Starting phenix.real_space_refine on Sun Aug 24 11:48:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zxd_60540/08_2025/8zxd_60540.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zxd_60540/08_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_60540/08_2025/8zxd_60540.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zxd_60540/08_2025/8zxd_60540.map" model { file = "/net/cci-nas-00/data/ceres_data/8zxd_60540/08_2025/8zxd_60540.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zxd_60540/08_2025/8zxd_60540.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.99, per 1000 atoms: 0.26 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: 1.80 Conformation dependent library (CDL) restraints added in 831.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.67 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: 3.60 Time building geometry restraints manager: 2.35 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 106 through 701) selection = (chain 'B' and resid 106 through 701) selection = (chain 'C' and resid 106 through 601) selection = (chain 'D' and resid 106 through 701) selection = (chain 'E' and resid 106 through 701) selection = (chain 'F' and resid 106 through 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.300 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 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:6.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.290 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.001 0.000 ARG F 391 TYR 0.014 0.001 TYR C 200 PHE 0.013 0.001 PHE A 481 TRP 0.006 0.001 TRP D 168 HIS 0.001 0.000 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00153 (19962) covalent geometry : angle 0.40659 (27048) hydrogen bonds : bond 0.12688 ( 1195) hydrogen bonds : angle 4.96929 ( 3465) *********************** 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 : 0.843 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: 0.6167 time to fit residues: 342.3119 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 : 0.749 ------------------------------------------------------------------------------- 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 216 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN A 305 HIS B 221 GLN B 293 ASN B 305 HIS C 293 ASN C 305 HIS D 293 ASN D 305 HIS D 395 GLN E 293 ASN E 418 HIS F 221 GLN F 293 ASN F 305 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.170997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.115161 restraints weight = 22269.857| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.68 r_work: 0.3326 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19962 Z= 0.174 Angle : 0.590 7.905 27048 Z= 0.300 Chirality : 0.040 0.139 3078 Planarity : 0.004 0.039 3318 Dihedral : 6.871 51.010 3566 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.52 % Allowed : 11.97 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.51 (0.18), residues: 2304 helix: 2.60 (0.14), residues: 1452 sheet: 1.00 (0.41), residues: 192 loop : -0.30 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 360 TYR 0.017 0.002 TYR A 453 PHE 0.021 0.002 PHE E 194 TRP 0.017 0.002 TRP B 458 HIS 0.008 0.001 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00416 (19962) covalent geometry : angle 0.58966 (27048) hydrogen bonds : bond 0.03874 ( 1195) hydrogen bonds : angle 3.84070 ( 3465) *********************** 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 417 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 366 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 131 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8306 (tp) REVERT: A 150 GLU cc_start: 0.7258 (tp30) cc_final: 0.6889 (mp0) REVERT: A 174 LYS cc_start: 0.7858 (mtpt) cc_final: 0.6821 (mmtt) REVERT: A 222 TYR cc_start: 0.8445 (t80) cc_final: 0.8177 (t80) REVERT: A 417 TYR cc_start: 0.7651 (m-10) cc_final: 0.7151 (m-10) REVERT: A 420 MET cc_start: 0.6546 (ttt) cc_final: 0.6011 (tpp) REVERT: A 435 MET cc_start: 0.8792 (mtp) cc_final: 0.8493 (mmm) REVERT: A 438 LYS cc_start: 0.7229 (mtmm) cc_final: 0.6971 (mttp) REVERT: A 469 GLU cc_start: 0.7704 (tt0) cc_final: 0.7205 (tt0) REVERT: B 131 ILE cc_start: 0.8311 (tp) cc_final: 0.8028 (tp) REVERT: B 150 GLU cc_start: 0.7299 (tp30) cc_final: 0.6919 (mp0) REVERT: B 174 LYS cc_start: 0.7962 (mtpt) cc_final: 0.6940 (mmtt) REVERT: B 263 ARG cc_start: 0.8024 (mmt90) cc_final: 0.7561 (mmt-90) REVERT: B 417 TYR cc_start: 0.7671 (m-80) cc_final: 0.7386 (m-10) REVERT: B 487 ASP cc_start: 0.8302 (t70) cc_final: 0.7868 (t0) REVERT: B 496 LYS cc_start: 0.8008 (tptm) cc_final: 0.7544 (tttt) REVERT: C 174 LYS cc_start: 0.7868 (mtpt) cc_final: 0.7043 (mmtt) REVERT: C 263 ARG cc_start: 0.8084 (mmt90) cc_final: 0.7582 (mmt-90) REVERT: C 417 TYR cc_start: 0.7490 (m-80) cc_final: 0.6899 (m-10) REVERT: C 456 ASP cc_start: 0.8701 (t0) cc_final: 0.8456 (p0) REVERT: C 496 LYS cc_start: 0.7825 (tptm) cc_final: 0.7449 (tptt) REVERT: D 150 GLU cc_start: 0.7242 (tp30) cc_final: 0.7002 (mp0) REVERT: D 174 LYS cc_start: 0.7800 (mtpt) cc_final: 0.6812 (mmtt) REVERT: D 388 MET cc_start: 0.6607 (pmt) cc_final: 0.6247 (pmt) REVERT: D 417 TYR cc_start: 0.7587 (m-10) cc_final: 0.7135 (m-10) REVERT: D 420 MET cc_start: 0.6784 (ttt) cc_final: 0.6145 (tpp) REVERT: D 438 LYS cc_start: 0.7258 (mtmm) cc_final: 0.6989 (mttp) REVERT: D 469 GLU cc_start: 0.7722 (tt0) cc_final: 0.7193 (tt0) REVERT: E 150 GLU cc_start: 0.7061 (tp30) cc_final: 0.6797 (mp0) REVERT: E 174 LYS cc_start: 0.7907 (mtpt) cc_final: 0.6904 (mmtt) REVERT: E 249 MET cc_start: 0.8616 (tpp) cc_final: 0.8218 (mmt) REVERT: E 263 ARG cc_start: 0.8029 (mmt90) cc_final: 0.7563 (mmt-90) REVERT: E 295 LEU cc_start: 0.6491 (mt) cc_final: 0.6274 (mm) REVERT: E 417 TYR cc_start: 0.7660 (m-10) cc_final: 0.7365 (m-10) REVERT: E 487 ASP cc_start: 0.8253 (t70) cc_final: 0.7803 (t0) REVERT: E 496 LYS cc_start: 0.7981 (tptm) cc_final: 0.7510 (tttt) REVERT: F 150 GLU cc_start: 0.7354 (tp30) cc_final: 0.7132 (mp0) REVERT: F 174 LYS cc_start: 0.7946 (mtpt) cc_final: 0.7090 (mmpt) REVERT: F 263 ARG cc_start: 0.8080 (mmt90) cc_final: 0.7585 (mmt-90) REVERT: F 334 ARG cc_start: 0.6697 (tmt170) cc_final: 0.6430 (mtp180) REVERT: F 417 TYR cc_start: 0.7526 (m-10) cc_final: 0.7153 (m-10) REVERT: F 456 ASP cc_start: 0.8703 (t0) cc_final: 0.8448 (p0) REVERT: F 487 ASP cc_start: 0.8164 (t70) cc_final: 0.7616 (t0) REVERT: F 496 LYS cc_start: 0.7821 (tptm) cc_final: 0.7465 (tptt) outliers start: 51 outliers final: 20 residues processed: 386 average time/residue: 0.5438 time to fit residues: 240.3130 Evaluate side-chains 305 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 284 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 150 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 206 optimal weight: 1.9990 chunk 114 optimal weight: 20.0000 chunk 167 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 B 416 ASN C 305 HIS ** D 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 GLN F 305 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.166245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.109858 restraints weight = 22406.502| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.65 r_work: 0.3267 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19962 Z= 0.167 Angle : 0.555 6.807 27048 Z= 0.283 Chirality : 0.039 0.141 3078 Planarity : 0.004 0.043 3318 Dihedral : 6.768 49.273 3556 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.02 % Allowed : 14.99 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.18), residues: 2304 helix: 2.57 (0.14), residues: 1428 sheet: 0.82 (0.40), residues: 192 loop : -0.27 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 360 TYR 0.013 0.002 TYR B 222 PHE 0.024 0.002 PHE A 194 TRP 0.020 0.002 TRP E 458 HIS 0.007 0.001 HIS B 305 Details of bonding type rmsd covalent geometry : bond 0.00408 (19962) covalent geometry : angle 0.55519 (27048) hydrogen bonds : bond 0.03865 ( 1195) hydrogen bonds : angle 3.71503 ( 3465) *********************** 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 380 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 319 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8337 (tp) REVERT: A 150 GLU cc_start: 0.7388 (tp30) cc_final: 0.6954 (mt-10) REVERT: A 174 LYS cc_start: 0.7915 (mtpt) cc_final: 0.6986 (mmtt) REVERT: A 235 TYR cc_start: 0.7292 (t80) cc_final: 0.6605 (t80) REVERT: A 417 TYR cc_start: 0.7711 (m-10) cc_final: 0.7055 (m-10) REVERT: A 420 MET cc_start: 0.6874 (ttt) cc_final: 0.6321 (tpp) REVERT: A 438 LYS cc_start: 0.7475 (mtmm) cc_final: 0.7168 (mtmm) REVERT: A 469 GLU cc_start: 0.7709 (tt0) cc_final: 0.7151 (tt0) REVERT: A 487 ASP cc_start: 0.8174 (t70) cc_final: 0.7411 (t0) REVERT: B 138 TRP cc_start: 0.7824 (m-90) cc_final: 0.7607 (m-90) REVERT: B 150 GLU cc_start: 0.7660 (tp30) cc_final: 0.7065 (mp0) REVERT: B 174 LYS cc_start: 0.8085 (mtpt) cc_final: 0.7011 (mmtt) REVERT: B 235 TYR cc_start: 0.7535 (t80) cc_final: 0.7307 (t80) REVERT: B 263 ARG cc_start: 0.8022 (mmt90) cc_final: 0.7551 (mmt-90) REVERT: B 401 MET cc_start: 0.8243 (ptt) cc_final: 0.7840 (ptt) REVERT: B 417 TYR cc_start: 0.7892 (m-80) cc_final: 0.7255 (m-80) REVERT: B 420 MET cc_start: 0.6839 (ttt) cc_final: 0.5965 (tpp) REVERT: B 487 ASP cc_start: 0.8241 (t70) cc_final: 0.7599 (t0) REVERT: B 496 LYS cc_start: 0.7965 (tptm) cc_final: 0.7611 (tttt) REVERT: C 138 TRP cc_start: 0.7669 (m-90) cc_final: 0.7286 (m-90) REVERT: C 174 LYS cc_start: 0.8049 (mtpt) cc_final: 0.7178 (mmpt) REVERT: C 263 ARG cc_start: 0.8176 (mmt90) cc_final: 0.7617 (mmt-90) REVERT: C 388 MET cc_start: 0.6827 (pmt) cc_final: 0.5959 (pmt) REVERT: C 410 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6882 (ttp-170) REVERT: C 417 TYR cc_start: 0.7677 (m-80) cc_final: 0.7074 (m-10) REVERT: D 150 GLU cc_start: 0.7748 (tp30) cc_final: 0.7281 (mp0) REVERT: D 174 LYS cc_start: 0.7902 (mtpt) cc_final: 0.6987 (mmtt) REVERT: D 235 TYR cc_start: 0.7369 (t80) cc_final: 0.6634 (t80) REVERT: D 299 LYS cc_start: 0.7164 (OUTLIER) cc_final: 0.6953 (mppt) REVERT: D 388 MET cc_start: 0.6507 (pmt) cc_final: 0.6237 (pmt) REVERT: D 417 TYR cc_start: 0.7550 (m-10) cc_final: 0.6993 (m-10) REVERT: D 420 MET cc_start: 0.7094 (ttt) cc_final: 0.6365 (tpp) REVERT: D 438 LYS cc_start: 0.7419 (mtmm) cc_final: 0.7101 (mtmm) REVERT: D 469 GLU cc_start: 0.7707 (tt0) cc_final: 0.7149 (tt0) REVERT: D 487 ASP cc_start: 0.8158 (t70) cc_final: 0.7389 (t0) REVERT: E 138 TRP cc_start: 0.7729 (m-90) cc_final: 0.7392 (m-90) REVERT: E 150 GLU cc_start: 0.7068 (tp30) cc_final: 0.6715 (mp0) REVERT: E 174 LYS cc_start: 0.8086 (mtpt) cc_final: 0.6945 (mmtt) REVERT: E 222 TYR cc_start: 0.8335 (t80) cc_final: 0.8018 (t80) REVERT: E 235 TYR cc_start: 0.7603 (t80) cc_final: 0.7382 (t80) REVERT: E 263 ARG cc_start: 0.8028 (mmt90) cc_final: 0.7551 (mmt-90) REVERT: E 417 TYR cc_start: 0.7807 (m-10) cc_final: 0.7357 (m-80) REVERT: E 420 MET cc_start: 0.6821 (OUTLIER) cc_final: 0.6064 (tpp) REVERT: E 487 ASP cc_start: 0.8266 (t70) cc_final: 0.7575 (t0) REVERT: E 496 LYS cc_start: 0.7983 (tptm) cc_final: 0.7608 (tttt) REVERT: F 138 TRP cc_start: 0.7705 (m-90) cc_final: 0.7303 (m-90) REVERT: F 150 GLU cc_start: 0.7593 (tp30) cc_final: 0.7158 (mp0) REVERT: F 174 LYS cc_start: 0.8143 (mtpt) cc_final: 0.7173 (mmpt) REVERT: F 263 ARG cc_start: 0.8173 (mmt90) cc_final: 0.7619 (mmt-90) REVERT: F 334 ARG cc_start: 0.6890 (tmt170) cc_final: 0.6607 (mtp180) REVERT: F 388 MET cc_start: 0.6751 (pmt) cc_final: 0.5885 (pmt) REVERT: F 410 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6893 (ttp-170) REVERT: F 417 TYR cc_start: 0.7711 (m-10) cc_final: 0.7268 (m-80) REVERT: F 456 ASP cc_start: 0.8641 (t0) cc_final: 0.8423 (p0) outliers start: 61 outliers final: 29 residues processed: 349 average time/residue: 0.5117 time to fit residues: 207.1863 Evaluate side-chains 317 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 283 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 249 MET Chi-restraints excluded: chain A residue 372 ILE 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 113 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 410 ARG Chi-restraints excluded: chain C residue 435 MET 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 249 MET Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 299 LYS 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 420 MET Chi-restraints excluded: chain E residue 471 VAL 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 435 MET 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 37 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 86 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 chunk 160 optimal weight: 0.7980 chunk 73 optimal weight: 0.1980 chunk 4 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN A 305 HIS B 221 GLN B 305 HIS B 473 ASN C 221 GLN C 473 ASN D 221 GLN E 305 HIS F 221 GLN F 473 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.166906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.111161 restraints weight = 22262.066| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.61 r_work: 0.3271 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.4158 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= 0.127 Angle : 0.525 7.843 27048 Z= 0.265 Chirality : 0.038 0.130 3078 Planarity : 0.004 0.045 3318 Dihedral : 6.511 46.852 3552 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.62 % Allowed : 16.86 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.18), residues: 2304 helix: 2.63 (0.14), residues: 1428 sheet: 0.69 (0.39), residues: 192 loop : -0.29 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 360 TYR 0.015 0.001 TYR B 222 PHE 0.029 0.001 PHE E 196 TRP 0.018 0.002 TRP E 458 HIS 0.006 0.001 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00298 (19962) covalent geometry : angle 0.52518 (27048) hydrogen bonds : bond 0.03441 ( 1195) hydrogen bonds : angle 3.61368 ( 3465) *********************** 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 358 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 305 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ILE cc_start: 0.8526 (mm) cc_final: 0.8239 (tp) REVERT: A 150 GLU cc_start: 0.7623 (tp30) cc_final: 0.7071 (mt-10) REVERT: A 174 LYS cc_start: 0.8032 (mtpt) cc_final: 0.6977 (mmtt) REVERT: A 235 TYR cc_start: 0.7228 (t80) cc_final: 0.6762 (t80) REVERT: A 417 TYR cc_start: 0.7740 (m-10) cc_final: 0.7114 (m-10) REVERT: A 420 MET cc_start: 0.6903 (ttt) cc_final: 0.6351 (tpp) REVERT: A 438 LYS cc_start: 0.7578 (mtmm) cc_final: 0.7295 (mtmm) REVERT: A 469 GLU cc_start: 0.7622 (tt0) cc_final: 0.7047 (tt0) REVERT: A 487 ASP cc_start: 0.8195 (t70) cc_final: 0.7924 (t70) REVERT: B 150 GLU cc_start: 0.7299 (tp30) cc_final: 0.6933 (mp0) REVERT: B 174 LYS cc_start: 0.8121 (mtpt) cc_final: 0.7066 (mmtt) REVERT: B 222 TYR cc_start: 0.8331 (t80) cc_final: 0.8091 (t80) REVERT: B 263 ARG cc_start: 0.8038 (mmt90) cc_final: 0.7555 (mmt-90) REVERT: B 401 MET cc_start: 0.8246 (ptt) cc_final: 0.7823 (ptt) REVERT: B 420 MET cc_start: 0.6805 (ttt) cc_final: 0.5958 (tpp) REVERT: B 487 ASP cc_start: 0.8267 (t70) cc_final: 0.7590 (t0) REVERT: B 496 LYS cc_start: 0.8036 (tptm) cc_final: 0.7678 (tttt) REVERT: C 174 LYS cc_start: 0.8019 (mtpt) cc_final: 0.7107 (mmpt) REVERT: C 263 ARG cc_start: 0.8159 (mmt90) cc_final: 0.7629 (mmt-90) REVERT: C 388 MET cc_start: 0.6813 (pmt) cc_final: 0.5948 (pmt) REVERT: C 417 TYR cc_start: 0.7761 (m-80) cc_final: 0.7169 (m-10) REVERT: C 443 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7874 (tpt170) REVERT: D 150 GLU cc_start: 0.7594 (tp30) cc_final: 0.7180 (mp0) REVERT: D 174 LYS cc_start: 0.8035 (mtpt) cc_final: 0.6970 (mmtt) REVERT: D 235 TYR cc_start: 0.7213 (t80) cc_final: 0.6706 (t80) REVERT: D 388 MET cc_start: 0.6491 (pmt) cc_final: 0.6243 (pmt) REVERT: D 417 TYR cc_start: 0.7671 (m-10) cc_final: 0.6944 (m-10) REVERT: D 420 MET cc_start: 0.7055 (ttt) cc_final: 0.6343 (tpp) REVERT: D 438 LYS cc_start: 0.7577 (mtmm) cc_final: 0.7291 (mtmm) REVERT: D 469 GLU cc_start: 0.7630 (tt0) cc_final: 0.7077 (tt0) REVERT: D 487 ASP cc_start: 0.8130 (t70) cc_final: 0.7878 (t70) REVERT: E 138 TRP cc_start: 0.7795 (m-90) cc_final: 0.7511 (m-90) REVERT: E 150 GLU cc_start: 0.6964 (tp30) cc_final: 0.6703 (mp0) REVERT: E 174 LYS cc_start: 0.8131 (mtpt) cc_final: 0.7061 (mmtt) REVERT: E 222 TYR cc_start: 0.8191 (t80) cc_final: 0.7802 (t80) REVERT: E 263 ARG cc_start: 0.8043 (mmt90) cc_final: 0.7561 (mmt-90) REVERT: E 417 TYR cc_start: 0.7818 (m-10) cc_final: 0.7366 (m-80) REVERT: E 420 MET cc_start: 0.6769 (OUTLIER) cc_final: 0.6024 (tpp) REVERT: E 442 GLU cc_start: 0.7481 (pp20) cc_final: 0.6846 (tp30) REVERT: E 487 ASP cc_start: 0.8236 (t70) cc_final: 0.7524 (t0) REVERT: E 496 LYS cc_start: 0.7974 (tptm) cc_final: 0.7512 (tttt) REVERT: F 138 TRP cc_start: 0.7671 (m-90) cc_final: 0.7403 (m-90) REVERT: F 150 GLU cc_start: 0.7466 (tp30) cc_final: 0.7095 (mp0) REVERT: F 174 LYS cc_start: 0.8027 (mtpt) cc_final: 0.7112 (mmpt) REVERT: F 263 ARG cc_start: 0.8166 (mmt90) cc_final: 0.7491 (mmt-90) REVERT: F 334 ARG cc_start: 0.6874 (tmt170) cc_final: 0.6592 (mtp180) REVERT: F 388 MET cc_start: 0.6746 (pmt) cc_final: 0.5892 (pmt) REVERT: F 410 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6920 (ttp-170) REVERT: F 417 TYR cc_start: 0.7673 (m-10) cc_final: 0.7135 (m-10) REVERT: F 443 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7858 (tpt170) outliers start: 53 outliers final: 29 residues processed: 335 average time/residue: 0.5302 time to fit residues: 204.4452 Evaluate side-chains 314 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 281 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 156 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 B residue 471 VAL Chi-restraints excluded: chain C residue 113 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 435 MET 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 200 TYR 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 355 LYS Chi-restraints excluded: chain E residue 420 MET 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 435 MET 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 36 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 221 optimal weight: 0.0970 chunk 192 optimal weight: 8.9990 chunk 175 optimal weight: 0.5980 chunk 166 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 GLN C 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.166505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.110647 restraints weight = 22183.519| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.61 r_work: 0.3267 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.4341 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= 0.125 Angle : 0.530 8.782 27048 Z= 0.266 Chirality : 0.038 0.130 3078 Planarity : 0.004 0.050 3318 Dihedral : 6.496 45.430 3552 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.12 % Allowed : 17.36 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.17), residues: 2304 helix: 2.59 (0.13), residues: 1446 sheet: 0.68 (0.39), residues: 192 loop : -0.35 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 476 TYR 0.023 0.001 TYR B 222 PHE 0.035 0.002 PHE C 196 TRP 0.017 0.002 TRP B 458 HIS 0.005 0.000 HIS D 305 Details of bonding type rmsd covalent geometry : bond 0.00294 (19962) covalent geometry : angle 0.52986 (27048) hydrogen bonds : bond 0.03376 ( 1195) hydrogen bonds : angle 3.58124 ( 3465) *********************** 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 362 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 299 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 PHE cc_start: 0.8393 (m-10) cc_final: 0.8106 (m-80) REVERT: A 131 ILE cc_start: 0.8517 (mm) cc_final: 0.8213 (tp) REVERT: A 150 GLU cc_start: 0.7574 (tp30) cc_final: 0.7018 (mt-10) REVERT: A 174 LYS cc_start: 0.8042 (mtpt) cc_final: 0.6967 (mmtt) REVERT: A 235 TYR cc_start: 0.7218 (t80) cc_final: 0.6816 (t80) REVERT: A 417 TYR cc_start: 0.7722 (m-10) cc_final: 0.7069 (m-10) REVERT: A 420 MET cc_start: 0.6894 (ttt) cc_final: 0.6326 (tpp) REVERT: A 438 LYS cc_start: 0.7574 (mtmm) cc_final: 0.7262 (mtmm) REVERT: A 469 GLU cc_start: 0.7632 (tt0) cc_final: 0.7044 (tt0) REVERT: A 487 ASP cc_start: 0.8201 (t70) cc_final: 0.7995 (t70) REVERT: B 130 PHE cc_start: 0.8232 (m-80) cc_final: 0.7793 (m-80) REVERT: B 150 GLU cc_start: 0.7260 (tp30) cc_final: 0.6852 (mp0) REVERT: B 174 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7150 (mmtt) REVERT: B 222 TYR cc_start: 0.8331 (t80) cc_final: 0.7757 (t80) REVERT: B 263 ARG cc_start: 0.8032 (mmt90) cc_final: 0.7551 (mmt-90) REVERT: B 401 MET cc_start: 0.8267 (ptt) cc_final: 0.7807 (ptt) REVERT: B 420 MET cc_start: 0.6814 (ttt) cc_final: 0.6023 (tpp) REVERT: B 442 GLU cc_start: 0.7380 (tm-30) cc_final: 0.6899 (tp30) REVERT: B 487 ASP cc_start: 0.8258 (t70) cc_final: 0.7539 (t0) REVERT: B 496 LYS cc_start: 0.7947 (tptm) cc_final: 0.7502 (tptt) REVERT: C 138 TRP cc_start: 0.7707 (m-90) cc_final: 0.7319 (m-90) REVERT: C 174 LYS cc_start: 0.8044 (mtpt) cc_final: 0.7137 (mmpt) REVERT: C 263 ARG cc_start: 0.8068 (mmt90) cc_final: 0.7367 (mmt-90) REVERT: C 388 MET cc_start: 0.6833 (pmt) cc_final: 0.5964 (pmt) REVERT: C 410 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6930 (ttp-170) REVERT: C 417 TYR cc_start: 0.7775 (m-80) cc_final: 0.7214 (m-10) REVERT: D 131 ILE cc_start: 0.8281 (mm) cc_final: 0.7961 (tp) REVERT: D 150 GLU cc_start: 0.7705 (tp30) cc_final: 0.7185 (mt-10) REVERT: D 174 LYS cc_start: 0.8053 (mtpt) cc_final: 0.6966 (mmtt) REVERT: D 226 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8526 (tp) REVERT: D 235 TYR cc_start: 0.7382 (t80) cc_final: 0.6860 (t80) REVERT: D 388 MET cc_start: 0.6509 (pmt) cc_final: 0.6251 (pmt) REVERT: D 417 TYR cc_start: 0.7736 (m-10) cc_final: 0.6996 (m-10) REVERT: D 420 MET cc_start: 0.7052 (ttt) cc_final: 0.6375 (tpp) REVERT: D 438 LYS cc_start: 0.7568 (mtmm) cc_final: 0.7250 (mtmm) REVERT: D 469 GLU cc_start: 0.7636 (tt0) cc_final: 0.7053 (tt0) REVERT: D 487 ASP cc_start: 0.8172 (t70) cc_final: 0.7960 (t70) REVERT: E 138 TRP cc_start: 0.7823 (m-90) cc_final: 0.7549 (m-90) REVERT: E 150 GLU cc_start: 0.7316 (tp30) cc_final: 0.6885 (mp0) REVERT: E 174 LYS cc_start: 0.8200 (mtpt) cc_final: 0.7155 (mmtt) REVERT: E 222 TYR cc_start: 0.8185 (t80) cc_final: 0.7760 (t80) REVERT: E 263 ARG cc_start: 0.8036 (mmt90) cc_final: 0.7557 (mmt-90) REVERT: E 417 TYR cc_start: 0.7832 (m-10) cc_final: 0.7351 (m-80) REVERT: E 420 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.6037 (tpp) REVERT: E 442 GLU cc_start: 0.7461 (pp20) cc_final: 0.6853 (tp30) REVERT: E 487 ASP cc_start: 0.8237 (t70) cc_final: 0.7538 (t0) REVERT: E 496 LYS cc_start: 0.7855 (tptm) cc_final: 0.7389 (tptt) REVERT: F 174 LYS cc_start: 0.8045 (mtpt) cc_final: 0.7136 (mmpt) REVERT: F 263 ARG cc_start: 0.8160 (mmt90) cc_final: 0.7624 (mmt-90) REVERT: F 334 ARG cc_start: 0.6887 (tmt170) cc_final: 0.6601 (mtp180) REVERT: F 388 MET cc_start: 0.6746 (pmt) cc_final: 0.5892 (pmt) REVERT: F 410 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6931 (ttp-170) REVERT: F 417 TYR cc_start: 0.7697 (m-10) cc_final: 0.7182 (m-10) REVERT: F 443 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7867 (tpt170) outliers start: 63 outliers final: 33 residues processed: 331 average time/residue: 0.4911 time to fit residues: 189.4955 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 : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 249 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 193 ILE Chi-restraints excluded: chain B residue 281 GLU 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 372 ILE Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 410 ARG Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 249 MET 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 281 GLU Chi-restraints excluded: chain E residue 355 LYS Chi-restraints excluded: chain E residue 420 MET 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 372 ILE Chi-restraints excluded: chain F residue 397 ILE Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain F residue 435 MET 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 19 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 193 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 158 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 473 ASN F 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.164689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.108632 restraints weight = 22118.394| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.60 r_work: 0.3244 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 19962 Z= 0.152 Angle : 0.544 6.872 27048 Z= 0.275 Chirality : 0.039 0.132 3078 Planarity : 0.004 0.049 3318 Dihedral : 6.678 48.042 3552 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.87 % Allowed : 18.30 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.17), residues: 2304 helix: 2.52 (0.13), residues: 1452 sheet: 0.66 (0.34), residues: 234 loop : -0.58 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 476 TYR 0.020 0.001 TYR B 222 PHE 0.031 0.002 PHE E 196 TRP 0.018 0.002 TRP D 458 HIS 0.005 0.000 HIS D 305 Details of bonding type rmsd covalent geometry : bond 0.00367 (19962) covalent geometry : angle 0.54381 (27048) hydrogen bonds : bond 0.03686 ( 1195) hydrogen bonds : angle 3.65779 ( 3465) *********************** 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 361 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 303 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ILE cc_start: 0.8574 (mm) cc_final: 0.8348 (tp) REVERT: A 150 GLU cc_start: 0.7535 (tp30) cc_final: 0.7051 (mt-10) REVERT: A 235 TYR cc_start: 0.7347 (t80) cc_final: 0.6882 (t80) REVERT: A 417 TYR cc_start: 0.7712 (m-10) cc_final: 0.7021 (m-10) REVERT: A 420 MET cc_start: 0.6918 (ttt) cc_final: 0.6350 (tpp) REVERT: A 438 LYS cc_start: 0.7591 (mtmm) cc_final: 0.7278 (mtmm) REVERT: A 487 ASP cc_start: 0.8205 (t70) cc_final: 0.7980 (t70) REVERT: B 130 PHE cc_start: 0.8159 (m-80) cc_final: 0.7774 (m-80) REVERT: B 150 GLU cc_start: 0.7272 (tp30) cc_final: 0.6831 (mp0) REVERT: B 174 LYS cc_start: 0.8278 (mtpt) cc_final: 0.7218 (mmtt) REVERT: B 222 TYR cc_start: 0.8356 (t80) cc_final: 0.8085 (t80) REVERT: B 263 ARG cc_start: 0.8006 (mmt90) cc_final: 0.7525 (mmt-90) REVERT: B 401 MET cc_start: 0.8203 (ptt) cc_final: 0.7681 (ptt) REVERT: B 420 MET cc_start: 0.6895 (ttt) cc_final: 0.6064 (tpp) REVERT: B 442 GLU cc_start: 0.7370 (tm-30) cc_final: 0.6928 (tp30) REVERT: B 487 ASP cc_start: 0.8268 (t70) cc_final: 0.7589 (t0) REVERT: C 138 TRP cc_start: 0.7799 (m-90) cc_final: 0.7471 (m-90) REVERT: C 174 LYS cc_start: 0.8094 (mtpt) cc_final: 0.7193 (mmpt) REVERT: C 263 ARG cc_start: 0.8143 (mmt90) cc_final: 0.7577 (mmt-90) REVERT: C 388 MET cc_start: 0.6793 (pmt) cc_final: 0.5960 (pmt) REVERT: C 410 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6881 (ttp-170) REVERT: C 417 TYR cc_start: 0.7779 (m-80) cc_final: 0.7182 (m-10) REVERT: C 420 MET cc_start: 0.6947 (ttt) cc_final: 0.6270 (tpp) REVERT: C 443 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7893 (tpt-90) REVERT: D 131 ILE cc_start: 0.8362 (mm) cc_final: 0.8039 (tp) REVERT: D 150 GLU cc_start: 0.7610 (tp30) cc_final: 0.7067 (mt-10) REVERT: D 235 TYR cc_start: 0.7339 (t80) cc_final: 0.6866 (t80) REVERT: D 417 TYR cc_start: 0.7821 (m-10) cc_final: 0.7124 (m-10) REVERT: D 420 MET cc_start: 0.7070 (ttt) cc_final: 0.6396 (tpp) REVERT: D 438 LYS cc_start: 0.7599 (mtmm) cc_final: 0.7228 (mtmm) REVERT: D 442 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7346 (tp30) REVERT: D 469 GLU cc_start: 0.7640 (tt0) cc_final: 0.7083 (tt0) REVERT: D 487 ASP cc_start: 0.8181 (t70) cc_final: 0.7964 (t70) REVERT: E 138 TRP cc_start: 0.7869 (m-90) cc_final: 0.7554 (m-90) REVERT: E 150 GLU cc_start: 0.7351 (tp30) cc_final: 0.6816 (mt-10) REVERT: E 174 LYS cc_start: 0.8272 (mtpt) cc_final: 0.7219 (mmtt) REVERT: E 222 TYR cc_start: 0.8123 (t80) cc_final: 0.7739 (t80) REVERT: E 263 ARG cc_start: 0.8015 (mmt90) cc_final: 0.7531 (mmt-90) REVERT: E 417 TYR cc_start: 0.7861 (m-10) cc_final: 0.7318 (m-80) REVERT: E 420 MET cc_start: 0.6785 (OUTLIER) cc_final: 0.6043 (tpp) REVERT: E 442 GLU cc_start: 0.7466 (pp20) cc_final: 0.6956 (tp30) REVERT: E 456 ASP cc_start: 0.8661 (t0) cc_final: 0.8407 (p0) REVERT: E 487 ASP cc_start: 0.8254 (t70) cc_final: 0.7551 (t0) REVERT: F 138 TRP cc_start: 0.7868 (m-90) cc_final: 0.7459 (m-90) REVERT: F 174 LYS cc_start: 0.8091 (mtpt) cc_final: 0.7191 (mmpt) REVERT: F 263 ARG cc_start: 0.8151 (mmt90) cc_final: 0.7594 (mmt-90) REVERT: F 334 ARG cc_start: 0.6918 (tmt170) cc_final: 0.6611 (mtp180) REVERT: F 388 MET cc_start: 0.6823 (pmt) cc_final: 0.5960 (pmt) REVERT: F 410 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6897 (ttp-170) REVERT: F 417 TYR cc_start: 0.7762 (m-10) cc_final: 0.7241 (m-10) REVERT: F 420 MET cc_start: 0.6964 (ttt) cc_final: 0.6277 (tpp) outliers start: 58 outliers final: 39 residues processed: 334 average time/residue: 0.4794 time to fit residues: 185.9535 Evaluate side-chains 324 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 281 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 281 GLU 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 193 ILE Chi-restraints excluded: chain B residue 281 GLU 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 372 ILE Chi-restraints excluded: chain C residue 410 ARG Chi-restraints excluded: chain C residue 435 MET 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 249 MET Chi-restraints excluded: chain D residue 281 GLU 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 294 LEU Chi-restraints excluded: chain E residue 355 LYS Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 471 VAL 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 372 ILE Chi-restraints excluded: chain F residue 397 ILE Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain F residue 435 MET Chi-restraints excluded: chain F residue 443 ARG Chi-restraints excluded: chain F residue 472 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 147 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 136 optimal weight: 0.0770 chunk 158 optimal weight: 0.9980 chunk 226 optimal weight: 0.6980 chunk 45 optimal weight: 0.1980 chunk 64 optimal weight: 9.9990 chunk 193 optimal weight: 10.0000 chunk 28 optimal weight: 0.5980 chunk 186 optimal weight: 3.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.167542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.111292 restraints weight = 22135.911| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.63 r_work: 0.3278 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.4613 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= 0.110 Angle : 0.523 9.173 27048 Z= 0.262 Chirality : 0.037 0.144 3078 Planarity : 0.004 0.056 3318 Dihedral : 6.501 49.937 3552 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.27 % Allowed : 19.98 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.49 (0.18), residues: 2304 helix: 2.68 (0.14), residues: 1428 sheet: 0.69 (0.34), residues: 234 loop : -0.40 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 476 TYR 0.024 0.001 TYR B 235 PHE 0.033 0.002 PHE C 196 TRP 0.015 0.002 TRP B 458 HIS 0.004 0.000 HIS D 305 Details of bonding type rmsd covalent geometry : bond 0.00250 (19962) covalent geometry : angle 0.52341 (27048) hydrogen bonds : bond 0.03152 ( 1195) hydrogen bonds : angle 3.54685 ( 3465) *********************** 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 356 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 310 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ILE cc_start: 0.8543 (mm) cc_final: 0.8318 (tp) REVERT: A 150 GLU cc_start: 0.7450 (tp30) cc_final: 0.6900 (mt-10) REVERT: A 174 LYS cc_start: 0.8076 (mtpt) cc_final: 0.6965 (mmtt) REVERT: A 222 TYR cc_start: 0.8335 (t80) cc_final: 0.7796 (t80) REVERT: A 235 TYR cc_start: 0.7325 (t80) cc_final: 0.7002 (t80) REVERT: A 417 TYR cc_start: 0.7690 (m-10) cc_final: 0.6992 (m-10) REVERT: A 420 MET cc_start: 0.6957 (ttt) cc_final: 0.6328 (tpp) REVERT: A 438 LYS cc_start: 0.7546 (mtmm) cc_final: 0.7237 (mtmm) REVERT: A 442 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7159 (tp30) REVERT: A 487 ASP cc_start: 0.8130 (t70) cc_final: 0.7884 (t70) REVERT: B 150 GLU cc_start: 0.7250 (tp30) cc_final: 0.6784 (mt-10) REVERT: B 174 LYS cc_start: 0.8244 (mtpt) cc_final: 0.7188 (mmtt) REVERT: B 222 TYR cc_start: 0.8403 (t80) cc_final: 0.7770 (t80) REVERT: B 263 ARG cc_start: 0.8002 (mmt90) cc_final: 0.7504 (mmt-90) REVERT: B 401 MET cc_start: 0.8257 (ptt) cc_final: 0.7720 (ptt) REVERT: B 420 MET cc_start: 0.6854 (ttt) cc_final: 0.6045 (tpp) REVERT: B 442 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6858 (tp30) REVERT: B 487 ASP cc_start: 0.8249 (t70) cc_final: 0.7543 (t0) REVERT: C 138 TRP cc_start: 0.7709 (m-90) cc_final: 0.7464 (m-90) REVERT: C 174 LYS cc_start: 0.8097 (mtpt) cc_final: 0.7213 (mmpt) REVERT: C 263 ARG cc_start: 0.8144 (mmt90) cc_final: 0.7433 (mmt-90) REVERT: C 388 MET cc_start: 0.6817 (pmt) cc_final: 0.5942 (pmt) REVERT: C 410 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.6815 (ttp-170) REVERT: C 417 TYR cc_start: 0.7767 (m-80) cc_final: 0.7240 (m-10) REVERT: C 443 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7884 (tpt-90) REVERT: D 131 ILE cc_start: 0.8396 (mm) cc_final: 0.8134 (tp) REVERT: D 150 GLU cc_start: 0.7588 (tp30) cc_final: 0.7045 (mt-10) REVERT: D 174 LYS cc_start: 0.8074 (mtpt) cc_final: 0.6976 (mmtt) REVERT: D 235 TYR cc_start: 0.7314 (t80) cc_final: 0.6938 (t80) REVERT: D 417 TYR cc_start: 0.7776 (m-10) cc_final: 0.7100 (m-10) REVERT: D 420 MET cc_start: 0.6947 (ttt) cc_final: 0.6321 (tpp) REVERT: D 438 LYS cc_start: 0.7540 (mtmm) cc_final: 0.7231 (mtmm) REVERT: D 442 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7184 (tp30) REVERT: D 469 GLU cc_start: 0.7598 (tt0) cc_final: 0.7011 (tt0) REVERT: D 487 ASP cc_start: 0.8142 (t70) cc_final: 0.7889 (t70) REVERT: E 130 PHE cc_start: 0.8159 (m-80) cc_final: 0.7818 (m-80) REVERT: E 138 TRP cc_start: 0.7868 (m-90) cc_final: 0.7587 (m-90) REVERT: E 150 GLU cc_start: 0.7254 (tp30) cc_final: 0.6804 (mt-10) REVERT: E 174 LYS cc_start: 0.8236 (mtpt) cc_final: 0.7187 (mmtt) REVERT: E 222 TYR cc_start: 0.8243 (t80) cc_final: 0.7865 (t80) REVERT: E 263 ARG cc_start: 0.8019 (mmt90) cc_final: 0.7518 (mmt-90) REVERT: E 417 TYR cc_start: 0.7847 (m-10) cc_final: 0.7380 (m-80) REVERT: E 420 MET cc_start: 0.6725 (OUTLIER) cc_final: 0.6044 (tpp) REVERT: E 442 GLU cc_start: 0.7484 (pp20) cc_final: 0.6943 (tp30) REVERT: E 456 ASP cc_start: 0.8637 (t0) cc_final: 0.8396 (p0) REVERT: E 487 ASP cc_start: 0.8236 (t70) cc_final: 0.7506 (t0) REVERT: F 138 TRP cc_start: 0.7732 (m-90) cc_final: 0.7261 (m-90) REVERT: F 174 LYS cc_start: 0.8088 (mtpt) cc_final: 0.7187 (mmpt) REVERT: F 263 ARG cc_start: 0.8140 (mmt90) cc_final: 0.7436 (mmt-90) REVERT: F 334 ARG cc_start: 0.6862 (tmt170) cc_final: 0.6578 (ttt-90) REVERT: F 388 MET cc_start: 0.6768 (pmt) cc_final: 0.5899 (pmt) REVERT: F 410 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6809 (ttp-170) REVERT: F 417 TYR cc_start: 0.7727 (m-10) cc_final: 0.7226 (m-10) REVERT: F 420 MET cc_start: 0.6953 (ttt) cc_final: 0.6271 (tpp) outliers start: 46 outliers final: 34 residues processed: 325 average time/residue: 0.5017 time to fit residues: 190.4680 Evaluate side-chains 318 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 280 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 249 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 193 ILE Chi-restraints excluded: chain B residue 281 GLU 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 281 GLU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 410 ARG Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 443 ARG Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 249 MET 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 281 GLU Chi-restraints excluded: chain E residue 355 LYS Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 459 LEU 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 410 ARG Chi-restraints excluded: chain F residue 435 MET 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 83 optimal weight: 0.1980 chunk 11 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 154 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 190 optimal weight: 20.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN B 221 GLN ** C 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.165574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.109209 restraints weight = 22200.263| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.61 r_work: 0.3256 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.4768 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= 0.134 Angle : 0.544 7.243 27048 Z= 0.274 Chirality : 0.038 0.131 3078 Planarity : 0.004 0.050 3318 Dihedral : 6.684 53.672 3552 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.57 % Allowed : 20.52 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.18), residues: 2304 helix: 2.56 (0.13), residues: 1446 sheet: 0.68 (0.34), residues: 234 loop : -0.55 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 476 TYR 0.017 0.001 TYR B 222 PHE 0.031 0.001 PHE E 196 TRP 0.016 0.002 TRP E 458 HIS 0.010 0.001 HIS C 234 Details of bonding type rmsd covalent geometry : bond 0.00318 (19962) covalent geometry : angle 0.54387 (27048) hydrogen bonds : bond 0.03451 ( 1195) hydrogen bonds : angle 3.62191 ( 3465) *********************** 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 342 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 290 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ILE cc_start: 0.8568 (mm) cc_final: 0.8290 (tp) REVERT: A 150 GLU cc_start: 0.7637 (tp30) cc_final: 0.7114 (mt-10) REVERT: A 235 TYR cc_start: 0.7381 (t80) cc_final: 0.6886 (t80) REVERT: A 417 TYR cc_start: 0.7770 (m-10) cc_final: 0.7096 (m-10) REVERT: A 420 MET cc_start: 0.6863 (ttt) cc_final: 0.6332 (tpp) REVERT: A 438 LYS cc_start: 0.7594 (mtmm) cc_final: 0.7222 (mtmm) REVERT: A 442 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7196 (tp30) REVERT: A 487 ASP cc_start: 0.8126 (t70) cc_final: 0.7893 (t70) REVERT: B 130 PHE cc_start: 0.8195 (m-80) cc_final: 0.7889 (m-80) REVERT: B 150 GLU cc_start: 0.7256 (tp30) cc_final: 0.6754 (mt-10) REVERT: B 174 LYS cc_start: 0.8288 (mtpt) cc_final: 0.7156 (mmtt) REVERT: B 222 TYR cc_start: 0.8409 (t80) cc_final: 0.7897 (t80) REVERT: B 263 ARG cc_start: 0.7997 (mmt90) cc_final: 0.7507 (mmt-90) REVERT: B 401 MET cc_start: 0.8282 (ptt) cc_final: 0.7665 (ptt) REVERT: B 420 MET cc_start: 0.7010 (ttt) cc_final: 0.6196 (tpp) REVERT: B 442 GLU cc_start: 0.7243 (tm-30) cc_final: 0.6914 (tp30) REVERT: B 487 ASP cc_start: 0.8230 (t70) cc_final: 0.7529 (t0) REVERT: C 174 LYS cc_start: 0.8111 (mtpt) cc_final: 0.7235 (mmtt) REVERT: C 263 ARG cc_start: 0.8146 (mmt90) cc_final: 0.7586 (mmt-90) REVERT: C 388 MET cc_start: 0.6840 (pmt) cc_final: 0.5963 (pmt) REVERT: C 417 TYR cc_start: 0.7809 (m-80) cc_final: 0.7278 (m-10) REVERT: C 420 MET cc_start: 0.6958 (ttt) cc_final: 0.6273 (tpp) REVERT: C 443 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7974 (tpt170) REVERT: D 131 ILE cc_start: 0.8445 (mm) cc_final: 0.8086 (tp) REVERT: D 150 GLU cc_start: 0.7514 (tp30) cc_final: 0.6985 (mt-10) REVERT: D 174 LYS cc_start: 0.8098 (mtpt) cc_final: 0.7006 (mmtt) REVERT: D 235 TYR cc_start: 0.7268 (t80) cc_final: 0.6813 (t80) REVERT: D 417 TYR cc_start: 0.7832 (m-10) cc_final: 0.7142 (m-10) REVERT: D 420 MET cc_start: 0.6969 (ttt) cc_final: 0.6347 (tpp) REVERT: D 438 LYS cc_start: 0.7574 (mtmm) cc_final: 0.7198 (mtmm) REVERT: D 442 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7226 (tp30) REVERT: D 469 GLU cc_start: 0.7619 (tt0) cc_final: 0.7030 (tt0) REVERT: D 487 ASP cc_start: 0.8103 (t70) cc_final: 0.7860 (t70) REVERT: E 130 PHE cc_start: 0.8162 (m-80) cc_final: 0.7879 (m-80) REVERT: E 138 TRP cc_start: 0.7871 (m-90) cc_final: 0.7557 (m-90) REVERT: E 150 GLU cc_start: 0.7291 (tp30) cc_final: 0.6774 (mt-10) REVERT: E 174 LYS cc_start: 0.8302 (mtpt) cc_final: 0.7190 (mmtt) REVERT: E 222 TYR cc_start: 0.8287 (t80) cc_final: 0.7926 (t80) REVERT: E 263 ARG cc_start: 0.7998 (mmt90) cc_final: 0.7506 (mmt-90) REVERT: E 417 TYR cc_start: 0.7843 (m-10) cc_final: 0.7339 (m-80) REVERT: E 420 MET cc_start: 0.6766 (OUTLIER) cc_final: 0.6058 (tpp) REVERT: E 442 GLU cc_start: 0.7434 (pp20) cc_final: 0.6952 (tp30) REVERT: E 456 ASP cc_start: 0.8649 (t0) cc_final: 0.8399 (p0) REVERT: E 487 ASP cc_start: 0.8260 (t70) cc_final: 0.7519 (t0) REVERT: F 138 TRP cc_start: 0.7770 (m-90) cc_final: 0.7316 (m-90) REVERT: F 174 LYS cc_start: 0.8109 (mtpt) cc_final: 0.7234 (mmtt) REVERT: F 263 ARG cc_start: 0.8149 (mmt90) cc_final: 0.7451 (mmt-90) REVERT: F 334 ARG cc_start: 0.6870 (tmt170) cc_final: 0.6546 (ttt-90) REVERT: F 388 MET cc_start: 0.6790 (pmt) cc_final: 0.5920 (pmt) REVERT: F 417 TYR cc_start: 0.7765 (m-10) cc_final: 0.7202 (m-10) REVERT: F 420 MET cc_start: 0.6965 (ttt) cc_final: 0.6284 (tpp) REVERT: F 443 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7843 (tpt-90) outliers start: 52 outliers final: 39 residues processed: 315 average time/residue: 0.4942 time to fit residues: 182.6212 Evaluate side-chains 322 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 280 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 249 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 193 ILE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain C residue 113 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 435 MET 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 249 MET 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 281 GLU Chi-restraints excluded: chain E residue 355 LYS Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 234 HIS 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 435 MET 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 206 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 212 optimal weight: 0.8980 chunk 131 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 190 optimal weight: 20.0000 chunk 169 optimal weight: 0.6980 chunk 173 optimal weight: 4.9990 chunk 76 optimal weight: 20.0000 chunk 105 optimal weight: 0.9990 chunk 174 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 234 HIS F 234 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.165059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.108960 restraints weight = 22050.127| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.59 r_work: 0.3245 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19962 Z= 0.141 Angle : 0.565 9.073 27048 Z= 0.284 Chirality : 0.039 0.174 3078 Planarity : 0.004 0.050 3318 Dihedral : 6.770 56.799 3552 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.57 % Allowed : 20.87 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.17), residues: 2304 helix: 2.54 (0.13), residues: 1446 sheet: 0.68 (0.34), residues: 234 loop : -0.55 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 476 TYR 0.016 0.001 TYR B 222 PHE 0.036 0.002 PHE C 196 TRP 0.017 0.002 TRP B 458 HIS 0.012 0.001 HIS F 234 Details of bonding type rmsd covalent geometry : bond 0.00339 (19962) covalent geometry : angle 0.56453 (27048) hydrogen bonds : bond 0.03502 ( 1195) hydrogen bonds : angle 3.63586 ( 3465) *********************** 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 327 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 275 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 GLU cc_start: 0.7592 (tp30) cc_final: 0.7043 (mt-10) REVERT: A 235 TYR cc_start: 0.7393 (t80) cc_final: 0.6891 (t80) REVERT: A 417 TYR cc_start: 0.7780 (m-10) cc_final: 0.7089 (m-10) REVERT: A 420 MET cc_start: 0.6857 (ttt) cc_final: 0.6328 (tpp) REVERT: A 438 LYS cc_start: 0.7574 (mtmm) cc_final: 0.7201 (mtmm) REVERT: A 442 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7200 (tp30) REVERT: A 487 ASP cc_start: 0.8147 (t70) cc_final: 0.7907 (t70) REVERT: B 130 PHE cc_start: 0.8195 (m-80) cc_final: 0.7888 (m-80) REVERT: B 150 GLU cc_start: 0.7260 (tp30) cc_final: 0.6744 (mt-10) REVERT: B 174 LYS cc_start: 0.8311 (mtpt) cc_final: 0.7203 (mmtt) REVERT: B 222 TYR cc_start: 0.8423 (t80) cc_final: 0.7930 (t80) REVERT: B 263 ARG cc_start: 0.7989 (mmt90) cc_final: 0.7501 (mmt-90) REVERT: B 401 MET cc_start: 0.8238 (ptt) cc_final: 0.7593 (ptt) REVERT: B 420 MET cc_start: 0.7013 (ttt) cc_final: 0.6205 (tpp) REVERT: B 442 GLU cc_start: 0.7306 (tm-30) cc_final: 0.6925 (tp30) REVERT: B 487 ASP cc_start: 0.8242 (t70) cc_final: 0.7532 (t0) REVERT: C 138 TRP cc_start: 0.7895 (m-90) cc_final: 0.7434 (m-90) REVERT: C 174 LYS cc_start: 0.8110 (mtpt) cc_final: 0.7239 (mmtt) REVERT: C 263 ARG cc_start: 0.8145 (mmt90) cc_final: 0.7587 (mmt-90) REVERT: C 388 MET cc_start: 0.6835 (pmt) cc_final: 0.5968 (pmt) REVERT: C 417 TYR cc_start: 0.7809 (m-80) cc_final: 0.7283 (m-10) REVERT: C 420 MET cc_start: 0.6960 (ttt) cc_final: 0.6281 (tpp) REVERT: D 150 GLU cc_start: 0.7518 (tp30) cc_final: 0.6979 (mt-10) REVERT: D 235 TYR cc_start: 0.7284 (t80) cc_final: 0.6816 (t80) REVERT: D 417 TYR cc_start: 0.7850 (m-10) cc_final: 0.7156 (m-10) REVERT: D 420 MET cc_start: 0.7085 (ttt) cc_final: 0.6405 (tpp) REVERT: D 438 LYS cc_start: 0.7576 (mtmm) cc_final: 0.7203 (mtmm) REVERT: D 442 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7353 (tp30) REVERT: D 469 GLU cc_start: 0.7598 (tt0) cc_final: 0.7035 (tt0) REVERT: D 487 ASP cc_start: 0.8113 (t70) cc_final: 0.7878 (t70) REVERT: E 130 PHE cc_start: 0.8186 (m-80) cc_final: 0.7893 (m-80) REVERT: E 138 TRP cc_start: 0.7857 (m-90) cc_final: 0.7514 (m-90) REVERT: E 150 GLU cc_start: 0.7298 (tp30) cc_final: 0.6769 (mt-10) REVERT: E 174 LYS cc_start: 0.8302 (mtpt) cc_final: 0.7217 (mmtt) REVERT: E 222 TYR cc_start: 0.8285 (t80) cc_final: 0.7906 (t80) REVERT: E 263 ARG cc_start: 0.8010 (mmt90) cc_final: 0.7519 (mmt-90) REVERT: E 417 TYR cc_start: 0.7855 (m-10) cc_final: 0.7355 (m-80) REVERT: E 420 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6171 (tpp) REVERT: E 442 GLU cc_start: 0.7436 (pp20) cc_final: 0.6983 (tp30) REVERT: E 487 ASP cc_start: 0.8298 (t70) cc_final: 0.7547 (t0) REVERT: F 138 TRP cc_start: 0.7798 (m-90) cc_final: 0.7531 (m-90) REVERT: F 174 LYS cc_start: 0.8129 (mtpt) cc_final: 0.7252 (mmtt) REVERT: F 263 ARG cc_start: 0.8145 (mmt90) cc_final: 0.7589 (mmt-90) REVERT: F 334 ARG cc_start: 0.6872 (tmt170) cc_final: 0.6548 (ttt-90) REVERT: F 388 MET cc_start: 0.6750 (pmt) cc_final: 0.5929 (pmt) REVERT: F 417 TYR cc_start: 0.7785 (m-10) cc_final: 0.7219 (m-10) REVERT: F 420 MET cc_start: 0.6963 (ttt) cc_final: 0.6297 (tpp) REVERT: F 443 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7941 (tpt-90) outliers start: 52 outliers final: 44 residues processed: 300 average time/residue: 0.4837 time to fit residues: 169.6425 Evaluate side-chains 318 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 272 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 239 VAL Chi-restraints excluded: chain A residue 249 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 193 ILE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 249 MET 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 435 MET 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 249 MET Chi-restraints excluded: chain D residue 294 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 281 GLU Chi-restraints excluded: chain E residue 355 LYS Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 372 ILE Chi-restraints excluded: chain F residue 435 MET 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 95 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 106 optimal weight: 0.3980 chunk 60 optimal weight: 0.5980 chunk 156 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 86 optimal weight: 0.0270 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 221 GLN F 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.166718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.110781 restraints weight = 22189.435| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.61 r_work: 0.3273 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.4809 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= 0.115 Angle : 0.551 9.137 27048 Z= 0.278 Chirality : 0.038 0.159 3078 Planarity : 0.004 0.050 3318 Dihedral : 6.737 59.005 3552 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.08 % Allowed : 21.56 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.18), residues: 2304 helix: 2.53 (0.14), residues: 1452 sheet: 0.68 (0.34), residues: 234 loop : -0.55 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 476 TYR 0.020 0.001 TYR D 222 PHE 0.034 0.001 PHE E 196 TRP 0.016 0.002 TRP B 458 HIS 0.012 0.001 HIS F 234 Details of bonding type rmsd covalent geometry : bond 0.00266 (19962) covalent geometry : angle 0.55149 (27048) hydrogen bonds : bond 0.03216 ( 1195) hydrogen bonds : angle 3.58457 ( 3465) ********************** 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 320 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 278 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 GLU cc_start: 0.7550 (tp30) cc_final: 0.6984 (mt-10) REVERT: A 174 LYS cc_start: 0.8093 (mtpt) cc_final: 0.6970 (mmtt) REVERT: A 235 TYR cc_start: 0.7379 (t80) cc_final: 0.6907 (t80) REVERT: A 417 TYR cc_start: 0.7744 (m-10) cc_final: 0.7106 (m-10) REVERT: A 420 MET cc_start: 0.6963 (ttt) cc_final: 0.6334 (tpp) REVERT: A 438 LYS cc_start: 0.7551 (mtmm) cc_final: 0.7238 (mtmm) REVERT: A 442 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7176 (tp30) REVERT: A 487 ASP cc_start: 0.8142 (t70) cc_final: 0.7896 (t70) REVERT: B 130 PHE cc_start: 0.8257 (m-80) cc_final: 0.7977 (m-80) REVERT: B 150 GLU cc_start: 0.7236 (tp30) cc_final: 0.6719 (mt-10) REVERT: B 174 LYS cc_start: 0.8309 (mtpt) cc_final: 0.7202 (mmtt) REVERT: B 222 TYR cc_start: 0.8422 (t80) cc_final: 0.7934 (t80) REVERT: B 263 ARG cc_start: 0.7991 (mmt90) cc_final: 0.7505 (mmt-90) REVERT: B 420 MET cc_start: 0.6990 (ttt) cc_final: 0.6186 (tpp) REVERT: B 487 ASP cc_start: 0.8226 (t70) cc_final: 0.7539 (t0) REVERT: C 138 TRP cc_start: 0.7801 (m-90) cc_final: 0.7405 (m-90) REVERT: C 174 LYS cc_start: 0.8117 (mtpt) cc_final: 0.7241 (mmtt) REVERT: C 263 ARG cc_start: 0.8131 (mmt90) cc_final: 0.7427 (mmt-90) REVERT: C 388 MET cc_start: 0.6823 (pmt) cc_final: 0.5946 (pmt) REVERT: C 417 TYR cc_start: 0.7793 (m-80) cc_final: 0.7301 (m-10) REVERT: C 420 MET cc_start: 0.6954 (ttt) cc_final: 0.6286 (tpp) REVERT: C 443 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7982 (tpt170) REVERT: D 150 GLU cc_start: 0.7514 (tp30) cc_final: 0.6955 (mt-10) REVERT: D 174 LYS cc_start: 0.8111 (mtpt) cc_final: 0.6976 (mmtt) REVERT: D 235 TYR cc_start: 0.7257 (t80) cc_final: 0.6803 (t80) REVERT: D 417 TYR cc_start: 0.7812 (m-10) cc_final: 0.7120 (m-10) REVERT: D 420 MET cc_start: 0.6931 (ttt) cc_final: 0.6316 (tpp) REVERT: D 438 LYS cc_start: 0.7559 (mtmm) cc_final: 0.7246 (mtmm) REVERT: D 442 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7198 (tp30) REVERT: D 469 GLU cc_start: 0.7551 (tt0) cc_final: 0.6964 (tt0) REVERT: D 487 ASP cc_start: 0.8114 (t70) cc_final: 0.7864 (t70) REVERT: E 130 PHE cc_start: 0.8268 (m-80) cc_final: 0.7993 (m-80) REVERT: E 138 TRP cc_start: 0.7774 (m-90) cc_final: 0.7492 (m-90) REVERT: E 150 GLU cc_start: 0.7340 (tp30) cc_final: 0.6825 (mt-10) REVERT: E 174 LYS cc_start: 0.8308 (mtpt) cc_final: 0.7199 (mmtt) REVERT: E 222 TYR cc_start: 0.8274 (t80) cc_final: 0.7908 (t80) REVERT: E 263 ARG cc_start: 0.8001 (mmt90) cc_final: 0.7499 (mmt-90) REVERT: E 417 TYR cc_start: 0.7851 (m-10) cc_final: 0.7360 (m-80) REVERT: E 420 MET cc_start: 0.6684 (OUTLIER) cc_final: 0.6077 (tpp) REVERT: E 442 GLU cc_start: 0.7442 (pp20) cc_final: 0.6996 (tp30) REVERT: E 487 ASP cc_start: 0.8246 (t70) cc_final: 0.7510 (t0) REVERT: F 138 TRP cc_start: 0.7809 (m-90) cc_final: 0.7395 (m-90) REVERT: F 174 LYS cc_start: 0.8134 (mtpt) cc_final: 0.7251 (mmtt) REVERT: F 221 GLN cc_start: 0.8313 (mt0) cc_final: 0.7967 (pm20) REVERT: F 263 ARG cc_start: 0.8132 (mmt90) cc_final: 0.7436 (mmt-90) REVERT: F 334 ARG cc_start: 0.6845 (tmt170) cc_final: 0.6533 (ttt-90) REVERT: F 388 MET cc_start: 0.6753 (pmt) cc_final: 0.5912 (pmt) REVERT: F 417 TYR cc_start: 0.7764 (m-10) cc_final: 0.7241 (m-10) REVERT: F 420 MET cc_start: 0.6939 (ttt) cc_final: 0.6270 (tpp) REVERT: F 443 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7945 (tpt-90) outliers start: 42 outliers final: 36 residues processed: 301 average time/residue: 0.4952 time to fit residues: 174.2478 Evaluate side-chains 313 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 274 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 239 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 397 ILE 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 281 GLU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 471 VAL 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 435 MET 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 249 MET 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 281 GLU Chi-restraints excluded: chain E residue 355 LYS Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 461 THR 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 435 MET 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 126 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 111 optimal weight: 0.0770 chunk 87 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 159 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 234 HIS F 234 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.165237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.109176 restraints weight = 22227.161| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.60 r_work: 0.3255 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.4865 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= 0.141 Angle : 0.572 9.109 27048 Z= 0.284 Chirality : 0.039 0.152 3078 Planarity : 0.004 0.049 3318 Dihedral : 6.839 59.591 3552 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.23 % Allowed : 21.76 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.27 (0.18), residues: 2304 helix: 2.47 (0.13), residues: 1452 sheet: 0.67 (0.34), residues: 234 loop : -0.55 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 476 TYR 0.021 0.001 TYR B 417 PHE 0.035 0.002 PHE F 196 TRP 0.017 0.002 TRP B 458 HIS 0.009 0.001 HIS F 234 Details of bonding type rmsd covalent geometry : bond 0.00341 (19962) covalent geometry : angle 0.57177 (27048) hydrogen bonds : bond 0.03466 ( 1195) hydrogen bonds : angle 3.63096 ( 3465) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6330.08 seconds wall clock time: 108 minutes 47.28 seconds (6527.28 seconds total)