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 2f4p-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2f4p-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2f4p-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4p-3.6-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/2f4p-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4p-3.6-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/2f4p-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4p-3.6-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 385 and 0 Target number of residues in the AU: 385 Target solvent content: 0.6283 Checking the provided sequence file Detected sequence length: 147 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 588 Adjusted target solvent content: 0.43 Input MTZ file: 2f4p-3.6-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: 170 Cell parameters: 71.746 71.746 188.600 90.000 90.000 120.000 Input sequence file: 2f4p-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 4704 target number of atoms Had to go as low as 0.65 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: 21.543 3.601 Wilson plot Bfac: 65.52 6336 reflections ( 99.48 % complete ) and 0 restraints for refining 5219 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3325 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3272 (Rfree = 0.000) for 5219 atoms. Found 28 (33 requested) and removed 82 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.38 3.71 Search for helices and strands: 0 residues in 0 chains, 5228 seeds are put forward NCS extension: 0 residues added, 5228 seeds are put forward Round 1: 219 peptides, 45 chains. Longest chain 10 peptides. Score 0.295 Round 2: 293 peptides, 49 chains. Longest chain 18 peptides. Score 0.459 Round 3: 325 peptides, 52 chains. Longest chain 12 peptides. Score 0.507 Round 4: 339 peptides, 52 chains. Longest chain 19 peptides. Score 0.541 Round 5: 341 peptides, 52 chains. Longest chain 14 peptides. Score 0.545 Taking the results from Round 5 Chains 52, Residues 289, Estimated correctness of the model 0.0 % 5 chains (21 residues) have been docked in sequence ------------------------------------------------------ 6336 reflections ( 99.48 % complete ) and 9665 restraints for refining 4264 atoms. 8501 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2722 (Rfree = 0.000) for 4264 atoms. Found 19 (27 requested) and removed 47 (13 requested) atoms. Cycle 2: After refmac, R = 0.2400 (Rfree = 0.000) for 4195 atoms. Found 22 (27 requested) and removed 32 (13 requested) atoms. Cycle 3: After refmac, R = 0.2261 (Rfree = 0.000) for 4161 atoms. Found 9 (26 requested) and removed 20 (13 requested) atoms. Cycle 4: After refmac, R = 0.2201 (Rfree = 0.000) for 4135 atoms. Found 5 (26 requested) and removed 17 (13 requested) atoms. Cycle 5: After refmac, R = 0.2148 (Rfree = 0.000) for 4118 atoms. Found 4 (26 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 3.67 Search for helices and strands: 0 residues in 0 chains, 4235 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 4253 seeds are put forward Round 1: 231 peptides, 45 chains. Longest chain 10 peptides. Score 0.332 Round 2: 269 peptides, 41 chains. Longest chain 17 peptides. Score 0.487 Round 3: 292 peptides, 43 chains. Longest chain 17 peptides. Score 0.522 Round 4: 318 peptides, 43 chains. Longest chain 23 peptides. Score 0.582 Round 5: 301 peptides, 42 chains. Longest chain 15 peptides. Score 0.554 Taking the results from Round 4 Chains 43, Residues 275, Estimated correctness of the model 7.4 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 6336 reflections ( 99.48 % complete ) and 9528 restraints for refining 4249 atoms. 8376 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2475 (Rfree = 0.000) for 4249 atoms. Found 25 (27 requested) and removed 49 (13 requested) atoms. Cycle 7: After refmac, R = 0.2342 (Rfree = 0.000) for 4202 atoms. Found 12 (27 requested) and removed 20 (13 requested) atoms. Cycle 8: After refmac, R = 0.2286 (Rfree = 0.000) for 4191 atoms. Found 3 (26 requested) and removed 17 (13 requested) atoms. Cycle 9: After refmac, R = 0.2251 (Rfree = 0.000) for 4176 atoms. Found 2 (26 requested) and removed 14 (13 requested) atoms. Cycle 10: After refmac, R = 0.2209 (Rfree = 0.000) for 4159 atoms. Found 4 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.34 3.67 Search for helices and strands: 0 residues in 0 chains, 4239 seeds are put forward NCS extension: 18 residues added (4 deleted due to clashes), 4257 seeds are put forward Round 1: 268 peptides, 47 chains. Longest chain 17 peptides. Score 0.415 Round 2: 318 peptides, 46 chains. Longest chain 20 peptides. Score 0.552 Round 3: 318 peptides, 43 chains. Longest chain 20 peptides. Score 0.582 Round 4: 309 peptides, 41 chains. Longest chain 21 peptides. Score 0.582 Round 5: 324 peptides, 55 chains. Longest chain 16 peptides. Score 0.473 Taking the results from Round 4 Chains 41, Residues 268, Estimated correctness of the model 7.4 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 6336 reflections ( 99.48 % complete ) and 9557 restraints for refining 4264 atoms. 8433 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2266 (Rfree = 0.000) for 4264 atoms. Found 20 (27 requested) and removed 29 (13 requested) atoms. Cycle 12: After refmac, R = 0.2127 (Rfree = 0.000) for 4234 atoms. Found 6 (27 requested) and removed 18 (13 requested) atoms. Cycle 13: After refmac, R = 0.2084 (Rfree = 0.000) for 4214 atoms. Found 9 (27 requested) and removed 18 (13 requested) atoms. Cycle 14: After refmac, R = 0.2023 (Rfree = 0.000) for 4205 atoms. Found 3 (26 requested) and removed 15 (13 requested) atoms. Cycle 15: After refmac, R = 0.1960 (Rfree = 0.000) for 4192 atoms. Found 5 (26 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.34 3.67 Search for helices and strands: 0 residues in 0 chains, 4261 seeds are put forward NCS extension: 28 residues added (6 deleted due to clashes), 4289 seeds are put forward Round 1: 273 peptides, 48 chains. Longest chain 14 peptides. Score 0.417 Round 2: 301 peptides, 46 chains. Longest chain 18 peptides. Score 0.512 Round 3: 315 peptides, 50 chains. Longest chain 14 peptides. Score 0.504 Round 4: 321 peptides, 46 chains. Longest chain 18 peptides. Score 0.559 Round 5: 310 peptides, 46 chains. Longest chain 17 peptides. Score 0.534 Taking the results from Round 4 Chains 46, Residues 275, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6336 reflections ( 99.48 % complete ) and 9827 restraints for refining 4263 atoms. 8773 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2158 (Rfree = 0.000) for 4263 atoms. Found 22 (27 requested) and removed 30 (13 requested) atoms. Cycle 17: After refmac, R = 0.2034 (Rfree = 0.000) for 4242 atoms. Found 15 (27 requested) and removed 19 (13 requested) atoms. Cycle 18: After refmac, R = 0.1949 (Rfree = 0.000) for 4236 atoms. Found 9 (27 requested) and removed 17 (13 requested) atoms. Cycle 19: After refmac, R = 0.1911 (Rfree = 0.000) for 4225 atoms. Found 11 (27 requested) and removed 16 (13 requested) atoms. Cycle 20: After refmac, R = 0.1874 (Rfree = 0.000) for 4219 atoms. Found 2 (27 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.33 3.66 Search for helices and strands: 0 residues in 0 chains, 4308 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 4322 seeds are put forward Round 1: 266 peptides, 45 chains. Longest chain 13 peptides. Score 0.433 Round 2: 286 peptides, 42 chains. Longest chain 15 peptides. Score 0.518 Round 3: 317 peptides, 47 chains. Longest chain 16 peptides. Score 0.540 Round 4: 318 peptides, 47 chains. Longest chain 16 peptides. Score 0.542 Round 5: 312 peptides, 48 chains. Longest chain 16 peptides. Score 0.518 Taking the results from Round 4 Chains 49, Residues 271, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6336 reflections ( 99.48 % complete ) and 9768 restraints for refining 4263 atoms. 8696 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2017 (Rfree = 0.000) for 4263 atoms. Found 17 (27 requested) and removed 18 (13 requested) atoms. Cycle 22: After refmac, R = 0.1909 (Rfree = 0.000) for 4245 atoms. Found 8 (27 requested) and removed 14 (13 requested) atoms. Cycle 23: After refmac, R = 0.1835 (Rfree = 0.000) for 4237 atoms. Found 7 (27 requested) and removed 15 (13 requested) atoms. Cycle 24: After refmac, R = 0.1824 (Rfree = 0.000) for 4226 atoms. Found 9 (27 requested) and removed 17 (13 requested) atoms. Cycle 25: After refmac, R = 0.1780 (Rfree = 0.000) for 4216 atoms. Found 5 (27 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 3.66 Search for helices and strands: 0 residues in 0 chains, 4313 seeds are put forward NCS extension: 17 residues added (4 deleted due to clashes), 4330 seeds are put forward Round 1: 229 peptides, 40 chains. Longest chain 13 peptides. Score 0.389 Round 2: 276 peptides, 41 chains. Longest chain 16 peptides. Score 0.505 Round 3: 277 peptides, 39 chains. Longest chain 21 peptides. Score 0.529 Round 4: 290 peptides, 42 chains. Longest chain 15 peptides. Score 0.528 Round 5: 284 peptides, 40 chains. Longest chain 18 peptides. Score 0.535 Taking the results from Round 5 Chains 41, Residues 244, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 6336 reflections ( 99.48 % complete ) and 9745 restraints for refining 4264 atoms. 8755 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1885 (Rfree = 0.000) for 4264 atoms. Found 11 (27 requested) and removed 19 (13 requested) atoms. Cycle 27: After refmac, R = 0.2009 (Rfree = 0.000) for 4242 atoms. Found 15 (27 requested) and removed 24 (13 requested) atoms. Cycle 28: After refmac, R = 0.1653 (Rfree = 0.000) for 4227 atoms. Found 6 (27 requested) and removed 20 (13 requested) atoms. Cycle 29: After refmac, R = 0.1629 (Rfree = 0.000) for 4204 atoms. Found 11 (27 requested) and removed 16 (13 requested) atoms. Cycle 30: After refmac, R = 0.1363 (Rfree = 0.000) for 4196 atoms. Found 5 (26 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.34 3.67 Search for helices and strands: 0 residues in 0 chains, 4282 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 4299 seeds are put forward Round 1: 229 peptides, 47 chains. Longest chain 10 peptides. Score 0.301 Round 2: 250 peptides, 42 chains. Longest chain 16 peptides. Score 0.425 Round 3: 258 peptides, 45 chains. Longest chain 16 peptides. Score 0.411 Round 4: 271 peptides, 46 chains. Longest chain 15 peptides. Score 0.435 Round 5: 273 peptides, 44 chains. Longest chain 16 peptides. Score 0.463 Taking the results from Round 5 Chains 44, Residues 229, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6336 reflections ( 99.48 % complete ) and 9897 restraints for refining 4264 atoms. 9012 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1669 (Rfree = 0.000) for 4264 atoms. Found 16 (27 requested) and removed 18 (13 requested) atoms. Cycle 32: After refmac, R = 0.1555 (Rfree = 0.000) for 4254 atoms. Found 12 (27 requested) and removed 19 (13 requested) atoms. Cycle 33: After refmac, R = 0.1525 (Rfree = 0.000) for 4240 atoms. Found 15 (27 requested) and removed 19 (13 requested) atoms. Cycle 34: After refmac, R = 0.1438 (Rfree = 0.000) for 4231 atoms. Found 13 (27 requested) and removed 16 (13 requested) atoms. Cycle 35: After refmac, R = 0.1401 (Rfree = 0.000) for 4224 atoms. Found 17 (27 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 3.69 Search for helices and strands: 0 residues in 0 chains, 4307 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 4325 seeds are put forward Round 1: 207 peptides, 43 chains. Longest chain 14 peptides. Score 0.284 Round 2: 231 peptides, 42 chains. Longest chain 18 peptides. Score 0.370 Round 3: 237 peptides, 42 chains. Longest chain 14 peptides. Score 0.388 Round 4: 253 peptides, 41 chains. Longest chain 18 peptides. Score 0.445 Round 5: 253 peptides, 44 chains. Longest chain 11 peptides. Score 0.409 Taking the results from Round 4 Chains 42, Residues 212, Estimated correctness of the model 0.0 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 6336 reflections ( 99.48 % complete ) and 9662 restraints for refining 4264 atoms. 8733 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1651 (Rfree = 0.000) for 4264 atoms. Found 12 (27 requested) and removed 26 (13 requested) atoms. Cycle 37: After refmac, R = 0.1588 (Rfree = 0.000) for 4239 atoms. Found 7 (27 requested) and removed 20 (13 requested) atoms. Cycle 38: After refmac, R = 0.1536 (Rfree = 0.000) for 4222 atoms. Found 14 (27 requested) and removed 19 (13 requested) atoms. Cycle 39: After refmac, R = 0.1581 (Rfree = 0.000) for 4209 atoms. Found 13 (27 requested) and removed 19 (13 requested) atoms. Cycle 40: After refmac, R = 0.1492 (Rfree = 0.000) for 4200 atoms. Found 10 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 3.68 Search for helices and strands: 0 residues in 0 chains, 4290 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 4320 seeds are put forward Round 1: 206 peptides, 41 chains. Longest chain 17 peptides. Score 0.307 Round 2: 244 peptides, 40 chains. Longest chain 17 peptides. Score 0.432 Round 3: 228 peptides, 40 chains. Longest chain 16 peptides. Score 0.387 Round 4: 241 peptides, 39 chains. Longest chain 25 peptides. Score 0.436 Round 5: 232 peptides, 34 chains. Longest chain 32 peptides. Score 0.471 Taking the results from Round 5 Chains 35, Residues 198, Estimated correctness of the model 0.0 % 2 chains (37 residues) have been docked in sequence ------------------------------------------------------ 6336 reflections ( 99.48 % complete ) and 9482 restraints for refining 4264 atoms. 8565 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1690 (Rfree = 0.000) for 4264 atoms. Found 16 (27 requested) and removed 31 (13 requested) atoms. Cycle 42: After refmac, R = 0.1530 (Rfree = 0.000) for 4237 atoms. Found 8 (27 requested) and removed 17 (13 requested) atoms. Cycle 43: After refmac, R = 0.1504 (Rfree = 0.000) for 4219 atoms. Found 11 (27 requested) and removed 19 (13 requested) atoms. Cycle 44: After refmac, R = 0.1431 (Rfree = 0.000) for 4207 atoms. Found 15 (26 requested) and removed 19 (13 requested) atoms. Cycle 45: After refmac, R = 0.1411 (Rfree = 0.000) for 4200 atoms. Found 3 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.34 3.67 Search for helices and strands: 0 residues in 0 chains, 4268 seeds are put forward NCS extension: 17 residues added (4 deleted due to clashes), 4285 seeds are put forward Round 1: 155 peptides, 33 chains. Longest chain 8 peptides. Score 0.250 Round 2: 209 peptides, 42 chains. Longest chain 15 peptides. Score 0.303 Round 3: 208 peptides, 38 chains. Longest chain 12 peptides. Score 0.353 Round 4: 202 peptides, 37 chains. Longest chain 11 peptides. Score 0.347 Round 5: 219 peptides, 36 chains. Longest chain 14 peptides. Score 0.411 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 183, 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 2f4p-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6336 reflections ( 99.48 % complete ) and 10250 restraints for refining 4264 atoms. 9554 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1583 (Rfree = 0.000) for 4264 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.1537 (Rfree = 0.000) for 4242 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.1589 (Rfree = 0.000) for 4226 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.1432 (Rfree = 0.000) for 4210 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:38:34 GMT 2018 Job finished. TimeTaking 70.61 Used memory is bytes: 17372160