R = 0.2377 (Rfree = 0.000) for 5129 atoms. Found 9 (28 requested) and removed 22 (14 requested) atoms. Cycle 8: After refmac, R = 0.2365 (Rfree = 0.000) for 5108 atoms. Found 11 (28 requested) and removed 23 (14 requested) atoms. Cycle 9: After refmac, R = 0.2268 (Rfree = 0.000) for 5085 atoms. Found 4 (28 requested) and removed 18 (14 requested) atoms. Cycle 10: After refmac, R = 0.2218 (Rfree = 0.000) for 5062 atoms. Found 7 (27 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.73 3.63 Search for helices and strands: 0 residues in 0 chains, 5232 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 5259 seeds are put forward Round 1: 338 peptides, 60 chains. Longest chain 11 peptides. Score 0.386 Round 2: 366 peptides, 51 chains. Longest chain 16 peptides. Score 0.512 Round 3: 384 peptides, 51 chains. Longest chain 18 peptides. Score 0.543 Round 4: 386 peptides, 49 chains. Longest chain 19 peptides. Score 0.561 Round 5: 403 peptides, 50 chains. Longest chain 25 peptides. Score 0.580 Taking the results from Round 5 Chains 52, Residues 353, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 8322 reflections ( 99.07 % complete ) and 11662 restraints for refining 5180 atoms. 10249 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2336 (Rfree = 0.000) for 5180 atoms. Found 4 (28 requested) and removed 27 (14 requested) atoms. Cycle 12: After refmac, R = 0.2169 (Rfree = 0.000) for 5135 atoms. Found 5 (28 requested) and removed 27 (14 requested) atoms. Cycle 13: After refmac, R = 0.2171 (Rfree = 0.000) for 5103 atoms. Found 5 (28 requested) and removed 24 (14 requested) atoms. Cycle 14: After refmac, R = 0.2138 (Rfree = 0.000) for 5078 atoms. Found 3 (27 requested) and removed 19 (13 requested) atoms. Cycle 15: After refmac, R = 0.2129 (Rfree = 0.000) for 5059 atoms. Found 2 (27 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.71 3.61 Search for helices and strands: 0 residues in 0 chains, 5194 seeds are put forward NCS extension: 28 residues added (5 deleted due to clashes), 5222 seeds are put forward Round 1: 337 peptides, 56 chains. Longest chain 13 peptides. Score 0.418 Round 2: 381 peptides, 52 chains. Longest chain 21 peptides. Score 0.530 Round 3: 374 peptides, 54 chains. Longest chain 15 peptides. Score 0.503 Round 4: 368 peptides, 52 chains. Longest chain 16 peptides. Score 0.508 Round 5: 379 peptides, 49 chains. Longest chain 15 peptides. Score 0.549 Taking the results from Round 5 Chains 49, Residues 330, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8322 reflections ( 99.07 % complete ) and 11924 restraints for refining 5180 atoms. 10653 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2401 (Rfree = 0.000) for 5180 atoms. Found 9 (28 requested) and removed 29 (14 requested) atoms. Cycle 17: After refmac, R = 0.2192 (Rfree = 0.000) for 5146 atoms. Found 3 (28 requested) and removed 26 (14 requested) atoms. Cycle 18: After refmac, R = 0.2162 (Rfree = 0.000) for 5116 atoms. Found 5 (28 requested) and removed 18 (14 requested) atoms. Cycle 19: After refmac, R = 0.2150 (Rfree = 0.000) for 5100 atoms. Found 4 (28 requested) and removed 26 (14 requested) atoms. Cycle 20: After refmac, R = 0.2131 (Rfree = 0.000) for 5070 atoms. Found 4 (27 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.71 3.61 Search for helices and strands: 0 residues in 0 chains, 5219 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 5238 seeds are put forward Round 1: 293 peptides, 57 chains. Longest chain 11 peptides. Score 0.318 Round 2: 337 peptides, 52 chains. Longest chain 15 peptides. Score 0.451 Round 3: 370 peptides, 54 chains. Longest chain 18 peptides. Score 0.496 Round 4: 350 peptides, 49 chains. Longest chain 28 peptides. Score 0.500 Round 5: 360 peptides, 50 chains. Longest chain 19 peptides. Score 0.509 Taking the results from Round 5 Chains 52, Residues 310, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 8322 reflections ( 99.07 % complete ) and 11837 restraints for refining 5181 atoms. 10580 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2414 (Rfree = 0.000) for 5181 atoms. Found 18 (28 requested) and removed 23 (14 requested) atoms. Cycle 22: After refmac, R = 0.2332 (Rfree = 0.000) for 5143 atoms. Found 13 (28 requested) and removed 21 (14 requested) atoms. Cycle 23: After refmac, R = 0.2144 (Rfree = 0.000) for 5116 atoms. Found 4 (28 requested) and removed 19 (14 requested) atoms. Cycle 24: After refmac, R = 0.2160 (Rfree = 0.000) for 5090 atoms. Found 6 (28 requested) and removed 26 (14 requested) atoms. Cycle 25: After refmac, R = 0.2041 (Rfree = 0.000) for 5067 atoms. Found 9 (27 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.68 3.58 Search for helices and strands: 0 residues in 0 chains, 5199 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 5227 seeds are put forward Round 1: 308 peptides, 58 chains. Longest chain 13 peptides. Score 0.341 Round 2: 330 peptides, 56 chains. Longest chain 15 peptides. Score 0.404 Round 3: 331 peptides, 50 chains. Longest chain 15 peptides. Score 0.457 Round 4: 344 peptides, 53 chains. Longest chain 14 peptides. Score 0.456 Round 5: 338 peptides, 50 chains. Longest chain 15 peptides. Score 0.470 Taking the results from Round 5 Chains 51, Residues 288, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 8322 reflections ( 99.07 % complete ) and 11984 restraints for refining 5180 atoms. 10809 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2317 (Rfree = 0.000) for 5180 atoms. Found 11 (28 requested) and removed 27 (14 requested) atoms. Cycle 27: After refmac, R = 0.2209 (Rfree = 0.000) for 5144 atoms. Found 11 (28 requested) and removed 20 (14 requested) atoms. Cycle 28: After refmac, R = 0.2173 (Rfree = 0.000) for 5126 atoms. Found 12 (28 requested) and removed 24 (14 requested) atoms. Cycle 29: After refmac, R = 0.2144 (Rfree = 0.000) for 5103 atoms. Found 15 (28 requested) and removed 15 (14 requested) atoms. Cycle 30: After refmac, R = 0.2102 (Rfree = 0.000) for 5096 atoms. Found 16 (28 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.72 3.62 Search for helices and strands: 0 residues in 0 chains, 5240 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 5253 seeds are put forward Round 1: 263 peptides, 54 chains. Longest chain 10 peptides. Score 0.280 Round 2: 307 peptides, 52 chains. Longest chain 14 peptides. Score 0.393 Round 3: 303 peptides, 50 chains. Longest chain 12 peptides. Score 0.402 Round 4: 303 peptides, 44 chains. Longest chain 20 peptides. Score 0.454 Round 5: 320 peptides, 49 chains. Longest chain 21 peptides. Score 0.444 Taking the results from Round 4 Chains 44, Residues 259, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 8322 reflections ( 99.07 % complete ) and 12300 restraints for refining 5180 atoms. 11286 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2451 (Rfree = 0.000) for 5180 atoms. Found 6 (28 requested) and removed 27 (14 requested) atoms. Cycle 32: After refmac, R = 0.2388 (Rfree = 0.000) for 5130 atoms. Found 16 (28 requested) and removed 23 (14 requested) atoms. Cycle 33: After refmac, R = 0.2228 (Rfree = 0.000) for 5108 atoms. Found 20 (28 requested) and removed 21 (14 requested) atoms. Cycle 34: After refmac, R = 0.1894 (Rfree = 0.000) for 5097 atoms. Found 5 (28 requested) and removed 18 (14 requested) atoms. Cycle 35: After refmac, R = 0.1863 (Rfree = 0.000) for 5075 atoms. Found 4 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.73 3.63 Search for helices and strands: 0 residues in 0 chains, 5189 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 5208 seeds are put forward Round 1: 242 peptides, 50 chains. Longest chain 9 peptides. Score 0.270 Round 2: 264 peptides, 47 chains. Longest chain 12 peptides. Score 0.348 Round 3: 284 peptides, 51 chains. Longest chain 11 peptides. Score 0.354 Round 4: 292 peptides, 50 chains. Longest chain 13 peptides. Score 0.380 Round 5: 294 peptides, 49 chains. Longest chain 15 peptides. Score 0.393 Taking the results from Round 5 Chains 49, Residues 245, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 8322 reflections ( 99.07 % complete ) and 12459 restraints for refining 5181 atoms. 11517 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2303 (Rfree = 0.000) for 5181 atoms. Found 11 (28 requested) and removed 24 (14 requested) atoms. Cycle 37: After refmac, R = 0.2328 (Rfree = 0.000) for 5140 atoms. Found 26 (28 requested) and removed 22 (14 requested) atoms. Cycle 38: After refmac, R = 0.2203 (Rfree = 0.000) for 5132 atoms. Found 22 (28 requested) and removed 25 (14 requested) atoms. Cycle 39: After refmac, R = 0.1843 (Rfree = 0.000) for 5118 atoms. Found 2 (28 requested) and removed 20 (14 requested) atoms. Cycle 40: After refmac, R = 0.1864 (Rfree = 0.000) for 5097 atoms. Found 1 (28 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 3.65 Search for helices and strands: 0 residues in 0 chains, 5234 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 5258 seeds are put forward Round 1: 245 peptides, 51 chains. Longest chain 14 peptides. Score 0.267 Round 2: 290 peptides, 54 chains. Longest chain 13 peptides. Score 0.339 Round 3: 277 peptides, 49 chains. Longest chain 13 peptides. Score 0.357 Round 4: 281 peptides, 49 chains. Longest chain 14 peptides. Score 0.366 Round 5: 289 peptides, 52 chains. Longest chain 13 peptides. Score 0.355 Taking the results from Round 4 Chains 49, Residues 232, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8322 reflections ( 99.07 % complete ) and 12320 restraints for refining 5181 atoms. 11441 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2215 (Rfree = 0.000) for 5181 atoms. Found 12 (28 requested) and removed 22 (14 requested) atoms. Cycle 42: After refmac, R = 0.2126 (Rfree = 0.000) for 5163 atoms. Found 13 (28 requested) and removed 22 (14 requested) atoms. Cycle 43: After refmac, R = 0.1959 (Rfree = 0.000) for 5148 atoms. Found 14 (28 requested) and removed 19 (14 requested) atoms. Cycle 44: After refmac, R = 0.1869 (Rfree = 0.000) for 5135 atoms. Found 10 (28 requested) and removed 18 (14 requested) atoms. Cycle 45: After refmac, R = 0.1811 (Rfree = 0.000) for 5125 atoms. Found 12 (28 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.66 3.56 Search for helices and strands: 0 residues in 0 chains, 5268 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 5291 seeds are put forward Round 1: 199 peptides, 44 chains. Longest chain 7 peptides. Score 0.227 Round 2: 255 peptides, 52 chains. Longest chain 10 peptides. Score 0.281 Round 3: 263 peptides, 52 chains. Longest chain 8 peptides. Score 0.299 Round 4: 268 peptides, 46 chains. Longest chain 12 peptides. Score 0.366 Round 5: 273 peptides, 48 chains. Longest chain 13 peptides. Score 0.358 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 46, Residues 222, 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 2oh1-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8322 reflections ( 99.07 % complete ) and 12274 restraints for refining 5181 atoms. 11432 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2021 (Rfree = 0.000) for 5181 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.1966 (Rfree = 0.000) for 5148 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.2022 (Rfree = 0.000) for 5127 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.1982 (Rfree = 0.000) for 5105 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:33:53 GMT 2018 Job finished. TimeTaking 70.72 Used memory is bytes: 18749784