Starting phenix.real_space_refine on Mon Feb 19 09:30:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh7_34754/02_2024/8hh7_34754_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh7_34754/02_2024/8hh7_34754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh7_34754/02_2024/8hh7_34754.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh7_34754/02_2024/8hh7_34754.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh7_34754/02_2024/8hh7_34754_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh7_34754/02_2024/8hh7_34754_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 77 5.16 5 C 15277 2.51 5 N 4214 2.21 5 O 4661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C GLU 320": "OE1" <-> "OE2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "E GLU 131": "OE1" <-> "OE2" Residue "F PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24250 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "C" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Chain: "D" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 23, 'TRANS': 446} Chain: "F" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "G" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2218 Classifications: {'peptide': 283} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 272} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.50, per 1000 atoms: 0.52 Number of scatterers: 24250 At special positions: 0 Unit cell: (126.72, 120.56, 154, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 77 16.00 P 16 15.00 Mg 5 11.99 O 4661 8.00 N 4214 7.00 C 15277 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.37 Conformation dependent library (CDL) restraints added in 4.4 seconds 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 121 helices and 22 sheets defined 42.5% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.29 Creating SS restraints... Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 186 removed outlier: 3.637A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 215 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 232 through 252 Proline residue: A 239 - end of helix removed outlier: 3.541A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.545A pdb=" N HIS A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 367 through 370 Processing helix chain 'A' and resid 373 through 395 removed outlier: 3.953A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ALA A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N PHE A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 401 removed outlier: 3.864A pdb=" N ASP A 401 " --> pdb=" O PHE A 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 398 through 401' Processing helix chain 'A' and resid 405 through 419 removed outlier: 3.825A pdb=" N ALA A 408 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 450 through 467 removed outlier: 3.752A pdb=" N VAL A 453 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ARG A 454 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'A' and resid 484 through 495 Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 188 removed outlier: 3.604A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ASP B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 215 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 232 through 252 Proline residue: B 239 - end of helix removed outlier: 3.852A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 288 through 300 removed outlier: 4.289A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 293 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU B 299 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 373 through 379 removed outlier: 3.853A pdb=" N VAL B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 398 removed outlier: 4.544A pdb=" N PHE B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 419 removed outlier: 3.501A pdb=" N ARG B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 441 Processing helix chain 'B' and resid 450 through 467 removed outlier: 5.149A pdb=" N ARG B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 459 " --> pdb=" O PHE B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'B' and resid 484 through 497 removed outlier: 3.582A pdb=" N THR B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 186 removed outlier: 3.538A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 215 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 232 through 252 Proline residue: C 239 - end of helix removed outlier: 3.783A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 290 through 300 removed outlier: 3.778A pdb=" N HIS C 294 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ARG C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 335 Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 373 through 379 Processing helix chain 'C' and resid 382 through 396 Processing helix chain 'C' and resid 404 through 419 Processing helix chain 'C' and resid 430 through 441 removed outlier: 3.588A pdb=" N LEU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 467 removed outlier: 4.979A pdb=" N ARG C 454 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN C 467 " --> pdb=" O LEU C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'C' and resid 484 through 497 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 164 through 178 removed outlier: 4.503A pdb=" N GLN D 177 " --> pdb=" O HIS D 173 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N GLU D 178 " --> pdb=" O ASN D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 207 through 210 Processing helix chain 'D' and resid 222 through 242 removed outlier: 5.108A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 removed outlier: 3.519A pdb=" N SER D 265 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA D 266 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 291 removed outlier: 4.446A pdb=" N ARG D 291 " --> pdb=" O GLN D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 311 No H-bonds generated for 'chain 'D' and resid 309 through 311' Processing helix chain 'D' and resid 316 through 324 removed outlier: 4.444A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N HIS D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 337 Processing helix chain 'D' and resid 356 through 359 No H-bonds generated for 'chain 'D' and resid 356 through 359' Processing helix chain 'D' and resid 361 through 387 removed outlier: 3.514A pdb=" N GLN D 381 " --> pdb=" O TYR D 377 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 409 removed outlier: 3.725A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 421 removed outlier: 3.706A pdb=" N GLU D 418 " --> pdb=" O HIS D 415 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLN D 419 " --> pdb=" O VAL D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 442 Processing helix chain 'D' and resid 450 through 453 Processing helix chain 'D' and resid 459 through 469 removed outlier: 3.548A pdb=" N VAL D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 125 through 127 No H-bonds generated for 'chain 'E' and resid 125 through 127' Processing helix chain 'E' and resid 140 through 145 Processing helix chain 'E' and resid 164 through 178 Processing helix chain 'E' and resid 192 through 205 Processing helix chain 'E' and resid 207 through 210 Processing helix chain 'E' and resid 222 through 241 removed outlier: 5.113A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 268 Processing helix chain 'E' and resid 281 through 291 removed outlier: 4.536A pdb=" N ARG E 291 " --> pdb=" O GLN E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 311 No H-bonds generated for 'chain 'E' and resid 309 through 311' Processing helix chain 'E' and resid 316 through 324 removed outlier: 3.508A pdb=" N SER E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N HIS E 324 " --> pdb=" O THR E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 338 Processing helix chain 'E' and resid 356 through 359 No H-bonds generated for 'chain 'E' and resid 356 through 359' Processing helix chain 'E' and resid 361 through 387 removed outlier: 3.570A pdb=" N GLN E 381 " --> pdb=" O TYR E 377 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 391 No H-bonds generated for 'chain 'E' and resid 389 through 391' Processing helix chain 'E' and resid 394 through 409 removed outlier: 3.617A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 421 removed outlier: 4.338A pdb=" N GLN E 419 " --> pdb=" O VAL E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 441 Processing helix chain 'E' and resid 450 through 453 Processing helix chain 'E' and resid 459 through 469 removed outlier: 3.592A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 125 through 127 No H-bonds generated for 'chain 'F' and resid 125 through 127' Processing helix chain 'F' and resid 140 through 145 Processing helix chain 'F' and resid 164 through 178 removed outlier: 4.396A pdb=" N GLN F 177 " --> pdb=" O HIS F 173 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLU F 178 " --> pdb=" O ASN F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 205 Processing helix chain 'F' and resid 207 through 210 Processing helix chain 'F' and resid 222 through 241 removed outlier: 5.043A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 268 removed outlier: 3.847A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 291 removed outlier: 4.220A pdb=" N ARG F 291 " --> pdb=" O GLN F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 316 through 320 Processing helix chain 'F' and resid 322 through 324 No H-bonds generated for 'chain 'F' and resid 322 through 324' Processing helix chain 'F' and resid 333 through 337 Processing helix chain 'F' and resid 356 through 359 No H-bonds generated for 'chain 'F' and resid 356 through 359' Processing helix chain 'F' and resid 361 through 387 removed outlier: 3.667A pdb=" N LEU F 380 " --> pdb=" O ARG F 376 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN F 381 " --> pdb=" O TYR F 377 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 409 removed outlier: 3.777A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 419 removed outlier: 3.568A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 416 through 419' Processing helix chain 'F' and resid 430 through 442 Processing helix chain 'F' and resid 450 through 453 Processing helix chain 'F' and resid 459 through 468 removed outlier: 3.591A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 57 removed outlier: 3.608A pdb=" N PHE G 42 " --> pdb=" O ASN G 38 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) Proline residue: G 44 - end of helix Processing helix chain 'G' and resid 91 through 106 removed outlier: 3.915A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'G' and resid 120 through 128 Processing helix chain 'G' and resid 146 through 161 removed outlier: 4.975A pdb=" N GLU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE G 160 " --> pdb=" O THR G 156 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA G 161 " --> pdb=" O VAL G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 282 removed outlier: 4.000A pdb=" N ASP G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) Proline residue: G 218 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.541A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N HIS A 42 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL A 31 " --> pdb=" O HIS A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= C, first strand: chain 'A' and resid 107 through 109 removed outlier: 8.556A pdb=" N VAL A 108 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL A 223 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N SER A 312 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N VAL A 258 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR A 314 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N TYR A 260 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 316 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 340 through 344 Processing sheet with id= E, first strand: chain 'B' and resid 28 through 30 removed outlier: 6.469A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N HIS B 42 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N VAL B 31 " --> pdb=" O HIS B 42 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.133A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 341 through 344 removed outlier: 6.642A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 221 through 226 removed outlier: 6.655A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER B 312 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL B 258 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N THR B 314 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N TYR B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU B 316 " --> pdb=" O TYR B 260 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 28 through 30 removed outlier: 6.547A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N HIS C 42 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL C 31 " --> pdb=" O HIS C 42 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.908A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 341 through 344 removed outlier: 6.738A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LEU C 344 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE C 168 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 221 through 226 removed outlier: 6.658A pdb=" N SER C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL C 224 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER C 312 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL C 258 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR C 314 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N TYR C 260 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU C 316 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 75 through 77 removed outlier: 6.770A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 84 through 86 Processing sheet with id= O, first strand: chain 'D' and resid 327 through 330 removed outlier: 7.814A pdb=" N ILE D 154 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N SER D 302 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU D 156 " --> pdb=" O SER D 302 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLN D 304 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N GLY D 158 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE D 306 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE D 182 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE D 250 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL D 184 " --> pdb=" O PHE D 250 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 75 through 77 removed outlier: 6.657A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 84 through 86 Processing sheet with id= R, first strand: chain 'E' and resid 327 through 330 removed outlier: 8.606A pdb=" N ILE E 154 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER E 302 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU E 156 " --> pdb=" O SER E 302 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLN E 304 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 75 through 77 removed outlier: 6.497A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 84 through 86 Processing sheet with id= U, first strand: chain 'F' and resid 327 through 330 removed outlier: 7.969A pdb=" N ILE F 154 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER F 302 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LEU F 156 " --> pdb=" O SER F 302 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN F 304 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N GLY F 158 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE F 306 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE F 182 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N PHE F 250 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL F 184 " --> pdb=" O PHE F 250 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 181 through 187 removed outlier: 6.303A pdb=" N GLY G 77 " --> pdb=" O TYR G 169 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N TYR G 171 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU G 79 " --> pdb=" O TYR G 171 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N ASN G 173 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N ILE G 81 " --> pdb=" O ASN G 173 " (cutoff:3.500A) removed outlier: 11.136A pdb=" N TYR G 175 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL G 117 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP G 136 " --> pdb=" O VAL G 117 " (cutoff:3.500A) 978 hydrogen bonds defined for protein. 2655 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.74 Time building geometry restraints manager: 10.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8201 1.34 - 1.45: 2641 1.45 - 1.57: 13638 1.57 - 1.69: 21 1.69 - 1.81: 154 Bond restraints: 24655 Sorted by residual: bond pdb=" O3 PO4 E 501 " pdb=" P PO4 E 501 " ideal model delta sigma weight residual 1.569 1.510 0.059 2.00e-02 2.50e+03 8.59e+00 bond pdb=" O4 PO4 E 501 " pdb=" P PO4 E 501 " ideal model delta sigma weight residual 1.568 1.510 0.058 2.00e-02 2.50e+03 8.51e+00 bond pdb=" O2 PO4 E 501 " pdb=" P PO4 E 501 " ideal model delta sigma weight residual 1.567 1.509 0.058 2.00e-02 2.50e+03 8.27e+00 bond pdb=" O1 PO4 E 501 " pdb=" P PO4 E 501 " ideal model delta sigma weight residual 1.565 1.509 0.056 2.00e-02 2.50e+03 7.74e+00 bond pdb=" O3 PO4 D 503 " pdb=" P PO4 D 503 " ideal model delta sigma weight residual 1.569 1.524 0.045 2.00e-02 2.50e+03 5.11e+00 ... (remaining 24650 not shown) Histogram of bond angle deviations from ideal: 99.02 - 107.18: 850 107.18 - 115.33: 15158 115.33 - 123.49: 16847 123.49 - 131.64: 564 131.64 - 139.80: 14 Bond angle restraints: 33433 Sorted by residual: angle pdb=" CA GLY B 340 " pdb=" C GLY B 340 " pdb=" N GLN B 341 " ideal model delta sigma weight residual 114.23 117.56 -3.33 8.80e-01 1.29e+00 1.43e+01 angle pdb=" N GLU G 273 " pdb=" CA GLU G 273 " pdb=" CB GLU G 273 " ideal model delta sigma weight residual 110.12 115.12 -5.00 1.47e+00 4.63e-01 1.16e+01 angle pdb=" CA GLN C 407 " pdb=" C GLN C 407 " pdb=" O GLN C 407 " ideal model delta sigma weight residual 120.70 117.28 3.42 1.03e+00 9.43e-01 1.10e+01 angle pdb=" N GLY F 88 " pdb=" CA GLY F 88 " pdb=" C GLY F 88 " ideal model delta sigma weight residual 111.56 114.72 -3.16 1.01e+00 9.80e-01 9.78e+00 angle pdb=" N THR G 138 " pdb=" CA THR G 138 " pdb=" CB THR G 138 " ideal model delta sigma weight residual 113.65 109.31 4.34 1.47e+00 4.63e-01 8.71e+00 ... (remaining 33428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.83: 14411 24.83 - 49.66: 532 49.66 - 74.49: 97 74.49 - 99.32: 18 99.32 - 124.14: 1 Dihedral angle restraints: 15059 sinusoidal: 6134 harmonic: 8925 Sorted by residual: dihedral pdb=" O1B ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PB ADP D 501 " pdb=" PA ADP D 501 " ideal model delta sinusoidal sigma weight residual 300.00 175.85 124.14 1 2.00e+01 2.50e-03 3.75e+01 dihedral pdb=" CA VAL A 353 " pdb=" C VAL A 353 " pdb=" N ARG A 354 " pdb=" CA ARG A 354 " ideal model delta harmonic sigma weight residual -180.00 -155.96 -24.04 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA PHE G 205 " pdb=" C PHE G 205 " pdb=" N GLU G 206 " pdb=" CA GLU G 206 " ideal model delta harmonic sigma weight residual 180.00 -156.93 -23.07 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 15056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2354 0.035 - 0.069: 1016 0.069 - 0.104: 322 0.104 - 0.139: 153 0.139 - 0.174: 7 Chirality restraints: 3852 Sorted by residual: chirality pdb=" CB THR C 406 " pdb=" CA THR C 406 " pdb=" OG1 THR C 406 " pdb=" CG2 THR C 406 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CG LEU B 52 " pdb=" CB LEU B 52 " pdb=" CD1 LEU B 52 " pdb=" CD2 LEU B 52 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CA GLU G 273 " pdb=" N GLU G 273 " pdb=" C GLU G 273 " pdb=" CB GLU G 273 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 3849 not shown) Planarity restraints: 4362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 269 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.57e+00 pdb=" C ALA G 269 " -0.033 2.00e-02 2.50e+03 pdb=" O ALA G 269 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE G 270 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 220 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO D 221 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 221 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 221 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 341 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO E 342 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO E 342 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 342 " -0.025 5.00e-02 4.00e+02 ... (remaining 4359 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 16 2.23 - 2.90: 9045 2.90 - 3.56: 34107 3.56 - 4.23: 57179 4.23 - 4.90: 99605 Nonbonded interactions: 199952 Sorted by model distance: nonbonded pdb=" CD1 TYR D 307 " pdb=" O2 PO4 D 503 " model vdw 1.560 3.340 nonbonded pdb=" NZ LYS D 164 " pdb=" O1 PO4 D 503 " model vdw 1.649 2.520 nonbonded pdb=" CE1 TYR D 307 " pdb=" O2 PO4 D 503 " model vdw 1.940 3.340 nonbonded pdb=" O1G ATP A 600 " pdb="MG MG A 601 " model vdw 1.952 2.170 nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 601 " model vdw 1.973 2.170 ... (remaining 199947 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 1 through 470) selection = (chain 'E' and resid 1 through 470) selection = (chain 'F' and resid 1 through 470) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.170 Check model and map are aligned: 0.400 Set scattering table: 0.250 Process input model: 63.640 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24655 Z= 0.288 Angle : 0.587 9.406 33433 Z= 0.334 Chirality : 0.046 0.174 3852 Planarity : 0.004 0.046 4362 Dihedral : 13.521 124.144 9347 Min Nonbonded Distance : 1.560 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.04 % Allowed : 0.23 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.15), residues: 3115 helix: 1.89 (0.15), residues: 1264 sheet: 1.08 (0.22), residues: 545 loop : 0.24 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 363 PHE 0.020 0.001 PHE D 257 TYR 0.018 0.001 TYR A 329 ARG 0.004 0.000 ARG D 240 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 3.034 Fit side-chains REVERT: C 95 MET cc_start: 0.8894 (tpt) cc_final: 0.8677 (tpt) outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 1.8158 time to fit residues: 251.8325 Evaluate side-chains 98 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 2.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 7.9990 chunk 234 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 242 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 281 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 294 HIS C 425 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 24655 Z= 0.424 Angle : 0.595 9.082 33433 Z= 0.313 Chirality : 0.048 0.185 3852 Planarity : 0.005 0.059 4362 Dihedral : 7.963 88.127 3546 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.43 % Allowed : 4.13 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.15), residues: 3115 helix: 1.63 (0.15), residues: 1262 sheet: 0.87 (0.22), residues: 559 loop : 0.02 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS F 363 PHE 0.018 0.002 PHE D 125 TYR 0.020 0.001 TYR A 329 ARG 0.008 0.001 ARG A 89 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 3.009 Fit side-chains REVERT: A 95 MET cc_start: 0.8230 (tpp) cc_final: 0.7898 (tpp) REVERT: B 390 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.6442 (mpt180) REVERT: C 189 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8020 (mm-40) outliers start: 11 outliers final: 4 residues processed: 115 average time/residue: 1.6793 time to fit residues: 219.2471 Evaluate side-chains 108 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 2.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 301 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 234 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 282 optimal weight: 8.9990 chunk 304 optimal weight: 0.9990 chunk 251 optimal weight: 1.9990 chunk 279 optimal weight: 0.0670 chunk 96 optimal weight: 3.9990 chunk 226 optimal weight: 1.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 HIS G 130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.0789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24655 Z= 0.173 Angle : 0.469 8.615 33433 Z= 0.245 Chirality : 0.043 0.148 3852 Planarity : 0.004 0.040 4362 Dihedral : 7.261 91.017 3546 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.62 % Allowed : 5.02 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.15), residues: 3115 helix: 1.80 (0.15), residues: 1266 sheet: 1.01 (0.22), residues: 556 loop : 0.14 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 363 PHE 0.011 0.001 PHE F 125 TYR 0.011 0.001 TYR A 329 ARG 0.006 0.000 ARG A 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 2.814 Fit side-chains REVERT: C 95 MET cc_start: 0.8912 (tpt) cc_final: 0.8668 (tpt) outliers start: 16 outliers final: 3 residues processed: 127 average time/residue: 1.5544 time to fit residues: 226.1380 Evaluate side-chains 105 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 2.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain D residue 301 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 4.9990 chunk 212 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 189 optimal weight: 6.9990 chunk 283 optimal weight: 4.9990 chunk 299 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 268 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 294 HIS C 425 HIS E 253 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 24655 Z= 0.400 Angle : 0.563 8.659 33433 Z= 0.294 Chirality : 0.047 0.170 3852 Planarity : 0.005 0.046 4362 Dihedral : 7.626 102.204 3546 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.93 % Allowed : 6.19 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.15), residues: 3115 helix: 1.60 (0.15), residues: 1258 sheet: 0.90 (0.22), residues: 550 loop : -0.01 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 363 PHE 0.018 0.002 PHE D 125 TYR 0.013 0.001 TYR A 329 ARG 0.005 0.000 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 106 time to evaluate : 3.013 Fit side-chains REVERT: B 390 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.6610 (mpt180) outliers start: 24 outliers final: 11 residues processed: 123 average time/residue: 1.5693 time to fit residues: 221.5137 Evaluate side-chains 117 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 253 ASN Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 301 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 4.9990 chunk 170 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 223 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 255 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 153 optimal weight: 1.9990 chunk 268 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 HIS E 253 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24655 Z= 0.211 Angle : 0.488 9.295 33433 Z= 0.254 Chirality : 0.043 0.156 3852 Planarity : 0.004 0.042 4362 Dihedral : 7.181 101.409 3546 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.05 % Allowed : 6.74 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.15), residues: 3115 helix: 1.73 (0.15), residues: 1260 sheet: 0.92 (0.22), residues: 561 loop : 0.01 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 363 PHE 0.013 0.001 PHE D 125 TYR 0.009 0.001 TYR A 329 ARG 0.006 0.000 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 106 time to evaluate : 3.178 Fit side-chains REVERT: B 390 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.6508 (mpt180) REVERT: C 95 MET cc_start: 0.8907 (tpt) cc_final: 0.8642 (tpt) REVERT: F 59 VAL cc_start: 0.9103 (OUTLIER) cc_final: 0.8900 (m) outliers start: 27 outliers final: 12 residues processed: 126 average time/residue: 1.5627 time to fit residues: 226.9487 Evaluate side-chains 115 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 2.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 253 ASN Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 301 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 1.9990 chunk 269 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 299 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 99 optimal weight: 0.1980 chunk 157 optimal weight: 5.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 HIS E 253 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 24655 Z= 0.307 Angle : 0.524 8.862 33433 Z= 0.273 Chirality : 0.045 0.162 3852 Planarity : 0.004 0.045 4362 Dihedral : 7.286 102.933 3546 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.09 % Allowed : 7.36 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.15), residues: 3115 helix: 1.67 (0.15), residues: 1256 sheet: 0.89 (0.22), residues: 551 loop : -0.00 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 363 PHE 0.015 0.001 PHE D 125 TYR 0.009 0.001 TYR C 251 ARG 0.005 0.000 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 104 time to evaluate : 2.803 Fit side-chains REVERT: B 390 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.6559 (mpt180) outliers start: 28 outliers final: 18 residues processed: 128 average time/residue: 1.5287 time to fit residues: 225.1396 Evaluate side-chains 120 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 2.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 301 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 0.9990 chunk 33 optimal weight: 0.0270 chunk 170 optimal weight: 0.6980 chunk 219 optimal weight: 0.0980 chunk 169 optimal weight: 0.7980 chunk 252 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 298 optimal weight: 9.9990 chunk 186 optimal weight: 0.9990 chunk 182 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 HIS E 253 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24655 Z= 0.120 Angle : 0.442 9.409 33433 Z= 0.227 Chirality : 0.041 0.150 3852 Planarity : 0.004 0.040 4362 Dihedral : 6.423 95.175 3546 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.78 % Allowed : 7.90 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.15), residues: 3115 helix: 1.96 (0.15), residues: 1257 sheet: 1.08 (0.22), residues: 543 loop : 0.14 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS E 363 PHE 0.011 0.001 PHE F 125 TYR 0.008 0.001 TYR A 438 ARG 0.007 0.000 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 3.342 Fit side-chains REVERT: A 95 MET cc_start: 0.8251 (tpp) cc_final: 0.7821 (ttp) REVERT: C 95 MET cc_start: 0.8891 (tpt) cc_final: 0.8660 (tpt) outliers start: 20 outliers final: 8 residues processed: 124 average time/residue: 1.6124 time to fit residues: 230.1643 Evaluate side-chains 109 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 101 time to evaluate : 2.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 301 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 189 optimal weight: 7.9990 chunk 203 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 27 optimal weight: 0.1980 chunk 234 optimal weight: 7.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 HIS E 253 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24655 Z= 0.127 Angle : 0.440 9.843 33433 Z= 0.225 Chirality : 0.041 0.153 3852 Planarity : 0.004 0.042 4362 Dihedral : 6.278 90.532 3546 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.78 % Allowed : 8.22 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.15), residues: 3115 helix: 2.06 (0.15), residues: 1257 sheet: 1.15 (0.22), residues: 543 loop : 0.21 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS E 363 PHE 0.011 0.001 PHE F 125 TYR 0.007 0.001 TYR A 329 ARG 0.007 0.000 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 2.657 Fit side-chains REVERT: A 95 MET cc_start: 0.8280 (tpp) cc_final: 0.7865 (ttp) REVERT: B 262 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7299 (t0) REVERT: B 390 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.6370 (mpt180) outliers start: 20 outliers final: 12 residues processed: 125 average time/residue: 1.5532 time to fit residues: 222.4296 Evaluate side-chains 116 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 3.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 301 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 5.9990 chunk 286 optimal weight: 0.0980 chunk 261 optimal weight: 0.5980 chunk 278 optimal weight: 0.9980 chunk 167 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 chunk 218 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 263 optimal weight: 0.8980 chunk 277 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 HIS E 253 ASN E 372 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24655 Z= 0.139 Angle : 0.442 9.557 33433 Z= 0.227 Chirality : 0.042 0.153 3852 Planarity : 0.004 0.042 4362 Dihedral : 6.218 86.659 3546 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.74 % Allowed : 8.26 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.15), residues: 3115 helix: 2.07 (0.15), residues: 1255 sheet: 1.18 (0.22), residues: 543 loop : 0.23 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 363 PHE 0.011 0.001 PHE F 125 TYR 0.007 0.001 TYR A 329 ARG 0.003 0.000 ARG A 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 3.159 Fit side-chains REVERT: A 95 MET cc_start: 0.8278 (tpp) cc_final: 0.7867 (ttp) REVERT: B 262 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.7295 (t0) REVERT: B 390 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.6452 (mpt180) outliers start: 19 outliers final: 12 residues processed: 119 average time/residue: 1.5433 time to fit residues: 211.7976 Evaluate side-chains 115 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 2.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 301 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 0.8980 chunk 294 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 204 optimal weight: 6.9990 chunk 308 optimal weight: 6.9990 chunk 284 optimal weight: 7.9990 chunk 245 optimal weight: 0.0770 chunk 25 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 HIS E 253 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24655 Z= 0.200 Angle : 0.470 8.917 33433 Z= 0.243 Chirality : 0.043 0.157 3852 Planarity : 0.004 0.043 4362 Dihedral : 6.384 86.898 3546 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.70 % Allowed : 8.33 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.15), residues: 3115 helix: 1.99 (0.15), residues: 1253 sheet: 1.11 (0.22), residues: 543 loop : 0.18 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 363 PHE 0.013 0.001 PHE D 125 TYR 0.008 0.001 TYR A 251 ARG 0.003 0.000 ARG A 89 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 2.859 Fit side-chains REVERT: A 95 MET cc_start: 0.8299 (tpp) cc_final: 0.7873 (ttp) REVERT: B 390 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.6363 (mpt180) outliers start: 18 outliers final: 12 residues processed: 121 average time/residue: 1.5196 time to fit residues: 211.0957 Evaluate side-chains 115 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 301 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 0.7980 chunk 261 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 226 optimal weight: 0.0870 chunk 36 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 246 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 252 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 HIS E 253 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.072841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.055786 restraints weight = 46338.409| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 2.29 r_work: 0.2613 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2488 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24655 Z= 0.198 Angle : 0.472 9.367 33433 Z= 0.243 Chirality : 0.043 0.157 3852 Planarity : 0.004 0.043 4362 Dihedral : 6.390 86.299 3546 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.78 % Allowed : 8.37 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.15), residues: 3115 helix: 1.96 (0.15), residues: 1253 sheet: 1.10 (0.22), residues: 543 loop : 0.16 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 363 PHE 0.012 0.001 PHE D 125 TYR 0.008 0.001 TYR A 292 ARG 0.003 0.000 ARG A 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5993.99 seconds wall clock time: 108 minutes 50.53 seconds (6530.53 seconds total)