Starting phenix.real_space_refine on Sat Aug 23 22:02:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wtz_37847/08_2025/8wtz_37847.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wtz_37847/08_2025/8wtz_37847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wtz_37847/08_2025/8wtz_37847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wtz_37847/08_2025/8wtz_37847.map" model { file = "/net/cci-nas-00/data/ceres_data/8wtz_37847/08_2025/8wtz_37847.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wtz_37847/08_2025/8wtz_37847.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.047 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 92 5.16 5 C 9862 2.51 5 N 2433 2.21 5 O 2541 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14930 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3695 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 12, 'TRANS': 434} Chain breaks: 1 Chain: "D" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3650 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 429} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3695 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 12, 'TRANS': 434} Chain breaks: 1 Chain: "B" Number of atoms: 3654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3654 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 12, 'TRANS': 429} Chain breaks: 1 Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 55 Unusual residues: {'PC1': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-1': 2, 'PC1:plan-2': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PC1:plan-1': 4, 'PC1:plan-2': 4} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 69 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-1': 3, 'PC1:plan-2': 3} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PC1:plan-1': 4, 'PC1:plan-2': 4} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 2.87, per 1000 atoms: 0.19 Number of scatterers: 14930 At special positions: 0 Unit cell: (98.8, 102.96, 127.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 2 15.00 O 2541 8.00 N 2433 7.00 C 9862 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 - 3.00 Amino acid : True - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 599.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3372 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 16 sheets defined 71.0% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'C' and resid 79 through 107 Proline residue: C 101 - end of helix Processing helix chain 'C' and resid 114 through 135 Processing helix chain 'C' and resid 148 through 159 removed outlier: 3.745A pdb=" N TYR C 156 " --> pdb=" O ILE C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 169 Processing helix chain 'C' and resid 170 through 178 Processing helix chain 'C' and resid 181 through 186 removed outlier: 3.717A pdb=" N ARG C 185 " --> pdb=" O LYS C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 193 removed outlier: 3.718A pdb=" N ILE C 190 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 208 removed outlier: 3.905A pdb=" N VAL C 198 " --> pdb=" O ARG C 194 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP C 208 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 242 removed outlier: 3.806A pdb=" N LEU C 221 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 251 removed outlier: 5.028A pdb=" N GLY C 249 " --> pdb=" O SER C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 269 Processing helix chain 'C' and resid 270 through 287 Processing helix chain 'C' and resid 298 through 329 Processing helix chain 'C' and resid 331 through 349 removed outlier: 3.905A pdb=" N ARG C 349 " --> pdb=" O ARG C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 379 removed outlier: 3.533A pdb=" N THR C 361 " --> pdb=" O ARG C 357 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY C 362 " --> pdb=" O GLY C 358 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR C 372 " --> pdb=" O TYR C 368 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR C 373 " --> pdb=" O GLU C 369 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA C 375 " --> pdb=" O SER C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 400 removed outlier: 3.727A pdb=" N LEU C 395 " --> pdb=" O GLN C 391 " (cutoff:3.500A) Proline residue: C 396 - end of helix removed outlier: 3.701A pdb=" N LYS C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 417 removed outlier: 3.892A pdb=" N ILE C 417 " --> pdb=" O ASN C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 478 removed outlier: 3.551A pdb=" N ILE C 476 " --> pdb=" O GLY C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 509 Processing helix chain 'C' and resid 509 through 524 removed outlier: 3.553A pdb=" N ARG C 514 " --> pdb=" O PHE C 510 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG C 515 " --> pdb=" O HIS C 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 107 removed outlier: 3.646A pdb=" N MET D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D 91 " --> pdb=" O MET D 87 " (cutoff:3.500A) Proline residue: D 101 - end of helix Processing helix chain 'D' and resid 111 through 135 removed outlier: 4.168A pdb=" N ILE D 116 " --> pdb=" O GLU D 112 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU D 117 " --> pdb=" O ASN D 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE D 133 " --> pdb=" O ILE D 129 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE D 134 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 159 removed outlier: 3.649A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR D 156 " --> pdb=" O ILE D 152 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS D 158 " --> pdb=" O LEU D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 168 Processing helix chain 'D' and resid 170 through 179 removed outlier: 3.565A pdb=" N GLY D 179 " --> pdb=" O TYR D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 186 Processing helix chain 'D' and resid 187 through 192 Processing helix chain 'D' and resid 193 through 207 removed outlier: 3.953A pdb=" N ARG D 197 " --> pdb=" O TYR D 193 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS D 207 " --> pdb=" O HIS D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 242 removed outlier: 3.718A pdb=" N ALA D 240 " --> pdb=" O PHE D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 removed outlier: 5.019A pdb=" N GLY D 249 " --> pdb=" O SER D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 269 Processing helix chain 'D' and resid 270 through 287 removed outlier: 3.604A pdb=" N THR D 276 " --> pdb=" O TRP D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 330 Processing helix chain 'D' and resid 333 through 349 removed outlier: 3.597A pdb=" N LYS D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG D 349 " --> pdb=" O ARG D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 370 removed outlier: 3.543A pdb=" N GLN D 359 " --> pdb=" O ASN D 355 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER D 370 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 381 Processing helix chain 'D' and resid 382 through 400 removed outlier: 3.967A pdb=" N LYS D 388 " --> pdb=" O SER D 384 " (cutoff:3.500A) Proline residue: D 396 - end of helix Processing helix chain 'D' and resid 401 through 405 Processing helix chain 'D' and resid 408 through 418 removed outlier: 3.586A pdb=" N ILE D 417 " --> pdb=" O ASN D 413 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG D 418 " --> pdb=" O GLN D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 479 Processing helix chain 'D' and resid 499 through 509 removed outlier: 3.646A pdb=" N ASN D 504 " --> pdb=" O GLN D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 524 Processing helix chain 'A' and resid 79 through 107 Proline residue: A 101 - end of helix Processing helix chain 'A' and resid 114 through 135 Processing helix chain 'A' and resid 148 through 159 removed outlier: 3.745A pdb=" N TYR A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 169 Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 181 through 186 removed outlier: 3.718A pdb=" N ARG A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 193 removed outlier: 3.718A pdb=" N ILE A 190 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 208 removed outlier: 3.904A pdb=" N VAL A 198 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP A 208 " --> pdb=" O LYS A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 242 removed outlier: 3.805A pdb=" N LEU A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 removed outlier: 5.028A pdb=" N GLY A 249 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 270 through 287 Processing helix chain 'A' and resid 298 through 329 Processing helix chain 'A' and resid 331 through 349 removed outlier: 3.904A pdb=" N ARG A 349 " --> pdb=" O ARG A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 379 removed outlier: 3.532A pdb=" N THR A 361 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY A 362 " --> pdb=" O GLY A 358 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR A 372 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 400 removed outlier: 3.726A pdb=" N LEU A 395 " --> pdb=" O GLN A 391 " (cutoff:3.500A) Proline residue: A 396 - end of helix removed outlier: 3.700A pdb=" N LYS A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 417 removed outlier: 3.892A pdb=" N ILE A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 478 removed outlier: 3.552A pdb=" N ILE A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 509 Processing helix chain 'A' and resid 509 through 524 removed outlier: 3.553A pdb=" N ARG A 514 " --> pdb=" O PHE A 510 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG A 515 " --> pdb=" O HIS A 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 107 removed outlier: 3.646A pdb=" N MET B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 90 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B 91 " --> pdb=" O MET B 87 " (cutoff:3.500A) Proline residue: B 101 - end of helix Processing helix chain 'B' and resid 111 through 135 removed outlier: 4.168A pdb=" N ILE B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU B 117 " --> pdb=" O ASN B 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE B 133 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 159 removed outlier: 3.648A pdb=" N ARG B 155 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR B 156 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 168 Processing helix chain 'B' and resid 170 through 179 removed outlier: 3.565A pdb=" N GLY B 179 " --> pdb=" O TYR B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 186 Processing helix chain 'B' and resid 187 through 192 Processing helix chain 'B' and resid 193 through 207 removed outlier: 3.953A pdb=" N ARG B 197 " --> pdb=" O TYR B 193 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 198 " --> pdb=" O ARG B 194 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS B 207 " --> pdb=" O HIS B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 242 removed outlier: 3.719A pdb=" N ALA B 240 " --> pdb=" O PHE B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 251 removed outlier: 5.018A pdb=" N GLY B 249 " --> pdb=" O SER B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 269 Processing helix chain 'B' and resid 270 through 287 removed outlier: 3.604A pdb=" N THR B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 330 Processing helix chain 'B' and resid 333 through 349 removed outlier: 3.598A pdb=" N LYS B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 349 " --> pdb=" O ARG B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 370 removed outlier: 3.543A pdb=" N GLN B 359 " --> pdb=" O ASN B 355 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'B' and resid 382 through 400 removed outlier: 3.966A pdb=" N LYS B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) Proline residue: B 396 - end of helix Processing helix chain 'B' and resid 401 through 405 Processing helix chain 'B' and resid 408 through 418 removed outlier: 3.586A pdb=" N ILE B 417 " --> pdb=" O ASN B 413 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG B 418 " --> pdb=" O GLN B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 479 Processing helix chain 'B' and resid 499 through 509 removed outlier: 3.645A pdb=" N ASN B 504 " --> pdb=" O GLN B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 524 Processing sheet with id=AA1, first strand: chain 'C' and resid 137 through 139 removed outlier: 3.802A pdb=" N TYR C 137 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE C 146 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP C 139 " --> pdb=" O ARG C 144 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ARG C 144 " --> pdb=" O ASP C 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 257 through 258 Processing sheet with id=AA3, first strand: chain 'C' and resid 420 through 424 removed outlier: 6.261A pdb=" N ARG C 493 " --> pdb=" O CYS C 444 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR C 441 " --> pdb=" O PHE C 471 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 463 through 465 removed outlier: 3.752A pdb=" N ALA C 463 " --> pdb=" O GLU C 450 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 138 through 139 removed outlier: 3.643A pdb=" N ASP D 139 " --> pdb=" O ARG D 144 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG D 144 " --> pdb=" O ASP D 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 257 through 258 Processing sheet with id=AA7, first strand: chain 'D' and resid 420 through 424 removed outlier: 3.564A pdb=" N PHE D 424 " --> pdb=" O CYS D 492 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N CYS D 492 " --> pdb=" O PHE D 424 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 463 through 465 removed outlier: 3.732A pdb=" N ALA D 463 " --> pdb=" O GLU D 450 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 137 through 139 removed outlier: 3.802A pdb=" N TYR A 137 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 146 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP A 139 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG A 144 " --> pdb=" O ASP A 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 257 through 258 Processing sheet with id=AB2, first strand: chain 'A' and resid 420 through 424 removed outlier: 6.262A pdb=" N ARG A 493 " --> pdb=" O CYS A 444 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR A 441 " --> pdb=" O PHE A 471 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 463 through 465 removed outlier: 3.751A pdb=" N ALA A 463 " --> pdb=" O GLU A 450 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.643A pdb=" N ASP B 139 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG B 144 " --> pdb=" O ASP B 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 257 through 258 Processing sheet with id=AB6, first strand: chain 'B' and resid 420 through 424 removed outlier: 3.563A pdb=" N PHE B 424 " --> pdb=" O CYS B 492 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N CYS B 492 " --> pdb=" O PHE B 424 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 463 through 465 removed outlier: 3.731A pdb=" N ALA B 463 " --> pdb=" O GLU B 450 " (cutoff:3.500A) 902 hydrogen bonds defined for protein. 2532 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: 2.35 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2233 1.31 - 1.44: 4380 1.44 - 1.56: 8498 1.56 - 1.69: 8 1.69 - 1.82: 156 Bond restraints: 15275 Sorted by residual: bond pdb=" C TYR B 372 " pdb=" O TYR B 372 " ideal model delta sigma weight residual 1.235 1.412 -0.176 1.26e-02 6.30e+03 1.96e+02 bond pdb=" C TYR D 372 " pdb=" O TYR D 372 " ideal model delta sigma weight residual 1.235 1.411 -0.176 1.26e-02 6.30e+03 1.95e+02 bond pdb=" C VAL B 377 " pdb=" O VAL B 377 " ideal model delta sigma weight residual 1.237 1.337 -0.100 1.14e-02 7.69e+03 7.75e+01 bond pdb=" C VAL D 377 " pdb=" O VAL D 377 " ideal model delta sigma weight residual 1.237 1.336 -0.099 1.14e-02 7.69e+03 7.61e+01 bond pdb=" N ILE B 381 " pdb=" CA ILE B 381 " ideal model delta sigma weight residual 1.461 1.561 -0.100 1.23e-02 6.61e+03 6.61e+01 ... (remaining 15270 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.86: 20413 3.86 - 7.72: 134 7.72 - 11.58: 18 11.58 - 15.45: 2 15.45 - 19.31: 8 Bond angle restraints: 20575 Sorted by residual: angle pdb=" N ASP D 380 " pdb=" CA ASP D 380 " pdb=" C ASP D 380 " ideal model delta sigma weight residual 110.06 129.37 -19.31 1.43e+00 4.89e-01 1.82e+02 angle pdb=" O SER D 371 " pdb=" C SER D 371 " pdb=" N TYR D 372 " ideal model delta sigma weight residual 122.59 104.70 17.89 1.33e+00 5.65e-01 1.81e+02 angle pdb=" N ASP B 380 " pdb=" CA ASP B 380 " pdb=" C ASP B 380 " ideal model delta sigma weight residual 110.06 129.27 -19.21 1.43e+00 4.89e-01 1.80e+02 angle pdb=" O SER B 371 " pdb=" C SER B 371 " pdb=" N TYR B 372 " ideal model delta sigma weight residual 122.59 104.85 17.74 1.33e+00 5.65e-01 1.78e+02 angle pdb=" N TYR B 372 " pdb=" CA TYR B 372 " pdb=" C TYR B 372 " ideal model delta sigma weight residual 110.80 129.69 -18.89 2.13e+00 2.20e-01 7.86e+01 ... (remaining 20570 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7631 17.98 - 35.97: 1014 35.97 - 53.95: 365 53.95 - 71.94: 55 71.94 - 89.92: 11 Dihedral angle restraints: 9076 sinusoidal: 3822 harmonic: 5254 Sorted by residual: dihedral pdb=" N ASP B 380 " pdb=" C ASP B 380 " pdb=" CA ASP B 380 " pdb=" CB ASP B 380 " ideal model delta harmonic sigma weight residual 122.80 137.50 -14.70 0 2.50e+00 1.60e-01 3.46e+01 dihedral pdb=" N ASP D 380 " pdb=" C ASP D 380 " pdb=" CA ASP D 380 " pdb=" CB ASP D 380 " ideal model delta harmonic sigma weight residual 122.80 137.47 -14.67 0 2.50e+00 1.60e-01 3.44e+01 dihedral pdb=" C ASP B 380 " pdb=" N ASP B 380 " pdb=" CA ASP B 380 " pdb=" CB ASP B 380 " ideal model delta harmonic sigma weight residual -122.60 -136.14 13.54 0 2.50e+00 1.60e-01 2.93e+01 ... (remaining 9073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 2221 0.145 - 0.290: 33 0.290 - 0.434: 8 0.434 - 0.579: 2 0.579 - 0.724: 2 Chirality restraints: 2266 Sorted by residual: chirality pdb=" CA ASP D 380 " pdb=" N ASP D 380 " pdb=" C ASP D 380 " pdb=" CB ASP D 380 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA ASP B 380 " pdb=" N ASP B 380 " pdb=" C ASP B 380 " pdb=" CB ASP B 380 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" C2 PC1 C 901 " pdb=" C1 PC1 C 901 " pdb=" C3 PC1 C 901 " pdb=" O21 PC1 C 901 " both_signs ideal model delta sigma weight residual False -2.49 -1.91 -0.58 2.00e-01 2.50e+01 8.35e+00 ... (remaining 2263 not shown) Planarity restraints: 2523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 371 " -0.072 2.00e-02 2.50e+03 1.27e-01 1.60e+02 pdb=" C SER D 371 " 0.219 2.00e-02 2.50e+03 pdb=" O SER D 371 " -0.079 2.00e-02 2.50e+03 pdb=" N TYR D 372 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 371 " 0.072 2.00e-02 2.50e+03 1.26e-01 1.60e+02 pdb=" C SER B 371 " -0.219 2.00e-02 2.50e+03 pdb=" O SER B 371 " 0.079 2.00e-02 2.50e+03 pdb=" N TYR B 372 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 372 " -0.030 2.00e-02 2.50e+03 5.48e-02 3.00e+01 pdb=" C TYR B 372 " 0.095 2.00e-02 2.50e+03 pdb=" O TYR B 372 " -0.035 2.00e-02 2.50e+03 pdb=" N THR B 373 " -0.030 2.00e-02 2.50e+03 ... (remaining 2520 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 22 2.30 - 2.95: 6584 2.95 - 3.60: 22192 3.60 - 4.25: 34761 4.25 - 4.90: 58082 Nonbonded interactions: 121641 Sorted by model distance: nonbonded pdb=" CE2 TYR C 346 " pdb=" CB ALA B 376 " model vdw 1.650 3.760 nonbonded pdb=" CB ALA D 376 " pdb=" CE2 TYR A 346 " model vdw 1.660 3.760 nonbonded pdb=" CD2 LEU C 364 " pdb=" OD2 ASP B 380 " model vdw 1.830 3.460 nonbonded pdb=" OD2 ASP D 380 " pdb=" CD2 LEU A 364 " model vdw 1.861 3.460 nonbonded pdb=" CD2 TYR C 346 " pdb=" CB ALA B 376 " model vdw 1.980 3.760 ... (remaining 121636 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 76 through 378 or (resid 379 and (name N or name CA or nam \ e C or name O or name CB )) or resid 380 through 524 or (resid 901 and (name C32 \ or name C33 or name C34 or name C35 or name C36 or name C37 or name C38)) or re \ sid 902 or (resid 903 and (name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38)))) selection = (chain 'B' and (resid 76 through 378 or (resid 379 and (name N or name CA or nam \ e C or name O or name CB )) or resid 380 through 524 or (resid 901 and (name C32 \ or name C33 or name C34 or name C35 or name C36 or name C37 or name C38)) or re \ sid 902 or (resid 903 and (name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38)))) selection = (chain 'C' and (resid 76 through 378 or (resid 379 and (name N or name CA or nam \ e C or name O or name CB )) or resid 380 through 524 or (resid 901 and (name C32 \ or name C33 or name C34 or name C35 or name C36 or name C37 or name C38)) or re \ sid 902 or (resid 903 and (name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38)))) selection = (chain 'D' and (resid 76 through 524 or (resid 901 and (name C32 or name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38)) or resid 902 or (resi \ d 903 and (name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38)))) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.050 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 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 : 0.006 0.215 15276 Z= 0.439 Angle : 0.849 19.307 20575 Z= 0.523 Chirality : 0.058 0.724 2266 Planarity : 0.006 0.127 2523 Dihedral : 18.201 89.923 5704 Min Nonbonded Distance : 1.650 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.57 % Allowed : 1.48 % Favored : 97.96 % Rotamer: Outliers : 2.15 % Allowed : 19.99 % Favored : 77.86 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.20), residues: 1762 helix: 0.07 (0.15), residues: 1080 sheet: 0.69 (0.43), residues: 128 loop : 0.34 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 496 TYR 0.013 0.001 TYR A 368 PHE 0.015 0.001 PHE A 115 TRP 0.013 0.001 TRP D 171 HIS 0.009 0.001 HIS A 445 Details of bonding type rmsd covalent geometry : bond 0.00570 (15275) covalent geometry : angle 0.84923 (20575) hydrogen bonds : bond 0.25502 ( 902) hydrogen bonds : angle 8.22613 ( 2532) Misc. bond : bond 0.21459 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 80 ARG cc_start: 0.7162 (ppt170) cc_final: 0.6236 (ptt180) REVERT: C 87 MET cc_start: 0.7855 (mmt) cc_final: 0.7648 (mmt) REVERT: C 183 GLU cc_start: 0.7494 (mp0) cc_final: 0.7054 (pm20) REVERT: C 216 THR cc_start: 0.8431 (t) cc_final: 0.8231 (m) REVERT: C 222 ILE cc_start: 0.8240 (tp) cc_final: 0.7976 (tp) REVERT: C 344 MET cc_start: 0.7239 (mtt) cc_final: 0.6942 (mtt) REVERT: D 87 MET cc_start: 0.8215 (tpp) cc_final: 0.7952 (tpp) REVERT: D 469 HIS cc_start: 0.7636 (m90) cc_final: 0.7373 (m90) REVERT: A 183 GLU cc_start: 0.7390 (mp0) cc_final: 0.6745 (pm20) REVERT: B 171 TRP cc_start: 0.8330 (m100) cc_final: 0.8068 (m100) REVERT: B 269 ILE cc_start: 0.8419 (mt) cc_final: 0.7796 (mm) REVERT: B 379 GLN cc_start: 0.5072 (OUTLIER) cc_final: 0.4828 (mt0) REVERT: B 422 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6792 (mm-30) REVERT: B 423 PHE cc_start: 0.7019 (m-80) cc_final: 0.6791 (m-80) outliers start: 34 outliers final: 9 residues processed: 240 average time/residue: 0.0993 time to fit residues: 35.5518 Evaluate side-chains 191 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 181 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 379 GLN Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 379 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 HIS C 482 GLN ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 GLN ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.240256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.141497 restraints weight = 15197.837| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.16 r_work: 0.3386 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15276 Z= 0.140 Angle : 0.605 16.609 20575 Z= 0.313 Chirality : 0.043 0.164 2266 Planarity : 0.005 0.056 2523 Dihedral : 9.630 85.020 2215 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.38 % Favored : 97.50 % Rotamer: Outliers : 2.59 % Allowed : 19.48 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.20), residues: 1762 helix: 0.72 (0.15), residues: 1126 sheet: -0.01 (0.43), residues: 136 loop : 0.74 (0.31), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 349 TYR 0.017 0.002 TYR D 82 PHE 0.017 0.001 PHE D 236 TRP 0.009 0.001 TRP C 81 HIS 0.006 0.001 HIS C 445 Details of bonding type rmsd covalent geometry : bond 0.00294 (15275) covalent geometry : angle 0.60504 (20575) hydrogen bonds : bond 0.04926 ( 902) hydrogen bonds : angle 5.17839 ( 2532) Misc. bond : bond 0.00037 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 183 GLU cc_start: 0.7861 (mp0) cc_final: 0.7002 (pm20) REVERT: C 216 THR cc_start: 0.8156 (t) cc_final: 0.7940 (m) REVERT: C 344 MET cc_start: 0.7200 (mtt) cc_final: 0.6925 (mtt) REVERT: C 386 ARG cc_start: 0.6804 (mtm-85) cc_final: 0.6603 (mtm-85) REVERT: C 485 THR cc_start: 0.1622 (OUTLIER) cc_final: 0.1248 (m) REVERT: D 80 ARG cc_start: 0.6604 (mtp-110) cc_final: 0.6242 (mmp80) REVERT: D 97 SER cc_start: 0.8609 (m) cc_final: 0.8363 (p) REVERT: D 171 TRP cc_start: 0.7712 (m100) cc_final: 0.7446 (m100) REVERT: D 309 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.6984 (mt) REVERT: D 329 LYS cc_start: 0.7241 (ttmm) cc_final: 0.6606 (tttp) REVERT: D 339 LYS cc_start: 0.6748 (mttt) cc_final: 0.6343 (mtmt) REVERT: D 420 HIS cc_start: 0.6299 (t-170) cc_final: 0.5997 (t-170) REVERT: D 469 HIS cc_start: 0.7523 (m90) cc_final: 0.7063 (m90) REVERT: D 503 MET cc_start: 0.6158 (mmm) cc_final: 0.5910 (mmm) REVERT: A 183 GLU cc_start: 0.7628 (mp0) cc_final: 0.6663 (pm20) REVERT: A 337 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7598 (ttp-170) REVERT: A 363 HIS cc_start: 0.7324 (OUTLIER) cc_final: 0.6912 (m90) REVERT: A 476 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7559 (mt) REVERT: B 269 ILE cc_start: 0.8298 (mt) cc_final: 0.8059 (mt) REVERT: B 309 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7081 (mt) REVERT: B 349 ARG cc_start: 0.7190 (mtp180) cc_final: 0.6714 (ptm160) outliers start: 41 outliers final: 13 residues processed: 220 average time/residue: 0.0983 time to fit residues: 31.7469 Evaluate side-chains 192 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 337 ARG Chi-restraints excluded: chain C residue 379 GLN Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 372 TYR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 485 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 104 optimal weight: 0.0980 chunk 111 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 156 optimal weight: 0.5980 chunk 108 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 391 GLN C 445 HIS ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 GLN D 482 GLN A 500 GLN B 482 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.238765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.140562 restraints weight = 15397.430| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.13 r_work: 0.3404 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15276 Z= 0.130 Angle : 0.557 16.848 20575 Z= 0.283 Chirality : 0.041 0.146 2266 Planarity : 0.004 0.056 2523 Dihedral : 7.972 59.792 2202 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.99 % Favored : 97.90 % Rotamer: Outliers : 3.10 % Allowed : 19.10 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.20), residues: 1762 helix: 1.03 (0.15), residues: 1142 sheet: -0.04 (0.43), residues: 136 loop : 0.74 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 365 TYR 0.016 0.001 TYR D 193 PHE 0.013 0.001 PHE D 236 TRP 0.012 0.001 TRP B 171 HIS 0.005 0.001 HIS C 445 Details of bonding type rmsd covalent geometry : bond 0.00281 (15275) covalent geometry : angle 0.55733 (20575) hydrogen bonds : bond 0.04255 ( 902) hydrogen bonds : angle 4.79229 ( 2532) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 171 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 183 GLU cc_start: 0.7984 (mp0) cc_final: 0.7070 (pm20) REVERT: C 222 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7419 (tp) REVERT: C 337 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.7243 (ttp-170) REVERT: C 344 MET cc_start: 0.7240 (mtt) cc_final: 0.6846 (mtt) REVERT: D 309 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7232 (mm) REVERT: D 329 LYS cc_start: 0.7382 (ttmm) cc_final: 0.6645 (tttp) REVERT: D 343 ILE cc_start: 0.7147 (OUTLIER) cc_final: 0.6853 (mp) REVERT: D 420 HIS cc_start: 0.6312 (t-170) cc_final: 0.5979 (t-170) REVERT: A 169 MET cc_start: 0.8218 (tpp) cc_final: 0.7994 (mmm) REVERT: A 363 HIS cc_start: 0.7257 (OUTLIER) cc_final: 0.6900 (m-70) REVERT: A 410 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7680 (mp0) REVERT: A 476 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7557 (mt) REVERT: B 309 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7322 (mt) outliers start: 49 outliers final: 15 residues processed: 207 average time/residue: 0.0966 time to fit residues: 30.2006 Evaluate side-chains 183 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 337 ARG Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 372 TYR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 309 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 38 optimal weight: 0.0270 chunk 21 optimal weight: 1.9990 chunk 171 optimal weight: 9.9990 chunk 55 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 123 optimal weight: 0.0770 chunk 120 optimal weight: 0.0060 chunk 36 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 165 optimal weight: 9.9990 overall best weight: 0.3212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 HIS ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 GLN B 482 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.241295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.144198 restraints weight = 15213.368| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.10 r_work: 0.3439 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15276 Z= 0.110 Angle : 0.532 16.399 20575 Z= 0.269 Chirality : 0.041 0.158 2266 Planarity : 0.004 0.057 2523 Dihedral : 7.415 59.836 2197 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.10 % Favored : 97.79 % Rotamer: Outliers : 2.97 % Allowed : 19.29 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.20), residues: 1762 helix: 1.24 (0.15), residues: 1150 sheet: -0.10 (0.42), residues: 136 loop : 0.79 (0.32), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 365 TYR 0.014 0.001 TYR C 213 PHE 0.020 0.001 PHE C 88 TRP 0.010 0.001 TRP C 85 HIS 0.005 0.001 HIS C 445 Details of bonding type rmsd covalent geometry : bond 0.00231 (15275) covalent geometry : angle 0.53166 (20575) hydrogen bonds : bond 0.03775 ( 902) hydrogen bonds : angle 4.51351 ( 2532) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 183 GLU cc_start: 0.7959 (mp0) cc_final: 0.7070 (pm20) REVERT: C 344 MET cc_start: 0.7080 (mtt) cc_final: 0.6787 (mtt) REVERT: D 139 ASP cc_start: 0.6383 (t0) cc_final: 0.6010 (t70) REVERT: D 309 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7166 (mt) REVERT: D 343 ILE cc_start: 0.7261 (OUTLIER) cc_final: 0.6901 (mp) REVERT: D 420 HIS cc_start: 0.6284 (t-170) cc_final: 0.6062 (t-170) REVERT: A 363 HIS cc_start: 0.7190 (OUTLIER) cc_final: 0.6862 (m90) REVERT: A 499 LYS cc_start: 0.7803 (mmtt) cc_final: 0.7560 (mtpt) REVERT: B 309 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7314 (mt) REVERT: B 345 ARG cc_start: 0.8400 (mtm-85) cc_final: 0.8188 (ttm170) REVERT: B 349 ARG cc_start: 0.7180 (mtp180) cc_final: 0.6649 (ptm160) outliers start: 47 outliers final: 19 residues processed: 204 average time/residue: 0.0885 time to fit residues: 28.5190 Evaluate side-chains 182 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 372 TYR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 443 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 146 optimal weight: 1.9990 chunk 170 optimal weight: 30.0000 chunk 163 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 39 optimal weight: 30.0000 chunk 89 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 52 optimal weight: 0.1980 chunk 72 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 HIS ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.236376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.136275 restraints weight = 15276.836| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.09 r_work: 0.3348 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15276 Z= 0.158 Angle : 0.568 16.846 20575 Z= 0.287 Chirality : 0.042 0.141 2266 Planarity : 0.004 0.059 2523 Dihedral : 7.727 59.368 2197 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.10 % Favored : 97.79 % Rotamer: Outliers : 2.59 % Allowed : 20.24 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.20), residues: 1762 helix: 1.17 (0.15), residues: 1136 sheet: 0.49 (0.44), residues: 116 loop : 0.66 (0.31), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 365 TYR 0.014 0.001 TYR A 275 PHE 0.028 0.001 PHE C 336 TRP 0.008 0.001 TRP A 85 HIS 0.004 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00365 (15275) covalent geometry : angle 0.56824 (20575) hydrogen bonds : bond 0.04104 ( 902) hydrogen bonds : angle 4.59950 ( 2532) Misc. bond : bond 0.00027 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 133 PHE cc_start: 0.7628 (OUTLIER) cc_final: 0.7347 (m-10) REVERT: C 183 GLU cc_start: 0.8035 (mp0) cc_final: 0.7092 (pm20) REVERT: C 344 MET cc_start: 0.7291 (mtt) cc_final: 0.7057 (mtt) REVERT: D 139 ASP cc_start: 0.6308 (t0) cc_final: 0.5958 (t70) REVERT: D 309 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7394 (mt) REVERT: D 343 ILE cc_start: 0.7205 (OUTLIER) cc_final: 0.6919 (mp) REVERT: D 347 MET cc_start: 0.8635 (mtm) cc_final: 0.8391 (mtm) REVERT: D 420 HIS cc_start: 0.6386 (t-170) cc_final: 0.6125 (t-170) REVERT: A 112 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7736 (mm-30) REVERT: A 363 HIS cc_start: 0.7342 (OUTLIER) cc_final: 0.7006 (m90) REVERT: A 499 LYS cc_start: 0.7763 (mmtt) cc_final: 0.7438 (mttp) REVERT: B 309 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7449 (mt) REVERT: B 349 ARG cc_start: 0.7482 (mtp180) cc_final: 0.6495 (ptt180) REVERT: B 503 MET cc_start: 0.5884 (mmm) cc_final: 0.5447 (mpp) outliers start: 41 outliers final: 27 residues processed: 205 average time/residue: 0.0888 time to fit residues: 28.4713 Evaluate side-chains 195 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 416 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 29 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 169 optimal weight: 20.0000 chunk 138 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 413 ASN C 445 HIS C 500 GLN D 367 GLN D 482 GLN B 482 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.234310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.132990 restraints weight = 15207.125| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.10 r_work: 0.3308 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15276 Z= 0.195 Angle : 0.608 17.768 20575 Z= 0.304 Chirality : 0.044 0.165 2266 Planarity : 0.005 0.060 2523 Dihedral : 7.989 59.461 2197 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.61 % Favored : 97.28 % Rotamer: Outliers : 2.91 % Allowed : 21.13 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.20), residues: 1762 helix: 1.06 (0.15), residues: 1132 sheet: 0.82 (0.47), residues: 104 loop : 0.64 (0.30), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 365 TYR 0.017 0.002 TYR C 275 PHE 0.025 0.002 PHE B 236 TRP 0.010 0.002 TRP A 272 HIS 0.004 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00465 (15275) covalent geometry : angle 0.60847 (20575) hydrogen bonds : bond 0.04297 ( 902) hydrogen bonds : angle 4.66473 ( 2532) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 173 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 133 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.7310 (m-10) REVERT: C 183 GLU cc_start: 0.8032 (mp0) cc_final: 0.7098 (pm20) REVERT: C 344 MET cc_start: 0.7485 (mtt) cc_final: 0.7238 (mtt) REVERT: D 139 ASP cc_start: 0.6397 (t0) cc_final: 0.5688 (p0) REVERT: D 309 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7440 (mt) REVERT: D 343 ILE cc_start: 0.7134 (OUTLIER) cc_final: 0.6890 (mp) REVERT: D 420 HIS cc_start: 0.6419 (t-170) cc_final: 0.6153 (t-170) REVERT: A 209 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7253 (mp) REVERT: B 139 ASP cc_start: 0.6214 (t70) cc_final: 0.5940 (t70) REVERT: B 309 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7307 (mt) REVERT: B 349 ARG cc_start: 0.7589 (mtp180) cc_final: 0.6519 (ptt180) REVERT: B 503 MET cc_start: 0.5844 (mmm) cc_final: 0.5379 (mpp) outliers start: 46 outliers final: 28 residues processed: 205 average time/residue: 0.0966 time to fit residues: 29.5853 Evaluate side-chains 196 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 499 LYS Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 443 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 149 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 20 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 169 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 391 GLN D 482 GLN A 363 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.236093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.136460 restraints weight = 15111.842| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.06 r_work: 0.3354 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15276 Z= 0.143 Angle : 0.581 17.587 20575 Z= 0.287 Chirality : 0.042 0.145 2266 Planarity : 0.004 0.059 2523 Dihedral : 7.623 59.825 2197 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.04 % Favored : 97.84 % Rotamer: Outliers : 2.40 % Allowed : 21.76 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.20), residues: 1762 helix: 1.24 (0.15), residues: 1132 sheet: 0.86 (0.47), residues: 104 loop : 0.66 (0.30), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 365 TYR 0.012 0.001 TYR A 275 PHE 0.021 0.001 PHE C 88 TRP 0.011 0.001 TRP B 171 HIS 0.004 0.001 HIS B 363 Details of bonding type rmsd covalent geometry : bond 0.00329 (15275) covalent geometry : angle 0.58109 (20575) hydrogen bonds : bond 0.03947 ( 902) hydrogen bonds : angle 4.51457 ( 2532) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: C 183 GLU cc_start: 0.7975 (mp0) cc_final: 0.6987 (pm20) REVERT: C 344 MET cc_start: 0.7436 (mtt) cc_final: 0.7166 (mtt) REVERT: D 139 ASP cc_start: 0.6418 (t0) cc_final: 0.5723 (p0) REVERT: D 309 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7440 (mt) REVERT: D 345 ARG cc_start: 0.8345 (mtm-85) cc_final: 0.6951 (tmm160) REVERT: D 349 ARG cc_start: 0.7027 (ptt180) cc_final: 0.6714 (ptt180) REVERT: D 420 HIS cc_start: 0.6293 (t-170) cc_final: 0.6029 (t-170) REVERT: D 482 GLN cc_start: 0.6023 (mm110) cc_final: 0.5718 (mm-40) REVERT: A 112 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.7902 (mm-30) REVERT: A 183 GLU cc_start: 0.7808 (mp0) cc_final: 0.6849 (pm20) REVERT: B 139 ASP cc_start: 0.6262 (t70) cc_final: 0.5975 (t70) REVERT: B 309 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7377 (mt) REVERT: B 349 ARG cc_start: 0.7634 (mtp180) cc_final: 0.6667 (ptt180) REVERT: B 503 MET cc_start: 0.5833 (mmm) cc_final: 0.5352 (mpp) outliers start: 38 outliers final: 23 residues processed: 195 average time/residue: 0.0917 time to fit residues: 27.5868 Evaluate side-chains 191 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 443 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 71 optimal weight: 0.0010 chunk 15 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 482 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.236821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.137553 restraints weight = 15133.933| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.05 r_work: 0.3366 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15276 Z= 0.134 Angle : 0.571 17.286 20575 Z= 0.282 Chirality : 0.041 0.145 2266 Planarity : 0.004 0.060 2523 Dihedral : 7.439 59.942 2197 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.44 % Favored : 97.45 % Rotamer: Outliers : 2.34 % Allowed : 21.95 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.20), residues: 1762 helix: 1.33 (0.15), residues: 1128 sheet: 0.91 (0.48), residues: 104 loop : 0.79 (0.31), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 365 TYR 0.011 0.001 TYR A 275 PHE 0.020 0.001 PHE C 88 TRP 0.015 0.001 TRP B 171 HIS 0.004 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00304 (15275) covalent geometry : angle 0.57058 (20575) hydrogen bonds : bond 0.03854 ( 902) hydrogen bonds : angle 4.43187 ( 2532) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 178 time to evaluate : 0.333 Fit side-chains REVERT: C 183 GLU cc_start: 0.7907 (mp0) cc_final: 0.6963 (pm20) REVERT: C 209 ILE cc_start: 0.7456 (OUTLIER) cc_final: 0.7120 (mp) REVERT: C 344 MET cc_start: 0.7426 (mtt) cc_final: 0.7136 (mtt) REVERT: C 499 LYS cc_start: 0.7771 (mmmt) cc_final: 0.7449 (mmtp) REVERT: D 139 ASP cc_start: 0.6369 (t0) cc_final: 0.5743 (p0) REVERT: D 309 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7328 (mt) REVERT: D 340 MET cc_start: 0.7467 (tpt) cc_final: 0.7069 (tpt) REVERT: D 345 ARG cc_start: 0.8277 (mtm-85) cc_final: 0.6830 (tmm160) REVERT: D 349 ARG cc_start: 0.7041 (ptt180) cc_final: 0.6720 (ptt180) REVERT: D 420 HIS cc_start: 0.6228 (t-170) cc_final: 0.5963 (t-170) REVERT: D 503 MET cc_start: 0.5813 (mmm) cc_final: 0.5347 (mpp) REVERT: A 112 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.7915 (mm-30) REVERT: A 183 GLU cc_start: 0.7754 (mp0) cc_final: 0.6797 (pm20) REVERT: B 139 ASP cc_start: 0.6321 (t70) cc_final: 0.6043 (t70) REVERT: B 309 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7269 (mt) REVERT: B 349 ARG cc_start: 0.7683 (mtp180) cc_final: 0.6702 (ptt180) REVERT: B 421 GLU cc_start: 0.7687 (pt0) cc_final: 0.7477 (pt0) REVERT: B 503 MET cc_start: 0.5855 (mmm) cc_final: 0.5369 (mpp) outliers start: 37 outliers final: 22 residues processed: 203 average time/residue: 0.0924 time to fit residues: 28.4945 Evaluate side-chains 195 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 443 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.2980 chunk 152 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 173 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 chunk 146 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 482 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.237167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.137318 restraints weight = 15189.517| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.11 r_work: 0.3341 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15276 Z= 0.133 Angle : 0.582 17.222 20575 Z= 0.286 Chirality : 0.042 0.139 2266 Planarity : 0.004 0.059 2523 Dihedral : 7.334 59.703 2197 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.33 % Favored : 97.56 % Rotamer: Outliers : 2.02 % Allowed : 22.07 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.20), residues: 1762 helix: 1.36 (0.15), residues: 1128 sheet: 0.90 (0.48), residues: 104 loop : 0.82 (0.31), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 365 TYR 0.011 0.001 TYR A 275 PHE 0.020 0.001 PHE C 88 TRP 0.017 0.001 TRP B 171 HIS 0.004 0.001 HIS B 363 Details of bonding type rmsd covalent geometry : bond 0.00305 (15275) covalent geometry : angle 0.58221 (20575) hydrogen bonds : bond 0.03839 ( 902) hydrogen bonds : angle 4.41600 ( 2532) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: C 183 GLU cc_start: 0.7921 (mp0) cc_final: 0.6985 (pm20) REVERT: C 209 ILE cc_start: 0.7518 (OUTLIER) cc_final: 0.7150 (mp) REVERT: C 344 MET cc_start: 0.7440 (mtt) cc_final: 0.7128 (mtt) REVERT: C 499 LYS cc_start: 0.7678 (mmmt) cc_final: 0.7392 (mmtp) REVERT: D 139 ASP cc_start: 0.6390 (t0) cc_final: 0.5780 (p0) REVERT: D 309 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7368 (mt) REVERT: D 343 ILE cc_start: 0.6829 (OUTLIER) cc_final: 0.6599 (mp) REVERT: D 345 ARG cc_start: 0.8303 (mtm-85) cc_final: 0.6971 (tmm160) REVERT: D 420 HIS cc_start: 0.6420 (t-170) cc_final: 0.6136 (t-170) REVERT: D 482 GLN cc_start: 0.5899 (mm110) cc_final: 0.5667 (mm-40) REVERT: A 112 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.7919 (mm-30) REVERT: B 139 ASP cc_start: 0.6367 (t70) cc_final: 0.6084 (t70) REVERT: B 309 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7394 (mm) REVERT: B 349 ARG cc_start: 0.7724 (mtp180) cc_final: 0.6838 (ptt180) REVERT: B 421 GLU cc_start: 0.7811 (pt0) cc_final: 0.7585 (pt0) REVERT: B 503 MET cc_start: 0.5867 (mmm) cc_final: 0.5373 (mpp) outliers start: 32 outliers final: 22 residues processed: 196 average time/residue: 0.0851 time to fit residues: 25.4340 Evaluate side-chains 198 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 443 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 110 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 82 optimal weight: 8.9990 chunk 166 optimal weight: 7.9990 chunk 126 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 145 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.237368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.138464 restraints weight = 15080.452| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.05 r_work: 0.3375 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15276 Z= 0.128 Angle : 0.587 17.061 20575 Z= 0.288 Chirality : 0.042 0.172 2266 Planarity : 0.004 0.060 2523 Dihedral : 7.223 59.726 2197 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.50 % Favored : 97.39 % Rotamer: Outliers : 1.90 % Allowed : 21.95 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.20), residues: 1762 helix: 1.40 (0.15), residues: 1128 sheet: 0.87 (0.47), residues: 104 loop : 0.81 (0.31), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 365 TYR 0.011 0.001 TYR A 275 PHE 0.020 0.001 PHE C 88 TRP 0.018 0.001 TRP B 171 HIS 0.004 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00290 (15275) covalent geometry : angle 0.58657 (20575) hydrogen bonds : bond 0.03803 ( 902) hydrogen bonds : angle 4.38557 ( 2532) Misc. bond : bond 0.00018 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: C 183 GLU cc_start: 0.7892 (mp0) cc_final: 0.6962 (pm20) REVERT: C 209 ILE cc_start: 0.7542 (OUTLIER) cc_final: 0.7178 (mp) REVERT: C 344 MET cc_start: 0.7454 (mtt) cc_final: 0.7141 (mtt) REVERT: C 499 LYS cc_start: 0.7631 (mmmt) cc_final: 0.7339 (mmtp) REVERT: D 139 ASP cc_start: 0.6375 (t0) cc_final: 0.5821 (p0) REVERT: D 169 MET cc_start: 0.6283 (tpt) cc_final: 0.6054 (tpt) REVERT: D 309 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7380 (mt) REVERT: D 345 ARG cc_start: 0.8328 (mtm-85) cc_final: 0.6949 (tmm160) REVERT: D 420 HIS cc_start: 0.6449 (t-170) cc_final: 0.6155 (t-170) REVERT: D 482 GLN cc_start: 0.5916 (mm110) cc_final: 0.5607 (mm-40) REVERT: A 112 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.7972 (mm-30) REVERT: B 139 ASP cc_start: 0.6432 (t70) cc_final: 0.6145 (t70) REVERT: B 309 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7322 (mt) REVERT: B 349 ARG cc_start: 0.7654 (mtp180) cc_final: 0.6796 (ptt180) REVERT: B 421 GLU cc_start: 0.7790 (pt0) cc_final: 0.7561 (pt0) REVERT: B 503 MET cc_start: 0.5868 (mmm) cc_final: 0.5366 (mpp) outliers start: 30 outliers final: 21 residues processed: 193 average time/residue: 0.0864 time to fit residues: 25.6607 Evaluate side-chains 189 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 443 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 109 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 107 optimal weight: 0.3980 chunk 157 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 379 GLN B 348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.237397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.138611 restraints weight = 15117.089| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.05 r_work: 0.3401 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15276 Z= 0.129 Angle : 0.583 16.965 20575 Z= 0.285 Chirality : 0.041 0.161 2266 Planarity : 0.004 0.059 2523 Dihedral : 7.172 59.758 2197 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.50 % Favored : 97.45 % Rotamer: Outliers : 1.83 % Allowed : 22.33 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.20), residues: 1762 helix: 1.41 (0.15), residues: 1132 sheet: 0.91 (0.47), residues: 104 loop : 0.82 (0.31), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 365 TYR 0.011 0.001 TYR A 275 PHE 0.020 0.001 PHE C 88 TRP 0.018 0.001 TRP B 171 HIS 0.004 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00292 (15275) covalent geometry : angle 0.58254 (20575) hydrogen bonds : bond 0.03783 ( 902) hydrogen bonds : angle 4.35988 ( 2532) Misc. bond : bond 0.00017 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4350.70 seconds wall clock time: 74 minutes 52.18 seconds (4492.18 seconds total)