Starting phenix.real_space_refine on Tue Jun 17 06:50:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zxd_60540/06_2025/8zxd_60540.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zxd_60540/06_2025/8zxd_60540.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zxd_60540/06_2025/8zxd_60540.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zxd_60540/06_2025/8zxd_60540.map" model { file = "/net/cci-nas-00/data/ceres_data/8zxd_60540/06_2025/8zxd_60540.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zxd_60540/06_2025/8zxd_60540.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.035 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 6 5.49 5 S 84 5.16 5 C 12804 2.51 5 N 3288 2.21 5 O 3336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19518 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3161 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 13, 'TRANS': 374} Chain breaks: 1 Chain: "B" Number of atoms: 3161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3161 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 13, 'TRANS': 374} Chain breaks: 1 Chain: "C" Number of atoms: 3161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3161 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 13, 'TRANS': 374} Chain breaks: 1 Chain: "D" Number of atoms: 3161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3161 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 13, 'TRANS': 374} Chain breaks: 1 Chain: "E" Number of atoms: 3161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3161 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 13, 'TRANS': 374} Chain breaks: 1 Chain: "F" Number of atoms: 3161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3161 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 13, 'TRANS': 374} Chain breaks: 1 Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 92 Unusual residues: {'MC3': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'MC3:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 92 Unusual residues: {'MC3': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'MC3:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 92 Unusual residues: {'MC3': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'MC3:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 92 Unusual residues: {'MC3': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'MC3:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 92 Unusual residues: {'MC3': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'MC3:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "F" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 92 Unusual residues: {'MC3': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'MC3:plan-2': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 11.57, per 1000 atoms: 0.59 Number of scatterers: 19518 At special positions: 0 Unit cell: (104.4, 99.6, 226.8, 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 84 16.00 P 6 15.00 O 3336 8.00 N 3288 7.00 C 12804 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=0, symmetry=0 Time building additional restraints: 4.30 Conformation dependent library (CDL) restraints added in 2.2 seconds 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4464 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 10 sheets defined 69.1% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 106 through 138 removed outlier: 3.600A pdb=" N VAL A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A 116 " --> pdb=" O GLY A 112 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Proline residue: A 127 - end of helix Proline residue: A 134 - end of helix Processing helix chain 'A' and resid 147 through 172 removed outlier: 3.641A pdb=" N ILE A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER A 155 " --> pdb=" O GLY A 151 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 208 removed outlier: 3.836A pdb=" N TYR A 200 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 208 " --> pdb=" O TYR A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 242 removed outlier: 4.274A pdb=" N GLN A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N TYR A 222 " --> pdb=" O GLY A 218 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 226 " --> pdb=" O TYR A 222 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE A 232 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 238 " --> pdb=" O HIS A 234 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 239 " --> pdb=" O TYR A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 287 removed outlier: 3.624A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 309 removed outlier: 4.062A pdb=" N LEU A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS A 304 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N HIS A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 Processing helix chain 'A' and resid 341 through 383 removed outlier: 3.988A pdb=" N TYR A 345 " --> pdb=" O ASN A 341 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 383 " --> pdb=" O GLU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 413 removed outlier: 4.102A pdb=" N ALA A 393 " --> pdb=" O ASP A 389 " (cutoff:3.500A) Proline residue: A 399 - end of helix removed outlier: 4.476A pdb=" N ARG A 403 " --> pdb=" O PRO A 399 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ALA A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 434 Processing helix chain 'A' and resid 436 through 446 removed outlier: 3.557A pdb=" N PHE A 440 " --> pdb=" O THR A 436 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 453 Processing helix chain 'A' and resid 454 through 458 Processing helix chain 'B' and resid 107 through 138 removed outlier: 3.599A pdb=" N VAL B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B 116 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) Proline residue: B 127 - end of helix Proline residue: B 134 - end of helix Processing helix chain 'B' and resid 147 through 172 removed outlier: 3.643A pdb=" N ILE B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 155 " --> pdb=" O GLY B 151 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 172 " --> pdb=" O TRP B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 208 removed outlier: 3.842A pdb=" N TYR B 200 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 208 " --> pdb=" O TYR B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 242 removed outlier: 4.273A pdb=" N GLN B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 226 " --> pdb=" O TYR B 222 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 232 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 238 " --> pdb=" O HIS B 234 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL B 239 " --> pdb=" O TYR B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 287 removed outlier: 3.622A pdb=" N TYR B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 309 removed outlier: 4.069A pdb=" N LEU B 295 " --> pdb=" O ASN B 291 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS B 304 " --> pdb=" O PHE B 300 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N HIS B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 338 Processing helix chain 'B' and resid 341 through 383 removed outlier: 3.975A pdb=" N TYR B 345 " --> pdb=" O ASN B 341 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 383 " --> pdb=" O GLU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 413 removed outlier: 4.103A pdb=" N ALA B 393 " --> pdb=" O ASP B 389 " (cutoff:3.500A) Proline residue: B 399 - end of helix removed outlier: 4.479A pdb=" N ARG B 403 " --> pdb=" O PRO B 399 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ALA B 404 " --> pdb=" O SER B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 434 Processing helix chain 'B' and resid 436 through 446 removed outlier: 3.551A pdb=" N PHE B 440 " --> pdb=" O THR B 436 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TYR B 444 " --> pdb=" O PHE B 440 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 453 Processing helix chain 'B' and resid 454 through 458 Processing helix chain 'C' and resid 107 through 138 removed outlier: 3.599A pdb=" N VAL C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA C 116 " --> pdb=" O GLY C 112 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 119 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY C 120 " --> pdb=" O ALA C 116 " (cutoff:3.500A) Proline residue: C 127 - end of helix Proline residue: C 134 - end of helix Processing helix chain 'C' and resid 147 through 172 removed outlier: 3.636A pdb=" N ILE C 154 " --> pdb=" O GLU C 150 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER C 155 " --> pdb=" O GLY C 151 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE C 172 " --> pdb=" O TRP C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 208 removed outlier: 3.844A pdb=" N TYR C 200 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 208 " --> pdb=" O TYR C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 242 removed outlier: 4.266A pdb=" N GLN C 221 " --> pdb=" O GLN C 217 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR C 222 " --> pdb=" O GLY C 218 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 226 " --> pdb=" O TYR C 222 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL C 227 " --> pdb=" O ALA C 223 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE C 232 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C 238 " --> pdb=" O HIS C 234 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL C 239 " --> pdb=" O TYR C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 287 removed outlier: 3.619A pdb=" N TYR C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS C 285 " --> pdb=" O GLU C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 309 removed outlier: 4.065A pdb=" N LEU C 295 " --> pdb=" O ASN C 291 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS C 304 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N HIS C 305 " --> pdb=" O ARG C 301 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET C 306 " --> pdb=" O ALA C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 338 Processing helix chain 'C' and resid 341 through 383 removed outlier: 3.986A pdb=" N TYR C 345 " --> pdb=" O ASN C 341 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN C 381 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 413 removed outlier: 4.102A pdb=" N ALA C 393 " --> pdb=" O ASP C 389 " (cutoff:3.500A) Proline residue: C 399 - end of helix removed outlier: 4.475A pdb=" N ARG C 403 " --> pdb=" O PRO C 399 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ALA C 404 " --> pdb=" O SER C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 434 Processing helix chain 'C' and resid 436 through 446 removed outlier: 3.558A pdb=" N PHE C 440 " --> pdb=" O THR C 436 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TYR C 444 " --> pdb=" O PHE C 440 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER C 446 " --> pdb=" O GLU C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 453 Processing helix chain 'C' and resid 454 through 458 Processing helix chain 'D' and resid 107 through 138 removed outlier: 3.607A pdb=" N VAL D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA D 116 " --> pdb=" O GLY D 112 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D 119 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY D 120 " --> pdb=" O ALA D 116 " (cutoff:3.500A) Proline residue: D 127 - end of helix Proline residue: D 134 - end of helix Processing helix chain 'D' and resid 147 through 172 removed outlier: 3.628A pdb=" N ILE D 154 " --> pdb=" O GLU D 150 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER D 155 " --> pdb=" O GLY D 151 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE D 172 " --> pdb=" O TRP D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 208 removed outlier: 3.844A pdb=" N TYR D 200 " --> pdb=" O PHE D 196 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE D 208 " --> pdb=" O TYR D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 242 removed outlier: 4.268A pdb=" N GLN D 221 " --> pdb=" O GLN D 217 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TYR D 222 " --> pdb=" O GLY D 218 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU D 226 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL D 227 " --> pdb=" O ALA D 223 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE D 232 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D 238 " --> pdb=" O HIS D 234 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL D 239 " --> pdb=" O TYR D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 287 removed outlier: 3.623A pdb=" N TYR D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS D 285 " --> pdb=" O GLU D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 309 removed outlier: 4.065A pdb=" N LEU D 295 " --> pdb=" O ASN D 291 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS D 304 " --> pdb=" O PHE D 300 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N HIS D 305 " --> pdb=" O ARG D 301 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 338 Processing helix chain 'D' and resid 341 through 383 removed outlier: 3.987A pdb=" N TYR D 345 " --> pdb=" O ASN D 341 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN D 381 " --> pdb=" O ALA D 377 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 413 removed outlier: 4.079A pdb=" N ALA D 393 " --> pdb=" O ASP D 389 " (cutoff:3.500A) Proline residue: D 399 - end of helix removed outlier: 4.477A pdb=" N ARG D 403 " --> pdb=" O PRO D 399 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ALA D 404 " --> pdb=" O SER D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 434 Processing helix chain 'D' and resid 436 through 446 removed outlier: 3.553A pdb=" N PHE D 440 " --> pdb=" O THR D 436 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR D 444 " --> pdb=" O PHE D 440 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER D 446 " --> pdb=" O GLU D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 453 Processing helix chain 'D' and resid 454 through 458 Processing helix chain 'E' and resid 107 through 138 removed outlier: 3.598A pdb=" N VAL E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA E 116 " --> pdb=" O GLY E 112 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU E 119 " --> pdb=" O VAL E 115 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY E 120 " --> pdb=" O ALA E 116 " (cutoff:3.500A) Proline residue: E 127 - end of helix Proline residue: E 134 - end of helix Processing helix chain 'E' and resid 147 through 172 removed outlier: 3.638A pdb=" N ILE E 154 " --> pdb=" O GLU E 150 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER E 155 " --> pdb=" O GLY E 151 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE E 172 " --> pdb=" O TRP E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 208 removed outlier: 3.843A pdb=" N TYR E 200 " --> pdb=" O PHE E 196 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE E 208 " --> pdb=" O TYR E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 242 removed outlier: 4.271A pdb=" N GLN E 221 " --> pdb=" O GLN E 217 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR E 222 " --> pdb=" O GLY E 218 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU E 226 " --> pdb=" O TYR E 222 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE E 232 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE E 238 " --> pdb=" O HIS E 234 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL E 239 " --> pdb=" O TYR E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 287 removed outlier: 3.625A pdb=" N TYR E 284 " --> pdb=" O LEU E 280 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 309 removed outlier: 4.066A pdb=" N LEU E 295 " --> pdb=" O ASN E 291 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS E 304 " --> pdb=" O PHE E 300 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N HIS E 305 " --> pdb=" O ARG E 301 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET E 306 " --> pdb=" O ALA E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 338 Processing helix chain 'E' and resid 341 through 383 removed outlier: 3.978A pdb=" N TYR E 345 " --> pdb=" O ASN E 341 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN E 381 " --> pdb=" O ALA E 377 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS E 382 " --> pdb=" O GLU E 378 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 413 removed outlier: 4.102A pdb=" N ALA E 393 " --> pdb=" O ASP E 389 " (cutoff:3.500A) Proline residue: E 399 - end of helix removed outlier: 4.477A pdb=" N ARG E 403 " --> pdb=" O PRO E 399 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ALA E 404 " --> pdb=" O SER E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 434 Processing helix chain 'E' and resid 436 through 446 removed outlier: 3.551A pdb=" N PHE E 440 " --> pdb=" O THR E 436 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TYR E 444 " --> pdb=" O PHE E 440 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER E 446 " --> pdb=" O GLU E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 453 Processing helix chain 'E' and resid 454 through 458 Processing helix chain 'F' and resid 107 through 138 removed outlier: 3.603A pdb=" N VAL F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA F 116 " --> pdb=" O GLY F 112 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU F 119 " --> pdb=" O VAL F 115 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY F 120 " --> pdb=" O ALA F 116 " (cutoff:3.500A) Proline residue: F 127 - end of helix Proline residue: F 134 - end of helix Processing helix chain 'F' and resid 147 through 172 removed outlier: 3.638A pdb=" N ILE F 154 " --> pdb=" O GLU F 150 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER F 155 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE F 172 " --> pdb=" O TRP F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 208 removed outlier: 3.849A pdb=" N TYR F 200 " --> pdb=" O PHE F 196 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE F 208 " --> pdb=" O TYR F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 242 removed outlier: 4.271A pdb=" N GLN F 221 " --> pdb=" O GLN F 217 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR F 222 " --> pdb=" O GLY F 218 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU F 226 " --> pdb=" O TYR F 222 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL F 227 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE F 232 " --> pdb=" O ASP F 228 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE F 238 " --> pdb=" O HIS F 234 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL F 239 " --> pdb=" O TYR F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 287 removed outlier: 3.618A pdb=" N TYR F 284 " --> pdb=" O LEU F 280 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS F 285 " --> pdb=" O GLU F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 309 removed outlier: 4.064A pdb=" N LEU F 295 " --> pdb=" O ASN F 291 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS F 304 " --> pdb=" O PHE F 300 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N HIS F 305 " --> pdb=" O ARG F 301 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET F 306 " --> pdb=" O ALA F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 338 Processing helix chain 'F' and resid 341 through 383 removed outlier: 3.986A pdb=" N TYR F 345 " --> pdb=" O ASN F 341 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS F 382 " --> pdb=" O GLU F 378 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 413 removed outlier: 4.103A pdb=" N ALA F 393 " --> pdb=" O ASP F 389 " (cutoff:3.500A) Proline residue: F 399 - end of helix removed outlier: 4.478A pdb=" N ARG F 403 " --> pdb=" O PRO F 399 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ALA F 404 " --> pdb=" O SER F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 434 Processing helix chain 'F' and resid 436 through 446 removed outlier: 3.556A pdb=" N PHE F 440 " --> pdb=" O THR F 436 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TYR F 444 " --> pdb=" O PHE F 440 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER F 446 " --> pdb=" O GLU F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 453 Processing helix chain 'F' and resid 454 through 458 Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 178 removed outlier: 3.642A pdb=" N LEU C 502 " --> pdb=" O ASP A 178 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TRP A 463 " --> pdb=" O ILE C 501 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 500 through 501 removed outlier: 6.825A pdb=" N ILE A 500 " --> pdb=" O ASP B 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 262 through 267 Processing sheet with id=AA4, first strand: chain 'B' and resid 500 through 501 removed outlier: 6.861A pdb=" N ILE B 500 " --> pdb=" O ASP C 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 262 through 267 Processing sheet with id=AA6, first strand: chain 'D' and resid 177 through 178 removed outlier: 3.653A pdb=" N LEU F 502 " --> pdb=" O ASP D 178 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TRP D 463 " --> pdb=" O ILE F 501 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 500 through 501 removed outlier: 6.844A pdb=" N ILE D 500 " --> pdb=" O ASP E 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 262 through 267 Processing sheet with id=AA9, first strand: chain 'E' and resid 500 through 501 removed outlier: 6.838A pdb=" N ILE E 500 " --> pdb=" O ASP F 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 262 through 267 1195 hydrogen bonds defined for protein. 3465 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: 5.68 Time building geometry restraints manager: 5.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3497 1.33 - 1.45: 4916 1.45 - 1.57: 11399 1.57 - 1.69: 12 1.69 - 1.81: 138 Bond restraints: 19962 Sorted by residual: bond pdb=" C PRO B 134 " pdb=" N PRO B 135 " ideal model delta sigma weight residual 1.335 1.344 -0.010 1.28e-02 6.10e+03 5.83e-01 bond pdb=" C PRO A 134 " pdb=" N PRO A 135 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.28e-02 6.10e+03 5.43e-01 bond pdb=" C PRO E 134 " pdb=" N PRO E 135 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.28e-02 6.10e+03 5.42e-01 bond pdb=" C PRO D 134 " pdb=" N PRO D 135 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.28e-02 6.10e+03 4.89e-01 bond pdb=" C PRO C 134 " pdb=" N PRO C 135 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.28e-02 6.10e+03 4.84e-01 ... (remaining 19957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 26642 1.24 - 2.48: 308 2.48 - 3.72: 63 3.72 - 4.97: 17 4.97 - 6.21: 18 Bond angle restraints: 27048 Sorted by residual: angle pdb=" C ASP F 487 " pdb=" N PHE F 488 " pdb=" CA PHE F 488 " ideal model delta sigma weight residual 121.85 118.45 3.40 1.77e+00 3.19e-01 3.68e+00 angle pdb=" C ASP C 487 " pdb=" N PHE C 488 " pdb=" CA PHE C 488 " ideal model delta sigma weight residual 121.85 118.47 3.38 1.77e+00 3.19e-01 3.65e+00 angle pdb=" C ASP B 487 " pdb=" N PHE B 488 " pdb=" CA PHE B 488 " ideal model delta sigma weight residual 121.85 118.49 3.36 1.77e+00 3.19e-01 3.60e+00 angle pdb=" C ASP E 487 " pdb=" N PHE E 488 " pdb=" CA PHE E 488 " ideal model delta sigma weight residual 121.85 118.51 3.34 1.77e+00 3.19e-01 3.55e+00 angle pdb=" C ASP A 487 " pdb=" N PHE A 488 " pdb=" CA PHE A 488 " ideal model delta sigma weight residual 121.85 118.52 3.33 1.77e+00 3.19e-01 3.53e+00 ... (remaining 27043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 11512 17.76 - 35.51: 892 35.51 - 53.27: 161 53.27 - 71.03: 11 71.03 - 88.79: 18 Dihedral angle restraints: 12594 sinusoidal: 5718 harmonic: 6876 Sorted by residual: dihedral pdb=" CB GLU F 421 " pdb=" CG GLU F 421 " pdb=" CD GLU F 421 " pdb=" OE1 GLU F 421 " ideal model delta sinusoidal sigma weight residual 0.00 88.79 -88.79 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU B 421 " pdb=" CG GLU B 421 " pdb=" CD GLU B 421 " pdb=" OE1 GLU B 421 " ideal model delta sinusoidal sigma weight residual 0.00 88.78 -88.78 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU E 421 " pdb=" CG GLU E 421 " pdb=" CD GLU E 421 " pdb=" OE1 GLU E 421 " ideal model delta sinusoidal sigma weight residual 0.00 88.77 -88.77 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 12591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2156 0.028 - 0.055: 579 0.055 - 0.083: 230 0.083 - 0.111: 97 0.111 - 0.139: 16 Chirality restraints: 3078 Sorted by residual: chirality pdb=" CA VAL C 480 " pdb=" N VAL C 480 " pdb=" C VAL C 480 " pdb=" CB VAL C 480 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA VAL B 480 " pdb=" N VAL B 480 " pdb=" C VAL B 480 " pdb=" CB VAL B 480 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA VAL D 480 " pdb=" N VAL D 480 " pdb=" C VAL D 480 " pdb=" CB VAL D 480 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 3075 not shown) Planarity restraints: 3318 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 133 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO B 134 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 134 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 134 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 133 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO E 134 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO E 134 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 134 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 133 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO D 134 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO D 134 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 134 " 0.019 5.00e-02 4.00e+02 ... (remaining 3315 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3969 2.78 - 3.31: 18779 3.31 - 3.84: 31125 3.84 - 4.37: 35504 4.37 - 4.90: 63047 Nonbonded interactions: 152424 Sorted by model distance: nonbonded pdb=" O TYR A 290 " pdb=" OH TYR A 417 " model vdw 2.255 3.040 nonbonded pdb=" O TYR E 290 " pdb=" OH TYR E 417 " model vdw 2.256 3.040 nonbonded pdb=" O TYR B 290 " pdb=" OH TYR B 417 " model vdw 2.257 3.040 nonbonded pdb=" O TYR F 290 " pdb=" OH TYR F 417 " model vdw 2.257 3.040 nonbonded pdb=" O TYR C 290 " pdb=" OH TYR C 417 " model vdw 2.258 3.040 ... (remaining 152419 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 106 through 505 or resid 701)) selection = (chain 'B' and (resid 106 through 505 or resid 701)) selection = (chain 'C' and (resid 106 through 505 or resid 601)) selection = (chain 'D' and (resid 106 through 505 or resid 701)) selection = (chain 'E' and (resid 106 through 505 or resid 701)) selection = (chain 'F' and (resid 106 through 505 or resid 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 41.400 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:13.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 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 : 0.002 0.020 19962 Z= 0.078 Angle : 0.407 6.207 27048 Z= 0.211 Chirality : 0.034 0.139 3078 Planarity : 0.003 0.035 3318 Dihedral : 12.722 88.786 8130 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.18), residues: 2304 helix: 2.76 (0.14), residues: 1416 sheet: 1.17 (0.40), residues: 192 loop : 0.09 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 168 HIS 0.001 0.000 HIS B 234 PHE 0.013 0.001 PHE A 481 TYR 0.014 0.001 TYR C 200 ARG 0.001 0.000 ARG F 391 Details of bonding type rmsd hydrogen bonds : bond 0.12688 ( 1195) hydrogen bonds : angle 4.96929 ( 3465) covalent geometry : bond 0.00153 (19962) covalent geometry : angle 0.40659 (27048) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 490 time to evaluate : 2.112 Fit side-chains revert: symmetry clash REVERT: A 150 GLU cc_start: 0.7407 (tp30) cc_final: 0.6974 (mp0) REVERT: A 153 PHE cc_start: 0.8109 (m-10) cc_final: 0.7507 (m-80) REVERT: A 249 MET cc_start: 0.8561 (tpp) cc_final: 0.8318 (tpt) REVERT: A 334 ARG cc_start: 0.7129 (mtt-85) cc_final: 0.6795 (ttm110) REVERT: A 435 MET cc_start: 0.8646 (mtp) cc_final: 0.8290 (mmm) REVERT: A 469 GLU cc_start: 0.7927 (tt0) cc_final: 0.7417 (tt0) REVERT: A 487 ASP cc_start: 0.8227 (t70) cc_final: 0.7907 (t70) REVERT: A 496 LYS cc_start: 0.7757 (tptm) cc_final: 0.7508 (tttt) REVERT: B 150 GLU cc_start: 0.7624 (tp30) cc_final: 0.7131 (mp0) REVERT: B 222 TYR cc_start: 0.8021 (t80) cc_final: 0.7762 (t80) REVERT: B 263 ARG cc_start: 0.7868 (mmt90) cc_final: 0.7613 (mmt-90) REVERT: B 334 ARG cc_start: 0.6862 (mtt-85) cc_final: 0.6455 (ttm110) REVERT: B 392 GLU cc_start: 0.7591 (pp20) cc_final: 0.7329 (pp20) REVERT: B 417 TYR cc_start: 0.7430 (m-10) cc_final: 0.7212 (m-10) REVERT: B 469 GLU cc_start: 0.7273 (tt0) cc_final: 0.6716 (tt0) REVERT: C 150 GLU cc_start: 0.7505 (tp30) cc_final: 0.7044 (mp0) REVERT: C 222 TYR cc_start: 0.7951 (t80) cc_final: 0.7433 (t80) REVERT: C 249 MET cc_start: 0.8645 (tpp) cc_final: 0.8156 (tpt) REVERT: C 258 THR cc_start: 0.8183 (p) cc_final: 0.7982 (p) REVERT: C 263 ARG cc_start: 0.7835 (mmt90) cc_final: 0.7497 (mmt-90) REVERT: C 417 TYR cc_start: 0.7301 (m-10) cc_final: 0.7094 (m-10) REVERT: C 421 GLU cc_start: 0.7936 (tp30) cc_final: 0.7710 (tp30) REVERT: C 456 ASP cc_start: 0.8527 (t0) cc_final: 0.8274 (p0) REVERT: C 496 LYS cc_start: 0.7488 (tptm) cc_final: 0.7128 (tttt) REVERT: D 150 GLU cc_start: 0.7399 (tp30) cc_final: 0.6968 (mp0) REVERT: D 153 PHE cc_start: 0.8069 (m-10) cc_final: 0.7612 (m-80) REVERT: D 249 MET cc_start: 0.8605 (tpp) cc_final: 0.8323 (tpt) REVERT: D 334 ARG cc_start: 0.7153 (mtt-85) cc_final: 0.6817 (ttm110) REVERT: D 376 GLN cc_start: 0.6919 (tt0) cc_final: 0.6675 (tt0) REVERT: D 469 GLU cc_start: 0.7942 (tt0) cc_final: 0.7439 (tt0) REVERT: D 487 ASP cc_start: 0.8176 (t70) cc_final: 0.7854 (t70) REVERT: D 496 LYS cc_start: 0.7723 (tptm) cc_final: 0.7484 (tttt) REVERT: E 150 GLU cc_start: 0.7326 (tp30) cc_final: 0.6856 (mp0) REVERT: E 153 PHE cc_start: 0.8314 (m-10) cc_final: 0.7870 (m-10) REVERT: E 222 TYR cc_start: 0.8135 (t80) cc_final: 0.7798 (t80) REVERT: E 249 MET cc_start: 0.8514 (tpp) cc_final: 0.8261 (tpt) REVERT: E 263 ARG cc_start: 0.7902 (mmt90) cc_final: 0.7647 (mmt-90) REVERT: E 392 GLU cc_start: 0.7591 (pp20) cc_final: 0.7275 (pp20) REVERT: E 421 GLU cc_start: 0.7784 (tp30) cc_final: 0.7363 (mm-30) REVERT: E 456 ASP cc_start: 0.8506 (t0) cc_final: 0.8303 (p0) REVERT: E 469 GLU cc_start: 0.7226 (tt0) cc_final: 0.6620 (tt0) REVERT: E 496 LYS cc_start: 0.7580 (tptm) cc_final: 0.7305 (tttt) REVERT: F 150 GLU cc_start: 0.7442 (tp30) cc_final: 0.6999 (mp0) REVERT: F 222 TYR cc_start: 0.7851 (t80) cc_final: 0.7413 (t80) REVERT: F 249 MET cc_start: 0.8659 (tpp) cc_final: 0.8163 (tpt) REVERT: F 258 THR cc_start: 0.8180 (p) cc_final: 0.7975 (p) REVERT: F 263 ARG cc_start: 0.7831 (mmt90) cc_final: 0.7503 (mmt-90) REVERT: F 421 GLU cc_start: 0.7957 (tp30) cc_final: 0.7728 (tp30) REVERT: F 456 ASP cc_start: 0.8542 (t0) cc_final: 0.8292 (p0) REVERT: F 496 LYS cc_start: 0.7493 (tptm) cc_final: 0.7068 (tttt) outliers start: 0 outliers final: 7 residues processed: 490 average time/residue: 1.1709 time to fit residues: 652.8807 Evaluate side-chains 329 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 322 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain F residue 294 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.1980 chunk 172 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 92 optimal weight: 0.0970 chunk 178 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 207 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN A 305 HIS ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN B 305 HIS C 293 ASN C 305 HIS C 418 HIS D 293 ASN D 305 HIS D 395 GLN E 293 ASN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 ASN F 305 HIS F 418 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.178113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.122966 restraints weight = 22227.505| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.71 r_work: 0.3431 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19962 Z= 0.125 Angle : 0.526 7.818 27048 Z= 0.266 Chirality : 0.038 0.132 3078 Planarity : 0.004 0.038 3318 Dihedral : 6.554 49.808 3566 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.47 % Allowed : 11.92 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.18), residues: 2304 helix: 2.77 (0.14), residues: 1452 sheet: 1.07 (0.41), residues: 192 loop : -0.22 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 458 HIS 0.008 0.001 HIS A 305 PHE 0.020 0.002 PHE E 194 TYR 0.013 0.002 TYR F 216 ARG 0.008 0.000 ARG B 360 Details of bonding type rmsd hydrogen bonds : bond 0.03280 ( 1195) hydrogen bonds : angle 3.69978 ( 3465) covalent geometry : bond 0.00286 (19962) covalent geometry : angle 0.52564 (27048) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 352 time to evaluate : 2.076 Fit side-chains REVERT: A 131 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8231 (tp) REVERT: A 150 GLU cc_start: 0.7189 (tp30) cc_final: 0.6927 (mp0) REVERT: A 174 LYS cc_start: 0.7813 (mtpt) cc_final: 0.6847 (mmtt) REVERT: A 417 TYR cc_start: 0.7705 (m-10) cc_final: 0.7322 (m-10) REVERT: A 435 MET cc_start: 0.8762 (mtp) cc_final: 0.8447 (mmm) REVERT: A 469 GLU cc_start: 0.7771 (tt0) cc_final: 0.7286 (tt0) REVERT: B 150 GLU cc_start: 0.7336 (tp30) cc_final: 0.6974 (mp0) REVERT: B 174 LYS cc_start: 0.7889 (mtpt) cc_final: 0.6936 (mmtt) REVERT: B 249 MET cc_start: 0.8230 (tpt) cc_final: 0.7851 (mmt) REVERT: B 263 ARG cc_start: 0.7987 (mmt90) cc_final: 0.7453 (mmt-90) REVERT: B 334 ARG cc_start: 0.6447 (mtt-85) cc_final: 0.6131 (mtm110) REVERT: B 417 TYR cc_start: 0.7549 (m-80) cc_final: 0.7281 (m-10) REVERT: B 487 ASP cc_start: 0.8364 (t70) cc_final: 0.8053 (t0) REVERT: C 174 LYS cc_start: 0.7834 (mtpt) cc_final: 0.7119 (mmpt) REVERT: C 249 MET cc_start: 0.8630 (tpp) cc_final: 0.8405 (tpt) REVERT: C 263 ARG cc_start: 0.7937 (mmt90) cc_final: 0.7286 (mmt-90) REVERT: C 417 TYR cc_start: 0.7477 (m-80) cc_final: 0.6908 (m-10) REVERT: C 456 ASP cc_start: 0.8680 (t0) cc_final: 0.8425 (p0) REVERT: C 487 ASP cc_start: 0.8209 (t70) cc_final: 0.7802 (t70) REVERT: C 496 LYS cc_start: 0.7699 (tptm) cc_final: 0.7365 (tttt) REVERT: D 150 GLU cc_start: 0.7227 (tp30) cc_final: 0.7002 (mp0) REVERT: D 153 PHE cc_start: 0.8034 (m-10) cc_final: 0.7619 (m-80) REVERT: D 174 LYS cc_start: 0.7715 (mtpt) cc_final: 0.6744 (mmtt) REVERT: D 334 ARG cc_start: 0.6953 (mtt-85) cc_final: 0.6649 (mtm110) REVERT: D 388 MET cc_start: 0.6514 (pmt) cc_final: 0.6215 (pmt) REVERT: D 417 TYR cc_start: 0.7600 (m-10) cc_final: 0.7290 (m-10) REVERT: D 420 MET cc_start: 0.6675 (ttt) cc_final: 0.5715 (tpp) REVERT: D 469 GLU cc_start: 0.7785 (tt0) cc_final: 0.7275 (tt0) REVERT: E 174 LYS cc_start: 0.7858 (mtpt) cc_final: 0.6964 (mmtt) REVERT: E 249 MET cc_start: 0.8613 (tpp) cc_final: 0.8071 (mmt) REVERT: E 263 ARG cc_start: 0.7993 (mmt90) cc_final: 0.7461 (mmt-90) REVERT: E 411 ILE cc_start: 0.8136 (tp) cc_final: 0.7901 (tp) REVERT: E 487 ASP cc_start: 0.8332 (t70) cc_final: 0.7993 (t0) REVERT: E 496 LYS cc_start: 0.7871 (tptm) cc_final: 0.7369 (tttt) REVERT: F 150 GLU cc_start: 0.7299 (tp30) cc_final: 0.7047 (mp0) REVERT: F 174 LYS cc_start: 0.7840 (mtpt) cc_final: 0.6919 (mmpt) REVERT: F 249 MET cc_start: 0.8629 (tpp) cc_final: 0.8377 (tpt) REVERT: F 263 ARG cc_start: 0.7914 (mmt90) cc_final: 0.7271 (mmt-90) REVERT: F 334 ARG cc_start: 0.6517 (tmt170) cc_final: 0.6301 (mtp180) REVERT: F 456 ASP cc_start: 0.8648 (t0) cc_final: 0.8434 (p0) REVERT: F 487 ASP cc_start: 0.8202 (t70) cc_final: 0.7804 (t70) REVERT: F 496 LYS cc_start: 0.7710 (tptm) cc_final: 0.7275 (tttt) outliers start: 50 outliers final: 21 residues processed: 369 average time/residue: 1.0755 time to fit residues: 456.5071 Evaluate side-chains 305 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 283 time to evaluate : 2.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 372 ILE Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 472 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 147 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 74 optimal weight: 0.0980 chunk 202 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 193 optimal weight: 0.0270 chunk 137 optimal weight: 0.5980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 HIS B 221 GLN B 305 HIS C 305 HIS C 418 HIS D 305 HIS F 221 GLN F 305 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.174094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.118489 restraints weight = 22068.947| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.65 r_work: 0.3378 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19962 Z= 0.115 Angle : 0.505 6.861 27048 Z= 0.255 Chirality : 0.037 0.130 3078 Planarity : 0.004 0.042 3318 Dihedral : 6.315 48.901 3552 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.18 % Allowed : 14.89 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.18), residues: 2304 helix: 2.79 (0.14), residues: 1428 sheet: 0.96 (0.41), residues: 192 loop : -0.15 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 458 HIS 0.008 0.001 HIS D 305 PHE 0.025 0.002 PHE A 194 TYR 0.016 0.001 TYR B 222 ARG 0.005 0.000 ARG B 360 Details of bonding type rmsd hydrogen bonds : bond 0.03090 ( 1195) hydrogen bonds : angle 3.54803 ( 3465) covalent geometry : bond 0.00262 (19962) covalent geometry : angle 0.50450 (27048) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 331 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8199 (tp) REVERT: A 150 GLU cc_start: 0.7433 (tp30) cc_final: 0.7042 (mp0) REVERT: A 174 LYS cc_start: 0.7939 (mtpt) cc_final: 0.6904 (mmtt) REVERT: A 401 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7679 (ptp) REVERT: A 417 TYR cc_start: 0.7651 (m-10) cc_final: 0.7140 (m-10) REVERT: A 420 MET cc_start: 0.6679 (OUTLIER) cc_final: 0.6173 (tpp) REVERT: A 469 GLU cc_start: 0.7665 (tt0) cc_final: 0.7171 (tt0) REVERT: A 487 ASP cc_start: 0.8279 (t70) cc_final: 0.7540 (t0) REVERT: B 131 ILE cc_start: 0.8308 (tp) cc_final: 0.8093 (tp) REVERT: B 138 TRP cc_start: 0.7995 (m-90) cc_final: 0.7544 (m-90) REVERT: B 150 GLU cc_start: 0.7382 (tp30) cc_final: 0.6989 (mp0) REVERT: B 174 LYS cc_start: 0.7888 (mtpt) cc_final: 0.6947 (mmtt) REVERT: B 221 GLN cc_start: 0.8069 (mt0) cc_final: 0.7778 (mt0) REVERT: B 249 MET cc_start: 0.8246 (tpt) cc_final: 0.7906 (mmt) REVERT: B 263 ARG cc_start: 0.8009 (mmt90) cc_final: 0.7487 (mmt-90) REVERT: B 334 ARG cc_start: 0.6511 (mtt-85) cc_final: 0.6169 (mtm110) REVERT: B 417 TYR cc_start: 0.7738 (m-80) cc_final: 0.7205 (m-80) REVERT: B 487 ASP cc_start: 0.8394 (t70) cc_final: 0.7838 (t0) REVERT: C 174 LYS cc_start: 0.7833 (mtpt) cc_final: 0.7063 (mmpt) REVERT: C 263 ARG cc_start: 0.7971 (mmt90) cc_final: 0.7277 (mmt-90) REVERT: C 417 TYR cc_start: 0.7558 (m-80) cc_final: 0.7000 (m-10) REVERT: C 456 ASP cc_start: 0.8680 (t0) cc_final: 0.8431 (p0) REVERT: D 131 ILE cc_start: 0.8432 (mm) cc_final: 0.8172 (tp) REVERT: D 150 GLU cc_start: 0.7472 (tp30) cc_final: 0.7190 (mp0) REVERT: D 174 LYS cc_start: 0.7929 (mtpt) cc_final: 0.6876 (mmtt) REVERT: D 334 ARG cc_start: 0.7150 (mtt-85) cc_final: 0.6770 (mtm110) REVERT: D 388 MET cc_start: 0.6512 (pmt) cc_final: 0.6188 (pmt) REVERT: D 417 TYR cc_start: 0.7530 (m-10) cc_final: 0.7083 (m-10) REVERT: D 420 MET cc_start: 0.6765 (ttt) cc_final: 0.5950 (tpp) REVERT: D 469 GLU cc_start: 0.7691 (tt0) cc_final: 0.7200 (tt0) REVERT: D 487 ASP cc_start: 0.8286 (t70) cc_final: 0.7553 (t0) REVERT: E 174 LYS cc_start: 0.7870 (mtpt) cc_final: 0.6915 (mmtt) REVERT: E 222 TYR cc_start: 0.8292 (t80) cc_final: 0.7991 (t80) REVERT: E 249 MET cc_start: 0.8620 (tpp) cc_final: 0.8289 (mmt) REVERT: E 263 ARG cc_start: 0.8003 (mmt90) cc_final: 0.7478 (mmt-90) REVERT: E 487 ASP cc_start: 0.8299 (t70) cc_final: 0.7724 (t0) REVERT: F 150 GLU cc_start: 0.7225 (tp30) cc_final: 0.6977 (mp0) REVERT: F 174 LYS cc_start: 0.7999 (mtpt) cc_final: 0.7158 (mmpt) REVERT: F 249 MET cc_start: 0.8633 (tpp) cc_final: 0.8391 (tpt) REVERT: F 263 ARG cc_start: 0.7961 (mmt90) cc_final: 0.7272 (mmt-90) REVERT: F 334 ARG cc_start: 0.6663 (tmt170) cc_final: 0.6450 (mtp180) REVERT: F 417 TYR cc_start: 0.7512 (m-10) cc_final: 0.7291 (m-10) REVERT: F 438 LYS cc_start: 0.6623 (mtmm) cc_final: 0.6423 (pttm) REVERT: F 496 LYS cc_start: 0.7770 (tptm) cc_final: 0.7391 (tptt) outliers start: 44 outliers final: 20 residues processed: 348 average time/residue: 1.0010 time to fit residues: 404.3921 Evaluate side-chains 308 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 285 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 472 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 113 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 165 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 226 optimal weight: 2.9990 chunk 132 optimal weight: 0.4980 chunk 169 optimal weight: 0.5980 chunk 173 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 ASN C 305 HIS C 473 ASN ** D 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 HIS E 418 HIS E 473 ASN F 305 HIS F 473 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.170231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.113992 restraints weight = 22222.277| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.66 r_work: 0.3319 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19962 Z= 0.124 Angle : 0.524 7.605 27048 Z= 0.263 Chirality : 0.038 0.129 3078 Planarity : 0.004 0.048 3318 Dihedral : 6.333 48.367 3552 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.47 % Allowed : 16.72 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.18), residues: 2304 helix: 2.61 (0.14), residues: 1452 sheet: 0.87 (0.40), residues: 192 loop : -0.29 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 458 HIS 0.006 0.001 HIS E 305 PHE 0.025 0.001 PHE E 194 TYR 0.013 0.001 TYR F 222 ARG 0.007 0.000 ARG C 476 Details of bonding type rmsd hydrogen bonds : bond 0.03258 ( 1195) hydrogen bonds : angle 3.54717 ( 3465) covalent geometry : bond 0.00290 (19962) covalent geometry : angle 0.52367 (27048) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 314 time to evaluate : 2.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ILE cc_start: 0.8517 (mm) cc_final: 0.8219 (tp) REVERT: A 138 TRP cc_start: 0.7604 (m-90) cc_final: 0.7262 (m-90) REVERT: A 150 GLU cc_start: 0.7554 (tp30) cc_final: 0.7138 (mp0) REVERT: A 174 LYS cc_start: 0.7866 (mtpt) cc_final: 0.6923 (mmtt) REVERT: A 235 TYR cc_start: 0.7278 (t80) cc_final: 0.6589 (t80) REVERT: A 417 TYR cc_start: 0.7725 (m-10) cc_final: 0.7116 (m-10) REVERT: A 420 MET cc_start: 0.6789 (OUTLIER) cc_final: 0.6324 (tpp) REVERT: A 469 GLU cc_start: 0.7687 (tt0) cc_final: 0.7183 (tt0) REVERT: A 487 ASP cc_start: 0.8142 (t70) cc_final: 0.7929 (t70) REVERT: B 138 TRP cc_start: 0.8019 (m-90) cc_final: 0.7586 (m-90) REVERT: B 150 GLU cc_start: 0.7329 (tp30) cc_final: 0.6942 (mp0) REVERT: B 174 LYS cc_start: 0.7935 (mtpt) cc_final: 0.7014 (mmtt) REVERT: B 196 PHE cc_start: 0.8807 (t80) cc_final: 0.8592 (t80) REVERT: B 249 MET cc_start: 0.8380 (tpt) cc_final: 0.7948 (mmt) REVERT: B 263 ARG cc_start: 0.8074 (mmt90) cc_final: 0.7594 (mmt-90) REVERT: B 417 TYR cc_start: 0.7884 (m-80) cc_final: 0.7340 (m-80) REVERT: B 487 ASP cc_start: 0.8252 (t70) cc_final: 0.7598 (t0) REVERT: B 496 LYS cc_start: 0.7920 (tptm) cc_final: 0.7558 (tttt) REVERT: C 138 TRP cc_start: 0.7927 (m-90) cc_final: 0.7676 (m-90) REVERT: C 174 LYS cc_start: 0.7859 (mtpt) cc_final: 0.7032 (mmpt) REVERT: C 263 ARG cc_start: 0.8005 (mmt90) cc_final: 0.7312 (mmt-90) REVERT: C 417 TYR cc_start: 0.7642 (m-80) cc_final: 0.7041 (m-10) REVERT: C 443 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7608 (tpt170) REVERT: D 131 ILE cc_start: 0.8428 (mm) cc_final: 0.8102 (tp) REVERT: D 138 TRP cc_start: 0.7970 (m-90) cc_final: 0.7666 (m-90) REVERT: D 150 GLU cc_start: 0.7780 (tp30) cc_final: 0.7351 (mp0) REVERT: D 174 LYS cc_start: 0.7983 (mtpt) cc_final: 0.6965 (mmtt) REVERT: D 235 TYR cc_start: 0.7245 (t80) cc_final: 0.6605 (t80) REVERT: D 334 ARG cc_start: 0.7204 (mtt-85) cc_final: 0.6797 (mtm110) REVERT: D 388 MET cc_start: 0.6603 (pmt) cc_final: 0.6271 (pmt) REVERT: D 417 TYR cc_start: 0.7591 (m-10) cc_final: 0.7030 (m-10) REVERT: D 420 MET cc_start: 0.7030 (ttt) cc_final: 0.6349 (tpp) REVERT: D 469 GLU cc_start: 0.7688 (tt0) cc_final: 0.7178 (tt0) REVERT: D 487 ASP cc_start: 0.8138 (t70) cc_final: 0.7926 (t70) REVERT: E 138 TRP cc_start: 0.7748 (m-90) cc_final: 0.7351 (m-90) REVERT: E 174 LYS cc_start: 0.8041 (mtpt) cc_final: 0.6961 (mmtt) REVERT: E 196 PHE cc_start: 0.8658 (t80) cc_final: 0.8412 (t80) REVERT: E 222 TYR cc_start: 0.8260 (t80) cc_final: 0.7880 (t80) REVERT: E 249 MET cc_start: 0.8638 (tpp) cc_final: 0.8312 (mmt) REVERT: E 263 ARG cc_start: 0.8033 (mmt90) cc_final: 0.7546 (mmt-90) REVERT: E 456 ASP cc_start: 0.8631 (t0) cc_final: 0.8379 (p0) REVERT: F 138 TRP cc_start: 0.7641 (m-90) cc_final: 0.7290 (m-90) REVERT: F 150 GLU cc_start: 0.7681 (tp30) cc_final: 0.7197 (mp0) REVERT: F 174 LYS cc_start: 0.7923 (mtpt) cc_final: 0.7033 (mmpt) REVERT: F 263 ARG cc_start: 0.8005 (mmt90) cc_final: 0.7320 (mmt-90) REVERT: F 334 ARG cc_start: 0.6807 (tmt170) cc_final: 0.6583 (mtp180) REVERT: F 401 MET cc_start: 0.8134 (ptt) cc_final: 0.7868 (pmm) REVERT: F 417 TYR cc_start: 0.7638 (m-10) cc_final: 0.7118 (m-10) REVERT: F 443 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7600 (tpt170) outliers start: 50 outliers final: 24 residues processed: 338 average time/residue: 0.9495 time to fit residues: 376.9270 Evaluate side-chains 313 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 286 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 443 ARG Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 397 ILE Chi-restraints excluded: chain F residue 443 ARG Chi-restraints excluded: chain F residue 472 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 147 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 165 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 200 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 HIS B 305 HIS D 221 GLN D 305 HIS E 305 HIS F 221 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.164688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.108015 restraints weight = 22446.913| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.64 r_work: 0.3240 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19962 Z= 0.175 Angle : 0.571 7.364 27048 Z= 0.290 Chirality : 0.040 0.132 3078 Planarity : 0.004 0.049 3318 Dihedral : 6.748 47.689 3552 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.17 % Allowed : 16.42 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.17), residues: 2304 helix: 2.42 (0.13), residues: 1452 sheet: 0.70 (0.39), residues: 192 loop : -0.42 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 458 HIS 0.005 0.001 HIS A 305 PHE 0.039 0.002 PHE C 196 TYR 0.014 0.002 TYR A 453 ARG 0.007 0.000 ARG B 476 Details of bonding type rmsd hydrogen bonds : bond 0.04001 ( 1195) hydrogen bonds : angle 3.71139 ( 3465) covalent geometry : bond 0.00428 (19962) covalent geometry : angle 0.57127 (27048) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 312 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ILE cc_start: 0.8547 (mm) cc_final: 0.8311 (tp) REVERT: A 138 TRP cc_start: 0.7782 (m-90) cc_final: 0.7452 (m-90) REVERT: A 150 GLU cc_start: 0.7649 (tp30) cc_final: 0.7099 (mt-10) REVERT: A 174 LYS cc_start: 0.8047 (mtpt) cc_final: 0.6984 (mmtt) REVERT: A 200 TYR cc_start: 0.7843 (OUTLIER) cc_final: 0.7491 (m-80) REVERT: A 222 TYR cc_start: 0.8121 (t80) cc_final: 0.7797 (t80) REVERT: A 235 TYR cc_start: 0.7280 (t80) cc_final: 0.6539 (t80) REVERT: A 420 MET cc_start: 0.6930 (OUTLIER) cc_final: 0.6389 (tpp) REVERT: A 469 GLU cc_start: 0.7747 (tt0) cc_final: 0.7242 (tt0) REVERT: B 131 ILE cc_start: 0.8202 (tp) cc_final: 0.7970 (tp) REVERT: B 138 TRP cc_start: 0.7889 (m-90) cc_final: 0.7502 (m-90) REVERT: B 150 GLU cc_start: 0.7463 (tp30) cc_final: 0.6976 (mp0) REVERT: B 174 LYS cc_start: 0.8201 (mtpt) cc_final: 0.7139 (mmtt) REVERT: B 196 PHE cc_start: 0.8723 (t80) cc_final: 0.8491 (t80) REVERT: B 249 MET cc_start: 0.8403 (tpt) cc_final: 0.8178 (mmm) REVERT: B 263 ARG cc_start: 0.8045 (mmt90) cc_final: 0.7542 (mmt-90) REVERT: B 417 TYR cc_start: 0.7966 (m-80) cc_final: 0.7303 (m-80) REVERT: B 420 MET cc_start: 0.6764 (ttt) cc_final: 0.5995 (tpp) REVERT: B 487 ASP cc_start: 0.8230 (t70) cc_final: 0.7482 (t0) REVERT: B 496 LYS cc_start: 0.7988 (tptm) cc_final: 0.7621 (tttt) REVERT: C 138 TRP cc_start: 0.8012 (m-90) cc_final: 0.7737 (m-90) REVERT: C 174 LYS cc_start: 0.7992 (mtpt) cc_final: 0.7104 (mmpt) REVERT: C 222 TYR cc_start: 0.8437 (t80) cc_final: 0.8234 (t80) REVERT: C 263 ARG cc_start: 0.8177 (mmt90) cc_final: 0.7502 (mmt-90) REVERT: C 388 MET cc_start: 0.6717 (pmt) cc_final: 0.5874 (pmt) REVERT: C 410 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6930 (ttp-170) REVERT: C 415 GLN cc_start: 0.8024 (pt0) cc_final: 0.7752 (pm20) REVERT: C 417 TYR cc_start: 0.7714 (m-80) cc_final: 0.7116 (m-10) REVERT: C 443 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7894 (tpt170) REVERT: C 461 THR cc_start: 0.8525 (m) cc_final: 0.8319 (m) REVERT: D 138 TRP cc_start: 0.8060 (m-90) cc_final: 0.7790 (m-90) REVERT: D 150 GLU cc_start: 0.7882 (tp30) cc_final: 0.7319 (mp0) REVERT: D 174 LYS cc_start: 0.8060 (mtpt) cc_final: 0.7007 (mmtt) REVERT: D 200 TYR cc_start: 0.7810 (OUTLIER) cc_final: 0.7605 (m-80) REVERT: D 235 TYR cc_start: 0.7322 (t80) cc_final: 0.6546 (t80) REVERT: D 388 MET cc_start: 0.6504 (pmt) cc_final: 0.6243 (pmt) REVERT: D 417 TYR cc_start: 0.7749 (m-10) cc_final: 0.7015 (m-10) REVERT: D 420 MET cc_start: 0.7101 (ttt) cc_final: 0.6393 (tpp) REVERT: D 469 GLU cc_start: 0.7734 (tt0) cc_final: 0.7233 (tt0) REVERT: E 138 TRP cc_start: 0.7800 (m-90) cc_final: 0.7437 (m-90) REVERT: E 174 LYS cc_start: 0.8195 (mtpt) cc_final: 0.7128 (mmtt) REVERT: E 222 TYR cc_start: 0.8238 (t80) cc_final: 0.7708 (t80) REVERT: E 249 MET cc_start: 0.8612 (tpp) cc_final: 0.8391 (mmp) REVERT: E 263 ARG cc_start: 0.8048 (mmt90) cc_final: 0.7524 (mmt-90) REVERT: E 420 MET cc_start: 0.6946 (ttt) cc_final: 0.6073 (tpp) REVERT: E 442 GLU cc_start: 0.7427 (tm-30) cc_final: 0.6885 (tp30) REVERT: E 456 ASP cc_start: 0.8675 (t0) cc_final: 0.8412 (p0) REVERT: E 487 ASP cc_start: 0.8314 (t0) cc_final: 0.7696 (t0) REVERT: E 496 LYS cc_start: 0.8035 (tptm) cc_final: 0.7628 (tttt) REVERT: F 138 TRP cc_start: 0.7830 (m-90) cc_final: 0.7514 (m-90) REVERT: F 174 LYS cc_start: 0.8027 (mtpt) cc_final: 0.7113 (mmpt) REVERT: F 263 ARG cc_start: 0.8154 (mmt90) cc_final: 0.7498 (mmt-90) REVERT: F 334 ARG cc_start: 0.6904 (tmt170) cc_final: 0.6607 (mtp180) REVERT: F 388 MET cc_start: 0.6731 (pmt) cc_final: 0.5874 (pmt) REVERT: F 410 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.6947 (ttp-170) REVERT: F 415 GLN cc_start: 0.7963 (pt0) cc_final: 0.7738 (pm20) REVERT: F 417 TYR cc_start: 0.7695 (m-10) cc_final: 0.7135 (m-10) REVERT: F 420 MET cc_start: 0.6886 (ttt) cc_final: 0.6266 (tpp) REVERT: F 443 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7972 (tpt170) outliers start: 64 outliers final: 31 residues processed: 349 average time/residue: 0.9679 time to fit residues: 395.3961 Evaluate side-chains 325 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 287 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 401 MET Chi-restraints excluded: chain C residue 410 ARG Chi-restraints excluded: chain C residue 443 ARG Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 281 GLU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 397 ILE Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain F residue 443 ARG Chi-restraints excluded: chain F residue 472 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 126 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 201 optimal weight: 0.9990 chunk 209 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 211 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN B 305 HIS B 416 ASN C 221 GLN E 416 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.162675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.106453 restraints weight = 22352.602| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.60 r_work: 0.3215 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 19962 Z= 0.213 Angle : 0.604 7.271 27048 Z= 0.306 Chirality : 0.041 0.138 3078 Planarity : 0.004 0.048 3318 Dihedral : 6.985 52.724 3552 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.17 % Allowed : 17.90 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.17), residues: 2304 helix: 2.25 (0.13), residues: 1452 sheet: 0.43 (0.38), residues: 198 loop : -0.60 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 458 HIS 0.003 0.001 HIS C 234 PHE 0.024 0.002 PHE E 194 TYR 0.017 0.002 TYR B 200 ARG 0.005 0.000 ARG B 476 Details of bonding type rmsd hydrogen bonds : bond 0.04319 ( 1195) hydrogen bonds : angle 3.79073 ( 3465) covalent geometry : bond 0.00527 (19962) covalent geometry : angle 0.60350 (27048) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 305 time to evaluate : 2.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 PHE cc_start: 0.8127 (m-10) cc_final: 0.7784 (m-80) REVERT: A 131 ILE cc_start: 0.8543 (mm) cc_final: 0.8229 (tp) REVERT: A 138 TRP cc_start: 0.7972 (m-90) cc_final: 0.7627 (m-90) REVERT: A 150 GLU cc_start: 0.7528 (tp30) cc_final: 0.6923 (mt-10) REVERT: A 222 TYR cc_start: 0.8304 (t80) cc_final: 0.8022 (t80) REVERT: A 235 TYR cc_start: 0.7507 (t80) cc_final: 0.6860 (t80) REVERT: A 417 TYR cc_start: 0.7831 (m-10) cc_final: 0.7120 (m-10) REVERT: A 420 MET cc_start: 0.6975 (OUTLIER) cc_final: 0.6445 (tpp) REVERT: B 138 TRP cc_start: 0.8205 (m-90) cc_final: 0.7845 (m-90) REVERT: B 150 GLU cc_start: 0.7497 (tp30) cc_final: 0.7063 (mt-10) REVERT: B 174 LYS cc_start: 0.8252 (mtpt) cc_final: 0.7174 (mmtt) REVERT: B 222 TYR cc_start: 0.8419 (t80) cc_final: 0.8102 (t80) REVERT: B 263 ARG cc_start: 0.8042 (mmt90) cc_final: 0.7544 (mmt-90) REVERT: B 420 MET cc_start: 0.6891 (ttt) cc_final: 0.6041 (tpp) REVERT: B 442 GLU cc_start: 0.7443 (tm-30) cc_final: 0.7128 (tp30) REVERT: B 487 ASP cc_start: 0.8332 (t70) cc_final: 0.7643 (t0) REVERT: B 496 LYS cc_start: 0.7991 (tptm) cc_final: 0.7669 (tttt) REVERT: C 138 TRP cc_start: 0.8116 (m-90) cc_final: 0.7833 (m-90) REVERT: C 174 LYS cc_start: 0.8069 (mtpt) cc_final: 0.7230 (mmtt) REVERT: C 263 ARG cc_start: 0.8172 (mmt90) cc_final: 0.7596 (mmt-90) REVERT: C 410 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6897 (ttp-170) REVERT: C 415 GLN cc_start: 0.8082 (pt0) cc_final: 0.7747 (pm20) REVERT: C 417 TYR cc_start: 0.7744 (m-80) cc_final: 0.7188 (m-10) REVERT: C 420 MET cc_start: 0.6993 (ttt) cc_final: 0.6305 (tpp) REVERT: D 130 PHE cc_start: 0.8180 (m-10) cc_final: 0.7720 (m-80) REVERT: D 138 TRP cc_start: 0.8023 (m-90) cc_final: 0.7721 (m-90) REVERT: D 150 GLU cc_start: 0.7772 (tp30) cc_final: 0.7246 (mt-10) REVERT: D 235 TYR cc_start: 0.7470 (t80) cc_final: 0.6770 (t80) REVERT: D 417 TYR cc_start: 0.7902 (m-10) cc_final: 0.7193 (m-10) REVERT: D 420 MET cc_start: 0.7178 (ttt) cc_final: 0.6433 (tpp) REVERT: E 138 TRP cc_start: 0.7842 (m-90) cc_final: 0.7470 (m-90) REVERT: E 174 LYS cc_start: 0.8241 (mtpt) cc_final: 0.7151 (mmtt) REVERT: E 263 ARG cc_start: 0.8040 (mmt90) cc_final: 0.7536 (mmt-90) REVERT: E 300 PHE cc_start: 0.7874 (m-10) cc_final: 0.7613 (t80) REVERT: E 420 MET cc_start: 0.6969 (ttt) cc_final: 0.6119 (tpp) REVERT: E 442 GLU cc_start: 0.7425 (tm-30) cc_final: 0.6909 (tp30) REVERT: E 456 ASP cc_start: 0.8802 (t0) cc_final: 0.8526 (p0) REVERT: E 487 ASP cc_start: 0.8374 (t0) cc_final: 0.7681 (t0) REVERT: E 496 LYS cc_start: 0.8027 (tptm) cc_final: 0.7618 (tttt) REVERT: F 138 TRP cc_start: 0.7615 (m-90) cc_final: 0.7383 (m-90) REVERT: F 174 LYS cc_start: 0.8147 (mtpt) cc_final: 0.7213 (mmtt) REVERT: F 263 ARG cc_start: 0.8161 (mmt90) cc_final: 0.7585 (mmt-90) REVERT: F 334 ARG cc_start: 0.6967 (tmt170) cc_final: 0.6644 (mtp180) REVERT: F 410 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6891 (ttp-170) REVERT: F 415 GLN cc_start: 0.8112 (pt0) cc_final: 0.7786 (pm20) REVERT: F 417 TYR cc_start: 0.7729 (m-10) cc_final: 0.7155 (m-10) REVERT: F 420 MET cc_start: 0.6918 (ttt) cc_final: 0.6298 (tpp) REVERT: F 443 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7968 (tpt170) outliers start: 64 outliers final: 35 residues processed: 341 average time/residue: 0.8858 time to fit residues: 355.9049 Evaluate side-chains 325 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 286 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 401 MET Chi-restraints excluded: chain C residue 410 ARG Chi-restraints excluded: chain C residue 443 ARG Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 249 MET Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain F residue 443 ARG Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 487 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 150 optimal weight: 1.9990 chunk 70 optimal weight: 0.0980 chunk 9 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 214 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 220 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.166850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.110658 restraints weight = 21998.122| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.62 r_work: 0.3271 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19962 Z= 0.117 Angle : 0.537 7.423 27048 Z= 0.272 Chirality : 0.038 0.146 3078 Planarity : 0.004 0.050 3318 Dihedral : 6.632 55.227 3552 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.13 % Allowed : 19.88 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.17), residues: 2304 helix: 2.42 (0.13), residues: 1452 sheet: 0.68 (0.34), residues: 234 loop : -0.65 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 458 HIS 0.003 0.000 HIS D 234 PHE 0.036 0.002 PHE C 196 TYR 0.018 0.001 TYR B 235 ARG 0.006 0.000 ARG A 360 Details of bonding type rmsd hydrogen bonds : bond 0.03374 ( 1195) hydrogen bonds : angle 3.60643 ( 3465) covalent geometry : bond 0.00271 (19962) covalent geometry : angle 0.53712 (27048) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 299 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 TRP cc_start: 0.7942 (m-90) cc_final: 0.7643 (m-90) REVERT: A 150 GLU cc_start: 0.7683 (tp30) cc_final: 0.7130 (mt-10) REVERT: A 174 LYS cc_start: 0.8073 (mtpt) cc_final: 0.6996 (mmtt) REVERT: A 235 TYR cc_start: 0.7299 (t80) cc_final: 0.6922 (t80) REVERT: A 417 TYR cc_start: 0.7726 (m-10) cc_final: 0.7048 (m-10) REVERT: A 420 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6391 (tpp) REVERT: B 138 TRP cc_start: 0.8202 (m-90) cc_final: 0.7788 (m-90) REVERT: B 150 GLU cc_start: 0.7298 (tp30) cc_final: 0.6779 (mt-10) REVERT: B 174 LYS cc_start: 0.8232 (mtpt) cc_final: 0.7159 (mmtt) REVERT: B 196 PHE cc_start: 0.8840 (t80) cc_final: 0.8635 (t80) REVERT: B 222 TYR cc_start: 0.8434 (t80) cc_final: 0.8124 (t80) REVERT: B 263 ARG cc_start: 0.8013 (mmt90) cc_final: 0.7512 (mmt-90) REVERT: B 420 MET cc_start: 0.6985 (ttt) cc_final: 0.6182 (tpp) REVERT: B 442 GLU cc_start: 0.7220 (tm-30) cc_final: 0.7003 (tp30) REVERT: B 487 ASP cc_start: 0.8249 (t70) cc_final: 0.7555 (t0) REVERT: B 496 LYS cc_start: 0.8066 (tptm) cc_final: 0.7619 (tttt) REVERT: C 138 TRP cc_start: 0.8047 (m-90) cc_final: 0.7697 (m-90) REVERT: C 174 LYS cc_start: 0.8156 (mtpt) cc_final: 0.7223 (mmpt) REVERT: C 263 ARG cc_start: 0.8180 (mmt90) cc_final: 0.7485 (mmt-90) REVERT: C 388 MET cc_start: 0.6774 (pmt) cc_final: 0.5938 (pmt) REVERT: C 417 TYR cc_start: 0.7737 (m-80) cc_final: 0.7202 (m-10) REVERT: C 420 MET cc_start: 0.6954 (ttt) cc_final: 0.6264 (tpp) REVERT: D 131 ILE cc_start: 0.8532 (mm) cc_final: 0.8256 (tp) REVERT: D 138 TRP cc_start: 0.8055 (m-90) cc_final: 0.7735 (m-90) REVERT: D 150 GLU cc_start: 0.7693 (tp30) cc_final: 0.7144 (mt-10) REVERT: D 174 LYS cc_start: 0.8064 (mtpt) cc_final: 0.6981 (mmtt) REVERT: D 235 TYR cc_start: 0.7391 (t80) cc_final: 0.6975 (t80) REVERT: D 417 TYR cc_start: 0.7794 (m-10) cc_final: 0.7133 (m-10) REVERT: D 420 MET cc_start: 0.6976 (ttt) cc_final: 0.6358 (tpp) REVERT: D 469 GLU cc_start: 0.7560 (tt0) cc_final: 0.6979 (tt0) REVERT: E 138 TRP cc_start: 0.7874 (m-90) cc_final: 0.7492 (m-90) REVERT: E 174 LYS cc_start: 0.8220 (mtpt) cc_final: 0.7195 (mmtt) REVERT: E 222 TYR cc_start: 0.8409 (t80) cc_final: 0.7900 (t80) REVERT: E 263 ARG cc_start: 0.8013 (mmt90) cc_final: 0.7510 (mmt-90) REVERT: E 295 LEU cc_start: 0.6384 (mm) cc_final: 0.5980 (mp) REVERT: E 420 MET cc_start: 0.6922 (ttt) cc_final: 0.6136 (tpp) REVERT: E 442 GLU cc_start: 0.7294 (tm-30) cc_final: 0.6792 (tp30) REVERT: E 487 ASP cc_start: 0.8351 (t0) cc_final: 0.7736 (t0) REVERT: F 174 LYS cc_start: 0.8107 (mtpt) cc_final: 0.7193 (mmpt) REVERT: F 263 ARG cc_start: 0.8160 (mmt90) cc_final: 0.7478 (mmt-90) REVERT: F 334 ARG cc_start: 0.6876 (tmt170) cc_final: 0.6595 (ttt-90) REVERT: F 388 MET cc_start: 0.6762 (pmt) cc_final: 0.5921 (pmt) REVERT: F 410 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6879 (ttp-170) REVERT: F 415 GLN cc_start: 0.7823 (pt0) cc_final: 0.7528 (pm20) REVERT: F 417 TYR cc_start: 0.7760 (m-10) cc_final: 0.7242 (m-10) REVERT: F 420 MET cc_start: 0.6957 (ttt) cc_final: 0.6278 (tpp) REVERT: F 443 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7915 (tpt-90) outliers start: 43 outliers final: 28 residues processed: 318 average time/residue: 0.9505 time to fit residues: 356.6792 Evaluate side-chains 313 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 282 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 397 ILE Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain F residue 443 ARG Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 487 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 133 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 214 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 183 optimal weight: 0.3980 chunk 52 optimal weight: 0.2980 chunk 198 optimal weight: 0.9990 chunk 157 optimal weight: 0.7980 chunk 182 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.166516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.109995 restraints weight = 22286.685| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.64 r_work: 0.3264 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19962 Z= 0.126 Angle : 0.546 7.519 27048 Z= 0.278 Chirality : 0.038 0.161 3078 Planarity : 0.004 0.050 3318 Dihedral : 6.690 57.527 3552 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.03 % Allowed : 20.62 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.17), residues: 2304 helix: 2.43 (0.14), residues: 1458 sheet: 0.71 (0.39), residues: 192 loop : -0.45 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 458 HIS 0.002 0.000 HIS A 234 PHE 0.028 0.002 PHE D 196 TYR 0.014 0.001 TYR D 222 ARG 0.006 0.000 ARG A 360 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 1195) hydrogen bonds : angle 3.62116 ( 3465) covalent geometry : bond 0.00295 (19962) covalent geometry : angle 0.54630 (27048) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 294 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 TRP cc_start: 0.7956 (m-90) cc_final: 0.7682 (m-90) REVERT: A 150 GLU cc_start: 0.7561 (tp30) cc_final: 0.6988 (mt-10) REVERT: A 174 LYS cc_start: 0.8087 (mtpt) cc_final: 0.7001 (mmtt) REVERT: A 222 TYR cc_start: 0.8447 (t80) cc_final: 0.8123 (t80) REVERT: A 235 TYR cc_start: 0.7448 (t80) cc_final: 0.7044 (t80) REVERT: A 417 TYR cc_start: 0.7752 (m-10) cc_final: 0.7041 (m-10) REVERT: A 420 MET cc_start: 0.6940 (OUTLIER) cc_final: 0.6429 (tpp) REVERT: B 138 TRP cc_start: 0.8191 (m-90) cc_final: 0.7801 (m-90) REVERT: B 150 GLU cc_start: 0.7282 (tp30) cc_final: 0.6765 (mt-10) REVERT: B 174 LYS cc_start: 0.8254 (mtpt) cc_final: 0.7155 (mmtt) REVERT: B 196 PHE cc_start: 0.8825 (t80) cc_final: 0.8610 (t80) REVERT: B 222 TYR cc_start: 0.8447 (t80) cc_final: 0.8089 (t80) REVERT: B 263 ARG cc_start: 0.8012 (mmt90) cc_final: 0.7522 (mmt-90) REVERT: B 420 MET cc_start: 0.6988 (ttt) cc_final: 0.6184 (tpp) REVERT: B 442 GLU cc_start: 0.7221 (tm-30) cc_final: 0.7003 (tp30) REVERT: B 487 ASP cc_start: 0.8246 (t70) cc_final: 0.7547 (t0) REVERT: B 496 LYS cc_start: 0.7961 (tptm) cc_final: 0.7517 (tptt) REVERT: C 138 TRP cc_start: 0.8030 (m-90) cc_final: 0.7532 (m-90) REVERT: C 174 LYS cc_start: 0.8160 (mtpt) cc_final: 0.7219 (mmpt) REVERT: C 221 GLN cc_start: 0.8184 (mt0) cc_final: 0.7763 (pm20) REVERT: C 263 ARG cc_start: 0.8165 (mmt90) cc_final: 0.7508 (mmt-90) REVERT: C 388 MET cc_start: 0.6745 (pmt) cc_final: 0.5927 (pmt) REVERT: C 415 GLN cc_start: 0.8012 (pt0) cc_final: 0.7660 (pm20) REVERT: C 417 TYR cc_start: 0.7765 (m-80) cc_final: 0.7187 (m-10) REVERT: C 420 MET cc_start: 0.6958 (ttt) cc_final: 0.6264 (tpp) REVERT: C 443 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7916 (tpt-90) REVERT: D 138 TRP cc_start: 0.8036 (m-90) cc_final: 0.7750 (m-90) REVERT: D 150 GLU cc_start: 0.7643 (tp30) cc_final: 0.7085 (mt-10) REVERT: D 174 LYS cc_start: 0.8082 (mtpt) cc_final: 0.6970 (mmtt) REVERT: D 235 TYR cc_start: 0.7295 (t80) cc_final: 0.6903 (t80) REVERT: D 417 TYR cc_start: 0.7848 (m-10) cc_final: 0.7141 (m-10) REVERT: D 420 MET cc_start: 0.6994 (ttt) cc_final: 0.6374 (tpp) REVERT: D 469 GLU cc_start: 0.7556 (tt0) cc_final: 0.6994 (tt0) REVERT: E 138 TRP cc_start: 0.7884 (m-90) cc_final: 0.7591 (m-90) REVERT: E 174 LYS cc_start: 0.8245 (mtpt) cc_final: 0.7158 (mmtt) REVERT: E 221 GLN cc_start: 0.8345 (mt0) cc_final: 0.7856 (pm20) REVERT: E 222 TYR cc_start: 0.8346 (t80) cc_final: 0.7954 (t80) REVERT: E 263 ARG cc_start: 0.8024 (mmt90) cc_final: 0.7521 (mmt-90) REVERT: E 420 MET cc_start: 0.6920 (ttt) cc_final: 0.6124 (tpp) REVERT: E 442 GLU cc_start: 0.7324 (tm-30) cc_final: 0.6808 (tp30) REVERT: E 487 ASP cc_start: 0.8335 (t0) cc_final: 0.7706 (t0) REVERT: E 496 LYS cc_start: 0.8003 (tptm) cc_final: 0.7556 (tptt) REVERT: F 174 LYS cc_start: 0.8146 (mtpt) cc_final: 0.7207 (mmpt) REVERT: F 263 ARG cc_start: 0.8163 (mmt90) cc_final: 0.7481 (mmt-90) REVERT: F 334 ARG cc_start: 0.6890 (tmt170) cc_final: 0.6616 (ttt-90) REVERT: F 388 MET cc_start: 0.6729 (pmt) cc_final: 0.5909 (pmt) REVERT: F 415 GLN cc_start: 0.7960 (pt0) cc_final: 0.7664 (pm20) REVERT: F 417 TYR cc_start: 0.7793 (m-10) cc_final: 0.7168 (m-10) REVERT: F 420 MET cc_start: 0.6963 (ttt) cc_final: 0.6282 (tpp) REVERT: F 443 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7913 (tpt-90) outliers start: 41 outliers final: 31 residues processed: 315 average time/residue: 0.8986 time to fit residues: 334.6450 Evaluate side-chains 310 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 276 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 443 ARG Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 372 ILE Chi-restraints excluded: chain F residue 397 ILE Chi-restraints excluded: chain F residue 443 ARG Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 487 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 224 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 222 optimal weight: 0.5980 chunk 1 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.165341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.109102 restraints weight = 22252.925| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.67 r_work: 0.3244 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19962 Z= 0.138 Angle : 0.562 7.870 27048 Z= 0.284 Chirality : 0.038 0.141 3078 Planarity : 0.004 0.052 3318 Dihedral : 6.821 59.385 3552 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.88 % Allowed : 21.46 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.17), residues: 2304 helix: 2.34 (0.14), residues: 1464 sheet: 0.72 (0.39), residues: 192 loop : -0.50 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 458 HIS 0.010 0.001 HIS F 234 PHE 0.036 0.002 PHE C 196 TYR 0.015 0.001 TYR D 222 ARG 0.005 0.000 ARG A 360 Details of bonding type rmsd hydrogen bonds : bond 0.03551 ( 1195) hydrogen bonds : angle 3.66693 ( 3465) covalent geometry : bond 0.00329 (19962) covalent geometry : angle 0.56233 (27048) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 290 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 TRP cc_start: 0.7975 (m-90) cc_final: 0.7708 (m-90) REVERT: A 150 GLU cc_start: 0.7589 (tp30) cc_final: 0.7021 (mt-10) REVERT: A 174 LYS cc_start: 0.8069 (mtpt) cc_final: 0.6939 (mmtt) REVERT: A 235 TYR cc_start: 0.7376 (t80) cc_final: 0.6856 (t80) REVERT: A 417 TYR cc_start: 0.7736 (m-10) cc_final: 0.7010 (m-10) REVERT: A 420 MET cc_start: 0.6861 (OUTLIER) cc_final: 0.6353 (tpp) REVERT: B 130 PHE cc_start: 0.8186 (m-80) cc_final: 0.7960 (m-80) REVERT: B 138 TRP cc_start: 0.8192 (m-90) cc_final: 0.7792 (m-90) REVERT: B 150 GLU cc_start: 0.7276 (tp30) cc_final: 0.6721 (mt-10) REVERT: B 174 LYS cc_start: 0.8244 (mtpt) cc_final: 0.7122 (mmtt) REVERT: B 196 PHE cc_start: 0.8802 (t80) cc_final: 0.8588 (t80) REVERT: B 222 TYR cc_start: 0.8366 (t80) cc_final: 0.8044 (t80) REVERT: B 263 ARG cc_start: 0.7963 (mmt90) cc_final: 0.7463 (mmt-90) REVERT: B 300 PHE cc_start: 0.7947 (m-10) cc_final: 0.7621 (t80) REVERT: B 420 MET cc_start: 0.6948 (ttt) cc_final: 0.6140 (tpp) REVERT: B 487 ASP cc_start: 0.8267 (t70) cc_final: 0.7574 (t0) REVERT: C 138 TRP cc_start: 0.8045 (m-90) cc_final: 0.7693 (m-90) REVERT: C 174 LYS cc_start: 0.8149 (mtpt) cc_final: 0.7287 (mmtt) REVERT: C 263 ARG cc_start: 0.8135 (mmt90) cc_final: 0.7566 (mmt-90) REVERT: C 388 MET cc_start: 0.6743 (pmt) cc_final: 0.5885 (pmt) REVERT: C 415 GLN cc_start: 0.8016 (pt0) cc_final: 0.7743 (pm20) REVERT: C 417 TYR cc_start: 0.7731 (m-80) cc_final: 0.7122 (m-10) REVERT: C 420 MET cc_start: 0.6915 (ttt) cc_final: 0.6233 (tpp) REVERT: C 443 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7899 (tpt-90) REVERT: D 138 TRP cc_start: 0.8146 (m-90) cc_final: 0.7801 (m-90) REVERT: D 150 GLU cc_start: 0.7582 (tp30) cc_final: 0.6986 (mt-10) REVERT: D 174 LYS cc_start: 0.8063 (mtpt) cc_final: 0.6932 (mmtt) REVERT: D 235 TYR cc_start: 0.7242 (t80) cc_final: 0.6799 (t80) REVERT: D 417 TYR cc_start: 0.7849 (m-10) cc_final: 0.7135 (m-10) REVERT: D 420 MET cc_start: 0.7054 (ttt) cc_final: 0.6376 (tpp) REVERT: D 469 GLU cc_start: 0.7543 (tt0) cc_final: 0.6975 (tt0) REVERT: E 130 PHE cc_start: 0.8098 (m-80) cc_final: 0.7832 (m-80) REVERT: E 131 ILE cc_start: 0.8180 (tp) cc_final: 0.7884 (tp) REVERT: E 138 TRP cc_start: 0.8043 (m-90) cc_final: 0.7719 (m-90) REVERT: E 174 LYS cc_start: 0.8246 (mtpt) cc_final: 0.7137 (mmtt) REVERT: E 222 TYR cc_start: 0.8183 (t80) cc_final: 0.7862 (t80) REVERT: E 263 ARG cc_start: 0.7981 (mmt90) cc_final: 0.7475 (mmt-90) REVERT: E 334 ARG cc_start: 0.6713 (mtp180) cc_final: 0.6264 (tmt170) REVERT: E 420 MET cc_start: 0.6870 (ttt) cc_final: 0.6071 (tpp) REVERT: E 442 GLU cc_start: 0.7312 (tm-30) cc_final: 0.6806 (tp30) REVERT: E 456 ASP cc_start: 0.8661 (t0) cc_final: 0.8390 (p0) REVERT: E 487 ASP cc_start: 0.8373 (t0) cc_final: 0.7749 (t0) REVERT: F 174 LYS cc_start: 0.8153 (mtpt) cc_final: 0.7198 (mmtt) REVERT: F 263 ARG cc_start: 0.8113 (mmt90) cc_final: 0.7557 (mmt-90) REVERT: F 334 ARG cc_start: 0.6837 (tmt170) cc_final: 0.6532 (ttt-90) REVERT: F 388 MET cc_start: 0.6717 (pmt) cc_final: 0.5905 (pmt) REVERT: F 415 GLN cc_start: 0.7962 (pt0) cc_final: 0.7670 (pm20) REVERT: F 417 TYR cc_start: 0.7737 (m-10) cc_final: 0.7143 (m-10) REVERT: F 420 MET cc_start: 0.7056 (ttt) cc_final: 0.6356 (tpp) REVERT: F 443 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7835 (tpt-90) outliers start: 38 outliers final: 32 residues processed: 311 average time/residue: 0.9055 time to fit residues: 331.1602 Evaluate side-chains 316 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 281 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 443 ARG Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 372 ILE Chi-restraints excluded: chain F residue 397 ILE Chi-restraints excluded: chain F residue 443 ARG Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 487 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 105 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 147 optimal weight: 0.5980 chunk 224 optimal weight: 2.9990 chunk 210 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.164660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.108706 restraints weight = 22216.731| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.60 r_work: 0.3244 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19962 Z= 0.149 Angle : 0.571 7.967 27048 Z= 0.289 Chirality : 0.039 0.178 3078 Planarity : 0.004 0.051 3318 Dihedral : 6.840 58.329 3552 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.78 % Allowed : 21.81 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.17), residues: 2304 helix: 2.36 (0.13), residues: 1452 sheet: 0.69 (0.39), residues: 192 loop : -0.51 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 458 HIS 0.009 0.001 HIS F 234 PHE 0.027 0.002 PHE E 194 TYR 0.021 0.001 TYR D 222 ARG 0.005 0.000 ARG A 360 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 1195) hydrogen bonds : angle 3.68443 ( 3465) covalent geometry : bond 0.00360 (19962) covalent geometry : angle 0.57106 (27048) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 285 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 TRP cc_start: 0.8009 (m-90) cc_final: 0.7747 (m-90) REVERT: A 150 GLU cc_start: 0.7514 (tp30) cc_final: 0.6972 (mt-10) REVERT: A 222 TYR cc_start: 0.8404 (t80) cc_final: 0.8053 (t80) REVERT: A 235 TYR cc_start: 0.7442 (t80) cc_final: 0.6890 (t80) REVERT: A 417 TYR cc_start: 0.7803 (m-10) cc_final: 0.7087 (m-10) REVERT: A 420 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6395 (tpp) REVERT: B 130 PHE cc_start: 0.8238 (m-80) cc_final: 0.7979 (m-80) REVERT: B 138 TRP cc_start: 0.8223 (m-90) cc_final: 0.7980 (m-90) REVERT: B 150 GLU cc_start: 0.7287 (tp30) cc_final: 0.6730 (mt-10) REVERT: B 174 LYS cc_start: 0.8280 (mtpt) cc_final: 0.7188 (mmtt) REVERT: B 222 TYR cc_start: 0.8406 (t80) cc_final: 0.8096 (t80) REVERT: B 263 ARG cc_start: 0.7984 (mmt90) cc_final: 0.7495 (mmt-90) REVERT: B 300 PHE cc_start: 0.7978 (m-10) cc_final: 0.7651 (t80) REVERT: B 420 MET cc_start: 0.7015 (ttt) cc_final: 0.6210 (tpp) REVERT: B 487 ASP cc_start: 0.8263 (t70) cc_final: 0.7568 (t0) REVERT: C 138 TRP cc_start: 0.8073 (m-90) cc_final: 0.7714 (m-90) REVERT: C 174 LYS cc_start: 0.8161 (mtpt) cc_final: 0.7321 (mmtt) REVERT: C 263 ARG cc_start: 0.8174 (mmt90) cc_final: 0.7614 (mmt-90) REVERT: C 388 MET cc_start: 0.6772 (pmt) cc_final: 0.5911 (pmt) REVERT: C 415 GLN cc_start: 0.8070 (pt0) cc_final: 0.7753 (pm20) REVERT: C 417 TYR cc_start: 0.7752 (m-80) cc_final: 0.7205 (m-10) REVERT: C 420 MET cc_start: 0.6967 (ttt) cc_final: 0.6295 (tpp) REVERT: D 138 TRP cc_start: 0.8164 (m-90) cc_final: 0.7803 (m-90) REVERT: D 150 GLU cc_start: 0.7586 (tp30) cc_final: 0.6991 (mt-10) REVERT: D 235 TYR cc_start: 0.7310 (t80) cc_final: 0.6835 (t80) REVERT: D 417 TYR cc_start: 0.7895 (m-10) cc_final: 0.7171 (m-10) REVERT: D 420 MET cc_start: 0.7145 (ttt) cc_final: 0.6452 (tpp) REVERT: D 469 GLU cc_start: 0.7580 (tt0) cc_final: 0.7010 (tt0) REVERT: E 138 TRP cc_start: 0.8138 (m-90) cc_final: 0.7867 (m-90) REVERT: E 174 LYS cc_start: 0.8282 (mtpt) cc_final: 0.7193 (mmtt) REVERT: E 222 TYR cc_start: 0.8206 (t80) cc_final: 0.7876 (t80) REVERT: E 263 ARG cc_start: 0.8029 (mmt90) cc_final: 0.7527 (mmt-90) REVERT: E 334 ARG cc_start: 0.6772 (mtp180) cc_final: 0.6317 (tmt170) REVERT: E 420 MET cc_start: 0.6911 (ttt) cc_final: 0.6116 (tpp) REVERT: E 442 GLU cc_start: 0.7386 (tm-30) cc_final: 0.6938 (tp30) REVERT: E 456 ASP cc_start: 0.8659 (t0) cc_final: 0.8401 (p0) REVERT: E 487 ASP cc_start: 0.8375 (t0) cc_final: 0.7739 (t0) REVERT: F 174 LYS cc_start: 0.8165 (mtpt) cc_final: 0.7237 (mmtt) REVERT: F 263 ARG cc_start: 0.8153 (mmt90) cc_final: 0.7598 (mmt-90) REVERT: F 334 ARG cc_start: 0.6901 (tmt170) cc_final: 0.6583 (ttt-90) REVERT: F 388 MET cc_start: 0.6749 (pmt) cc_final: 0.5889 (pmt) REVERT: F 415 GLN cc_start: 0.8011 (pt0) cc_final: 0.7716 (pm20) REVERT: F 417 TYR cc_start: 0.7776 (m-10) cc_final: 0.7178 (m-10) REVERT: F 420 MET cc_start: 0.7094 (ttt) cc_final: 0.6411 (tpp) REVERT: F 443 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7936 (tpt-90) outliers start: 36 outliers final: 34 residues processed: 305 average time/residue: 0.9802 time to fit residues: 362.4574 Evaluate side-chains 313 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 277 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 443 ARG Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 372 ILE Chi-restraints excluded: chain F residue 443 ARG Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 487 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 133 optimal weight: 0.0570 chunk 179 optimal weight: 3.9990 chunk 205 optimal weight: 0.7980 chunk 38 optimal weight: 20.0000 chunk 121 optimal weight: 0.5980 chunk 105 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 209 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.166761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.110779 restraints weight = 22329.669| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.63 r_work: 0.3268 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19962 Z= 0.116 Angle : 0.554 8.235 27048 Z= 0.280 Chirality : 0.038 0.165 3078 Planarity : 0.004 0.052 3318 Dihedral : 6.738 58.925 3552 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.83 % Allowed : 22.06 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.18), residues: 2304 helix: 2.42 (0.14), residues: 1452 sheet: 0.76 (0.40), residues: 192 loop : -0.52 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 458 HIS 0.010 0.000 HIS F 234 PHE 0.035 0.002 PHE C 196 TYR 0.019 0.001 TYR D 222 ARG 0.005 0.000 ARG A 360 Details of bonding type rmsd hydrogen bonds : bond 0.03301 ( 1195) hydrogen bonds : angle 3.61315 ( 3465) covalent geometry : bond 0.00266 (19962) covalent geometry : angle 0.55375 (27048) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12503.07 seconds wall clock time: 213 minutes 35.09 seconds (12815.09 seconds total)