Mon 24 Dec 00:23:11 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 2f4p-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2f4p-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2f4p-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4p-3.6-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/2f4p-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4p-3.6-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 00:23:16 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/2f4p-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4p-3.6-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 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-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: 170 Cell parameters: 71.746 71.746 188.600 90.000 90.000 120.000 Input sequence file: 2f4p-3.6-parrot-mrncs.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 5244 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3281 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3146 (Rfree = 0.000) for 5244 atoms. Found 33 (33 requested) and removed 89 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.37 3.70 Search for helices and strands: 0 residues in 0 chains, 5273 seeds are put forward NCS extension: 0 residues added, 5273 seeds are put forward Round 1: 214 peptides, 42 chains. Longest chain 11 peptides. Score 0.319 Round 2: 289 peptides, 47 chains. Longest chain 17 peptides. Score 0.471 Round 3: 302 peptides, 48 chains. Longest chain 15 peptides. Score 0.493 Round 4: 316 peptides, 44 chains. Longest chain 15 peptides. Score 0.568 Round 5: 315 peptides, 42 chains. Longest chain 18 peptides. Score 0.585 Taking the results from Round 5 Chains 42, Residues 273, Estimated correctness of the model 8.6 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6336 reflections ( 99.48 % complete ) and 9702 restraints for refining 4263 atoms. 8631 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2587 (Rfree = 0.000) for 4263 atoms. Found 26 (27 requested) and removed 48 (13 requested) atoms. Cycle 2: After refmac, R = 0.2212 (Rfree = 0.000) for 4169 atoms. Found 27 (27 requested) and removed 49 (13 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2050 (Rfree = 0.000) for 4126 atoms. Found 7 (26 requested) and removed 22 (13 requested) atoms. Cycle 4: After refmac, R = 0.1980 (Rfree = 0.000) for 4103 atoms. Found 12 (26 requested) and removed 34 (13 requested) atoms. Cycle 5: After refmac, R = 0.1866 (Rfree = 0.000) for 4075 atoms. Found 4 (26 requested) and removed 23 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.33 3.66 Search for helices and strands: 0 residues in 0 chains, 4170 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 4185 seeds are put forward Round 1: 265 peptides, 50 chains. Longest chain 14 peptides. Score 0.371 Round 2: 300 peptides, 47 chains. Longest chain 16 peptides. Score 0.499 Round 3: 291 peptides, 43 chains. Longest chain 24 peptides. Score 0.520 Round 4: 310 peptides, 41 chains. Longest chain 17 peptides. Score 0.584 Round 5: 307 peptides, 40 chains. Longest chain 27 peptides. Score 0.587 Taking the results from Round 5 Chains 40, Residues 267, Estimated correctness of the model 9.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6336 reflections ( 99.48 % complete ) and 9538 restraints for refining 4213 atoms. 8510 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2182 (Rfree = 0.000) for 4213 atoms. Found 27 (27 requested) and removed 52 (13 requested) atoms. Cycle 7: After refmac, R = 0.1995 (Rfree = 0.000) for 4160 atoms. Found 14 (26 requested) and removed 34 (13 requested) atoms. Cycle 8: After refmac, R = 0.1851 (Rfree = 0.000) for 4131 atoms. Found 12 (26 requested) and removed 25 (13 requested) atoms. Cycle 9: After refmac, R = 0.1754 (Rfree = 0.000) for 4110 atoms. Found 9 (26 requested) and removed 29 (13 requested) atoms. Cycle 10: After refmac, R = 0.1638 (Rfree = 0.000) for 4085 atoms. Found 10 (26 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.28 3.60 Search for helices and strands: 0 residues in 0 chains, 4179 seeds are put forward NCS extension: 27 residues added (9 deleted due to clashes), 4206 seeds are put forward Round 1: 248 peptides, 45 chains. Longest chain 13 peptides. Score 0.383 Round 2: 297 peptides, 46 chains. Longest chain 16 peptides. Score 0.502 Round 3: 308 peptides, 43 chains. Longest chain 17 peptides. Score 0.560 Round 4: 314 peptides, 45 chains. Longest chain 17 peptides. Score 0.553 Round 5: 308 peptides, 40 chains. Longest chain 21 peptides. Score 0.589 Taking the results from Round 5 Chains 42, Residues 268, Estimated correctness of the model 10.2 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 6336 reflections ( 99.48 % complete ) and 9301 restraints for refining 4264 atoms. 8171 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2093 (Rfree = 0.000) for 4264 atoms. Found 27 (27 requested) and removed 44 (13 requested) atoms. Cycle 12: After refmac, R = 0.1903 (Rfree = 0.000) for 4218 atoms. Found 15 (27 requested) and removed 24 (13 requested) atoms. Cycle 13: After refmac, R = 0.1841 (Rfree = 0.000) for 4200 atoms. Found 11 (26 requested) and removed 20 (13 requested) atoms. Cycle 14: After refmac, R = 0.1777 (Rfree = 0.000) for 4184 atoms. Found 7 (26 requested) and removed 15 (13 requested) atoms. Cycle 15: After refmac, R = 0.1752 (Rfree = 0.000) for 4174 atoms. Found 6 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.28 3.60 Search for helices and strands: 0 residues in 0 chains, 4281 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 4297 seeds are put forward Round 1: 258 peptides, 46 chains. Longest chain 16 peptides. Score 0.399 Round 2: 302 peptides, 44 chains. Longest chain 23 peptides. Score 0.536 Round 3: 302 peptides, 43 chains. Longest chain 17 peptides. Score 0.546 Round 4: 317 peptides, 45 chains. Longest chain 18 peptides. Score 0.560 Round 5: 322 peptides, 42 chains. Longest chain 19 peptides. Score 0.600 Taking the results from Round 5 Chains 42, Residues 280, Estimated correctness of the model 14.6 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 6336 reflections ( 99.48 % complete ) and 9414 restraints for refining 4261 atoms. 8246 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2104 (Rfree = 0.000) for 4261 atoms. Found 24 (27 requested) and removed 42 (13 requested) atoms. Cycle 17: After refmac, R = 0.1758 (Rfree = 0.000) for 4217 atoms. Found 16 (27 requested) and removed 22 (13 requested) atoms. Cycle 18: After refmac, R = 0.1644 (Rfree = 0.000) for 4198 atoms. Found 9 (26 requested) and removed 21 (13 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1568 (Rfree = 0.000) for 4170 atoms. Found 6 (26 requested) and removed 15 (13 requested) atoms. Cycle 20: After refmac, R = 0.1500 (Rfree = 0.000) for 4149 atoms. Found 10 (26 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.32 3.65 Search for helices and strands: 0 residues in 0 chains, 4257 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 4284 seeds are put forward Round 1: 257 peptides, 47 chains. Longest chain 11 peptides. Score 0.384 Round 2: 302 peptides, 45 chains. Longest chain 14 peptides. Score 0.525 Round 3: 296 peptides, 45 chains. Longest chain 15 peptides. Score 0.511 Round 4: 301 peptides, 46 chains. Longest chain 21 peptides. Score 0.512 Round 5: 304 peptides, 39 chains. Longest chain 21 peptides. Score 0.590 Taking the results from Round 5 Chains 40, Residues 265, Estimated correctness of the model 10.6 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 6336 reflections ( 99.48 % complete ) and 9598 restraints for refining 4264 atoms. 8520 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1806 (Rfree = 0.000) for 4264 atoms. Found 17 (27 requested) and removed 32 (13 requested) atoms. Cycle 22: After refmac, R = 0.1581 (Rfree = 0.000) for 4230 atoms. Found 9 (27 requested) and removed 21 (13 requested) atoms. Cycle 23: After refmac, R = 0.1506 (Rfree = 0.000) for 4207 atoms. Found 7 (27 requested) and removed 15 (13 requested) atoms. Cycle 24: After refmac, R = 0.1565 (Rfree = 0.000) for 4192 atoms. Found 7 (26 requested) and removed 19 (13 requested) atoms. Cycle 25: After refmac, R = 0.1435 (Rfree = 0.000) for 4177 atoms. Found 4 (26 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.30 3.62 Search for helices and strands: 0 residues in 0 chains, 4273 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4290 seeds are put forward Round 1: 226 peptides, 45 chains. Longest chain 11 peptides. Score 0.317 Round 2: 263 peptides, 45 chains. Longest chain 12 peptides. Score 0.425 Round 3: 267 peptides, 43 chains. Longest chain 13 peptides. Score 0.459 Round 4: 280 peptides, 46 chains. Longest chain 13 peptides. Score 0.459 Round 5: 291 peptides, 47 chains. Longest chain 12 peptides. Score 0.476 Taking the results from Round 5 Chains 47, Residues 244, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6336 reflections ( 99.48 % complete ) and 9637 restraints for refining 4263 atoms. 8656 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1760 (Rfree = 0.000) for 4263 atoms. Found 25 (27 requested) and removed 17 (13 requested) atoms. Cycle 27: After refmac, R = 0.1610 (Rfree = 0.000) for 4255 atoms. Found 12 (27 requested) and removed 20 (13 requested) atoms. Cycle 28: After refmac, R = 0.1511 (Rfree = 0.000) for 4242 atoms. Found 6 (27 requested) and removed 19 (13 requested) atoms. Cycle 29: After refmac, R = 0.1522 (Rfree = 0.000) for 4226 atoms. Found 12 (27 requested) and removed 18 (13 requested) atoms. Cycle 30: After refmac, R = 0.1381 (Rfree = 0.000) for 4216 atoms. Found 9 (27 requested) and removed 22 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.35 3.68 Search for helices and strands: 0 residues in 0 chains, 4335 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 4348 seeds are put forward Round 1: 241 peptides, 48 chains. Longest chain 11 peptides. Score 0.325 Round 2: 246 peptides, 44 chains. Longest chain 11 peptides. Score 0.389 Round 3: 263 peptides, 44 chains. Longest chain 15 peptides. Score 0.437 Round 4: 266 peptides, 43 chains. Longest chain 11 peptides. Score 0.456 Round 5: 274 peptides, 43 chains. Longest chain 11 peptides. Score 0.477 Taking the results from Round 5 Chains 44, Residues 231, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 6336 reflections ( 99.48 % complete ) and 9738 restraints for refining 4264 atoms. 8795 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1823 (Rfree = 0.000) for 4264 atoms. Found 26 (27 requested) and removed 20 (13 requested) atoms. Cycle 32: After refmac, R = 0.1656 (Rfree = 0.000) for 4253 atoms. Found 6 (27 requested) and removed 17 (13 requested) atoms. Cycle 33: After refmac, R = 0.1632 (Rfree = 0.000) for 4235 atoms. Found 3 (27 requested) and removed 17 (13 requested) atoms. Cycle 34: After refmac, R = 0.1644 (Rfree = 0.000) for 4219 atoms. Found 5 (27 requested) and removed 14 (13 requested) atoms. Cycle 35: After refmac, R = 0.1625 (Rfree = 0.000) for 4210 atoms. Found 1 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.34 3.67 Search for helices and strands: 0 residues in 0 chains, 4296 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 4307 seeds are put forward Round 1: 202 peptides, 38 chains. Longest chain 12 peptides. Score 0.334 Round 2: 245 peptides, 38 chains. Longest chain 13 peptides. Score 0.458 Round 3: 250 peptides, 39 chains. Longest chain 15 peptides. Score 0.460 Round 4: 255 peptides, 39 chains. Longest chain 14 peptides. Score 0.473 Round 5: 248 peptides, 34 chains. Longest chain 18 peptides. Score 0.512 Taking the results from Round 5 Chains 35, Residues 214, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 6336 reflections ( 99.48 % complete ) and 9745 restraints for refining 4264 atoms. 8856 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1906 (Rfree = 0.000) for 4264 atoms. Found 24 (27 requested) and removed 19 (13 requested) atoms. Cycle 37: After refmac, R = 0.1770 (Rfree = 0.000) for 4264 atoms. Found 13 (27 requested) and removed 13 (13 requested) atoms. Cycle 38: After refmac, R = 0.1724 (Rfree = 0.000) for 4261 atoms. Found 7 (27 requested) and removed 13 (13 requested) atoms. Cycle 39: After refmac, R = 0.1686 (Rfree = 0.000) for 4251 atoms. Found 4 (27 requested) and removed 13 (13 requested) atoms. Cycle 40: After refmac, R = 0.1628 (Rfree = 0.000) for 4240 atoms. Found 3 (27 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 3.64 Search for helices and strands: 0 residues in 0 chains, 4325 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 4345 seeds are put forward Round 1: 186 peptides, 34 chains. Longest chain 18 peptides. Score 0.338 Round 2: 213 peptides, 32 chains. Longest chain 13 peptides. Score 0.443 Round 3: 216 peptides, 33 chains. Longest chain 19 peptides. Score 0.439 Round 4: 228 peptides, 38 chains. Longest chain 13 peptides. Score 0.411 Round 5: 237 peptides, 35 chains. Longest chain 17 peptides. Score 0.472 Taking the results from Round 5 Chains 35, Residues 202, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6336 reflections ( 99.48 % complete ) and 10059 restraints for refining 4264 atoms. 9286 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1905 (Rfree = 0.000) for 4264 atoms. Found 27 (27 requested) and removed 14 (13 requested) atoms. Cycle 42: After refmac, R = 0.1767 (Rfree = 0.000) for 4276 atoms. Found 11 (27 requested) and removed 15 (13 requested) atoms. Cycle 43: After refmac, R = 0.1711 (Rfree = 0.000) for 4271 atoms. Found 11 (27 requested) and removed 14 (13 requested) atoms. Cycle 44: After refmac, R = 0.1652 (Rfree = 0.000) for 4266 atoms. Found 2 (27 requested) and removed 14 (13 requested) atoms. Cycle 45: After refmac, R = 0.1624 (Rfree = 0.000) for 4252 atoms. Found 3 (27 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 3.66 Search for helices and strands: 0 residues in 0 chains, 4346 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 4372 seeds are put forward Round 1: 204 peptides, 38 chains. Longest chain 11 peptides. Score 0.341 Round 2: 229 peptides, 38 chains. Longest chain 14 peptides. Score 0.414 Round 3: 230 peptides, 38 chains. Longest chain 13 peptides. Score 0.417 Round 4: 229 peptides, 37 chains. Longest chain 12 peptides. Score 0.427 Round 5: 232 peptides, 35 chains. Longest chain 20 peptides. Score 0.459 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 197, Estimated correctness of the model 0.0 % 3 chains (30 residues) have been docked in sequence Sequence coverage is 15 % Consider running further cycles of model building using 2f4p-3_warpNtrace.pdb as input Building loops using Loopy2018 35 chains (197 residues) following loop building 3 chains (30 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6336 reflections ( 99.48 % complete ) and 9674 restraints for refining 4264 atoms. 8790 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1778 (Rfree = 0.000) for 4264 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.1668 (Rfree = 0.000) for 4238 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.1640 (Rfree = 0.000) for 4220 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.1615 (Rfree = 0.000) for 4203 atoms. TimeTaking 57.13