Starting phenix.real_space_refine on Thu Aug 6 11:48:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x0c_66432/08_2026/9x0c_66432.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x0c_66432/08_2026/9x0c_66432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9x0c_66432/08_2026/9x0c_66432.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x0c_66432/08_2026/9x0c_66432.map" model { file = "/net/cci-nas-00/data/ceres_data/9x0c_66432/08_2026/9x0c_66432.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x0c_66432/08_2026/9x0c_66432.cif" } resolution = 2.6 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= -0.000 sd= 0.025 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: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 9536 2.51 5 N 2452 2.21 5 O 2540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14592 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3648 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 15, 'TRANS': 433} Chain: "C" Number of atoms: 3648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3648 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 15, 'TRANS': 433} Chain: "A" Number of atoms: 3648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3648 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 15, 'TRANS': 433} Chain: "D" Number of atoms: 3648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3648 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 15, 'TRANS': 433} Time building chain proxies: 3.44, per 1000 atoms: 0.24 Number of scatterers: 14592 At special positions: 0 Unit cell: (97.35, 97.35, 117.975, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 2540 8.00 N 2452 7.00 C 9536 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: 0.70 Conformation dependent library (CDL) restraints added in 460.3 milliseconds 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3416 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 12 sheets defined 69.2% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'B' and resid 75 through 102 removed outlier: 3.936A pdb=" N ILE B 87 " --> pdb=" O TRP B 83 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 88 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TRP B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Proline residue: B 97 - end of helix Processing helix chain 'B' and resid 107 through 129 removed outlier: 4.477A pdb=" N LEU B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 121 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASP B 124 " --> pdb=" O PHE B 120 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE B 129 " --> pdb=" O ILE B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 155 removed outlier: 3.861A pdb=" N ILE B 148 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N TRP B 150 " --> pdb=" O LYS B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 165 removed outlier: 3.641A pdb=" N VAL B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL B 162 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 176 removed outlier: 3.870A pdb=" N HIS B 175 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASN B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 186 removed outlier: 4.228A pdb=" N TYR B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 190 Processing helix chain 'B' and resid 191 through 205 removed outlier: 3.919A pdb=" N VAL B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG B 201 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LEU B 202 " --> pdb=" O CYS B 198 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B 203 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 239 removed outlier: 3.510A pdb=" N ILE B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 removed outlier: 3.895A pdb=" N ALA B 251 " --> pdb=" O PHE B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 276 Processing helix chain 'B' and resid 287 through 320 removed outlier: 3.687A pdb=" N LEU B 315 " --> pdb=" O ASN B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 340 Processing helix chain 'B' and resid 343 through 360 removed outlier: 3.538A pdb=" N GLU B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 351 " --> pdb=" O GLN B 347 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR B 358 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 375 through 387 Processing helix chain 'B' and resid 387 through 394 removed outlier: 3.707A pdb=" N VAL B 391 " --> pdb=" O PHE B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 411 Processing helix chain 'B' and resid 446 through 450 removed outlier: 3.598A pdb=" N VAL B 450 " --> pdb=" O VAL B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 471 removed outlier: 3.630A pdb=" N VAL B 468 " --> pdb=" O GLY B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 501 Processing helix chain 'B' and resid 503 through 518 removed outlier: 3.594A pdb=" N ILE B 507 " --> pdb=" O GLY B 503 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS B 515 " --> pdb=" O ASN B 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 102 removed outlier: 3.936A pdb=" N ILE C 87 " --> pdb=" O TRP C 83 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 88 " --> pdb=" O PHE C 84 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TRP C 94 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Proline residue: C 97 - end of helix Processing helix chain 'C' and resid 107 through 129 removed outlier: 4.411A pdb=" N LEU C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASP C 124 " --> pdb=" O PHE C 120 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE C 129 " --> pdb=" O ILE C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 155 removed outlier: 3.847A pdb=" N ILE C 148 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TRP C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 165 Processing helix chain 'C' and resid 169 through 176 removed outlier: 3.870A pdb=" N HIS C 175 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASN C 176 " --> pdb=" O LEU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 186 removed outlier: 4.229A pdb=" N TYR C 181 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY C 182 " --> pdb=" O ILE C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 190 Processing helix chain 'C' and resid 191 through 205 removed outlier: 3.890A pdb=" N VAL C 195 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ARG C 201 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LEU C 202 " --> pdb=" O CYS C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 239 removed outlier: 3.565A pdb=" N THR C 216 " --> pdb=" O TRP C 212 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE C 236 " --> pdb=" O PHE C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 252 removed outlier: 3.895A pdb=" N ALA C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 276 Processing helix chain 'C' and resid 287 through 320 removed outlier: 3.772A pdb=" N LEU C 315 " --> pdb=" O ASN C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 340 Processing helix chain 'C' and resid 343 through 358 removed outlier: 3.538A pdb=" N GLU C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C 351 " --> pdb=" O GLN C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 375 through 387 Processing helix chain 'C' and resid 387 through 394 Processing helix chain 'C' and resid 401 through 411 Processing helix chain 'C' and resid 446 through 450 Processing helix chain 'C' and resid 464 through 471 removed outlier: 3.524A pdb=" N VAL C 468 " --> pdb=" O GLY C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 501 Processing helix chain 'C' and resid 503 through 518 removed outlier: 3.593A pdb=" N ILE C 507 " --> pdb=" O GLY C 503 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS C 515 " --> pdb=" O ASN C 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 102 removed outlier: 3.937A pdb=" N ILE A 87 " --> pdb=" O TRP A 83 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TRP A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Proline residue: A 97 - end of helix Processing helix chain 'A' and resid 107 through 129 removed outlier: 4.482A pdb=" N LEU A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP A 124 " --> pdb=" O PHE A 120 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A 129 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 165 removed outlier: 3.641A pdb=" N VAL A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 176 removed outlier: 3.870A pdb=" N HIS A 175 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASN A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 186 removed outlier: 4.229A pdb=" N TYR A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 182 " --> pdb=" O ILE A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 190 Processing helix chain 'A' and resid 191 through 205 removed outlier: 3.915A pdb=" N VAL A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG A 201 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEU A 202 " --> pdb=" O CYS A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 239 removed outlier: 3.630A pdb=" N THR A 216 " --> pdb=" O TRP A 212 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 removed outlier: 3.895A pdb=" N ALA A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 276 Processing helix chain 'A' and resid 287 through 320 removed outlier: 3.771A pdb=" N LEU A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 340 Processing helix chain 'A' and resid 343 through 360 removed outlier: 3.538A pdb=" N GLU A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 351 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 375 through 387 Processing helix chain 'A' and resid 387 through 394 removed outlier: 3.706A pdb=" N VAL A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 411 Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 464 through 471 removed outlier: 3.762A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 501 Processing helix chain 'A' and resid 503 through 518 removed outlier: 3.594A pdb=" N ILE A 507 " --> pdb=" O GLY A 503 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS A 515 " --> pdb=" O ASN A 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 102 removed outlier: 3.936A pdb=" N ILE D 87 " --> pdb=" O TRP D 83 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU D 88 " --> pdb=" O PHE D 84 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TRP D 94 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Proline residue: D 97 - end of helix Processing helix chain 'D' and resid 107 through 129 removed outlier: 4.483A pdb=" N LEU D 113 " --> pdb=" O PRO D 109 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE D 121 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASP D 124 " --> pdb=" O PHE D 120 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE D 129 " --> pdb=" O ILE D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 155 Processing helix chain 'D' and resid 157 through 165 removed outlier: 3.667A pdb=" N VAL D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL D 162 " --> pdb=" O ILE D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 177 removed outlier: 3.870A pdb=" N HIS D 175 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASN D 176 " --> pdb=" O LEU D 173 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR D 177 " --> pdb=" O LEU D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 188 removed outlier: 3.579A pdb=" N GLY D 182 " --> pdb=" O ILE D 178 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG D 188 " --> pdb=" O PHE D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 205 removed outlier: 3.883A pdb=" N VAL D 195 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG D 201 " --> pdb=" O LYS D 197 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LEU D 202 " --> pdb=" O CYS D 198 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU D 203 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 239 removed outlier: 3.510A pdb=" N ILE D 236 " --> pdb=" O PHE D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 252 removed outlier: 3.895A pdb=" N ALA D 251 " --> pdb=" O PHE D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 276 Processing helix chain 'D' and resid 287 through 320 removed outlier: 3.772A pdb=" N LEU D 315 " --> pdb=" O ASN D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 340 Processing helix chain 'D' and resid 343 through 360 removed outlier: 3.537A pdb=" N GLU D 348 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL D 351 " --> pdb=" O GLN D 347 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR D 358 " --> pdb=" O LEU D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 369 Processing helix chain 'D' and resid 375 through 387 Processing helix chain 'D' and resid 387 through 394 removed outlier: 3.707A pdb=" N VAL D 391 " --> pdb=" O PHE D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 411 Processing helix chain 'D' and resid 464 through 471 removed outlier: 3.798A pdb=" N VAL D 468 " --> pdb=" O GLY D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 501 Processing helix chain 'D' and resid 503 through 518 removed outlier: 3.593A pdb=" N ILE D 507 " --> pdb=" O GLY D 503 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS D 515 " --> pdb=" O ASN D 511 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 134 through 135 Processing sheet with id=AA2, first strand: chain 'B' and resid 413 through 417 Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 457 removed outlier: 6.376A pdb=" N ILE B 443 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLU B 456 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL B 441 " --> pdb=" O GLU B 456 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 134 through 135 Processing sheet with id=AA5, first strand: chain 'C' and resid 413 through 417 Processing sheet with id=AA6, first strand: chain 'C' and resid 422 through 424 removed outlier: 6.623A pdb=" N VAL C 478 " --> pdb=" O VAL C 423 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AA8, first strand: chain 'A' and resid 413 through 417 removed outlier: 6.793A pdb=" N ALA A 440 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU A 483 " --> pdb=" O THR A 438 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR A 438 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N GLN A 485 " --> pdb=" O MET A 436 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N MET A 436 " --> pdb=" O GLN A 485 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU A 487 " --> pdb=" O TYR A 434 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYR A 434 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LEU A 489 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASP A 432 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 441 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU A 456 " --> pdb=" O VAL A 441 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE A 443 " --> pdb=" O VAL A 454 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 422 through 424 removed outlier: 6.624A pdb=" N VAL A 478 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ALA A 440 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU A 483 " --> pdb=" O THR A 438 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR A 438 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N GLN A 485 " --> pdb=" O MET A 436 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N MET A 436 " --> pdb=" O GLN A 485 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU A 487 " --> pdb=" O TYR A 434 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYR A 434 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LEU A 489 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASP A 432 " --> pdb=" O LEU A 489 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 134 through 135 Processing sheet with id=AB2, first strand: chain 'D' and resid 413 through 417 Processing sheet with id=AB3, first strand: chain 'D' and resid 422 through 424 removed outlier: 6.687A pdb=" N VAL D 478 " --> pdb=" O VAL D 423 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL D 441 " --> pdb=" O GLU D 456 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU D 456 " --> pdb=" O VAL D 441 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE D 443 " --> pdb=" O VAL D 454 " (cutoff:3.500A) 873 hydrogen bonds defined for protein. 2502 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: 1.98 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3990 1.34 - 1.45: 2694 1.45 - 1.57: 8192 1.57 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 14980 Sorted by residual: bond pdb=" N VAL C 437 " pdb=" CA VAL C 437 " ideal model delta sigma weight residual 1.458 1.492 -0.034 9.00e-03 1.23e+04 1.47e+01 bond pdb=" CA SER D 235 " pdb=" CB SER D 235 " ideal model delta sigma weight residual 1.530 1.475 0.056 1.58e-02 4.01e+03 1.23e+01 bond pdb=" CA SER C 235 " pdb=" CB SER C 235 " ideal model delta sigma weight residual 1.530 1.475 0.056 1.58e-02 4.01e+03 1.23e+01 bond pdb=" CA SER B 235 " pdb=" CB SER B 235 " ideal model delta sigma weight residual 1.530 1.475 0.056 1.58e-02 4.01e+03 1.23e+01 bond pdb=" CA SER A 235 " pdb=" CB SER A 235 " ideal model delta sigma weight residual 1.530 1.475 0.055 1.58e-02 4.01e+03 1.23e+01 ... (remaining 14975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 13604 1.48 - 2.95: 5534 2.95 - 4.43: 1037 4.43 - 5.90: 184 5.90 - 7.38: 17 Bond angle restraints: 20376 Sorted by residual: angle pdb=" N VAL C 423 " pdb=" CA VAL C 423 " pdb=" C VAL C 423 " ideal model delta sigma weight residual 111.56 107.26 4.30 8.60e-01 1.35e+00 2.50e+01 angle pdb=" CA PHE C 433 " pdb=" CB PHE C 433 " pdb=" CG PHE C 433 " ideal model delta sigma weight residual 113.80 118.74 -4.94 1.00e+00 1.00e+00 2.44e+01 angle pdb=" N ILE A 213 " pdb=" CA ILE A 213 " pdb=" C ILE A 213 " ideal model delta sigma weight residual 111.45 106.88 4.57 9.30e-01 1.16e+00 2.41e+01 angle pdb=" CA PHE D 433 " pdb=" CB PHE D 433 " pdb=" CG PHE D 433 " ideal model delta sigma weight residual 113.80 118.67 -4.87 1.00e+00 1.00e+00 2.37e+01 angle pdb=" N VAL C 437 " pdb=" CA VAL C 437 " pdb=" C VAL C 437 " ideal model delta sigma weight residual 111.62 107.79 3.83 7.90e-01 1.60e+00 2.35e+01 ... (remaining 20371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.98: 7459 12.98 - 25.96: 706 25.96 - 38.94: 313 38.94 - 51.92: 122 51.92 - 64.90: 128 Dihedral angle restraints: 8728 sinusoidal: 3432 harmonic: 5296 Sorted by residual: dihedral pdb=" C ASN A 511 " pdb=" N ASN A 511 " pdb=" CA ASN A 511 " pdb=" CB ASN A 511 " ideal model delta harmonic sigma weight residual -122.60 -131.26 8.66 0 2.50e+00 1.60e-01 1.20e+01 dihedral pdb=" C ASN B 511 " pdb=" N ASN B 511 " pdb=" CA ASN B 511 " pdb=" CB ASN B 511 " ideal model delta harmonic sigma weight residual -122.60 -131.22 8.62 0 2.50e+00 1.60e-01 1.19e+01 dihedral pdb=" C ASN C 511 " pdb=" N ASN C 511 " pdb=" CA ASN C 511 " pdb=" CB ASN C 511 " ideal model delta harmonic sigma weight residual -122.60 -131.22 8.62 0 2.50e+00 1.60e-01 1.19e+01 ... (remaining 8725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 839 0.052 - 0.104: 731 0.104 - 0.157: 494 0.157 - 0.209: 184 0.209 - 0.261: 44 Chirality restraints: 2292 Sorted by residual: chirality pdb=" CA ILE D 158 " pdb=" N ILE D 158 " pdb=" C ILE D 158 " pdb=" CB ILE D 158 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ILE A 158 " pdb=" N ILE A 158 " pdb=" C ILE A 158 " pdb=" CB ILE A 158 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ILE B 158 " pdb=" N ILE B 158 " pdb=" C ILE B 158 " pdb=" CB ILE B 158 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 2289 not shown) Planarity restraints: 2556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 422 " -0.024 2.00e-02 2.50e+03 4.83e-02 2.33e+01 pdb=" C ASP B 422 " 0.084 2.00e-02 2.50e+03 pdb=" O ASP B 422 " -0.031 2.00e-02 2.50e+03 pdb=" N VAL B 423 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 357 " -0.286 9.50e-02 1.11e+02 1.28e-01 1.01e+01 pdb=" NE ARG D 357 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG D 357 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG D 357 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 357 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 191 " -0.269 9.50e-02 1.11e+02 1.21e-01 8.97e+00 pdb=" NE ARG A 191 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 191 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 191 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 191 " -0.008 2.00e-02 2.50e+03 ... (remaining 2553 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 5799 2.87 - 3.38: 14923 3.38 - 3.89: 26726 3.89 - 4.39: 30863 4.39 - 4.90: 49088 Nonbonded interactions: 127399 Sorted by model distance: nonbonded pdb=" O SER A 276 " pdb=" OG1 THR A 277 " model vdw 2.368 3.040 nonbonded pdb=" O SER D 276 " pdb=" OG1 THR D 277 " model vdw 2.368 3.040 nonbonded pdb=" O SER B 276 " pdb=" OG1 THR B 277 " model vdw 2.368 3.040 nonbonded pdb=" O SER C 276 " pdb=" OG1 THR C 277 " model vdw 2.368 3.040 nonbonded pdb=" OD1 ASP C 442 " pdb=" CD LYS C 481 " model vdw 2.382 3.440 ... (remaining 127394 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 8.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 12.140 Find NCS groups from input model: 0.250 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:5.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 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 : 0.013 0.056 14980 Z= 0.958 Angle : 1.561 7.380 20376 Z= 1.203 Chirality : 0.097 0.261 2292 Planarity : 0.013 0.128 2556 Dihedral : 15.919 64.900 5312 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.77 % Favored : 93.18 % Rotamer: Outliers : 10.94 % Allowed : 12.28 % Favored : 76.78 % 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 are not related in a simple way. whole: -3.77 (0.17), residues: 1788 helix: -2.38 (0.12), residues: 1120 sheet: -1.47 (0.46), residues: 104 loop : -2.52 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 327 TYR 0.017 0.002 TYR B 434 PHE 0.023 0.002 PHE C 463 TRP 0.018 0.004 TRP A 94 HIS 0.005 0.002 HIS D 193 Details of bonding type rmsd/Z covalent geometry : bond 0.01289 / 0.96 (14980) covalent geometry : angle 1.56141 / 1.20 (20376) hydrogen bonds : bond 0.23065 / 15.19 ( 868) hydrogen bonds : angle 8.70561 / 6.34 ( 2502) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 335 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 125 ILE cc_start: 0.6406 (pt) cc_final: 0.5858 (pt) REVERT: B 146 LYS cc_start: 0.5916 (OUTLIER) cc_final: 0.5373 (tptt) REVERT: B 160 ASP cc_start: 0.6159 (t0) cc_final: 0.5898 (t0) REVERT: B 190 TRP cc_start: 0.6637 (t-100) cc_final: 0.6240 (t-100) REVERT: B 206 ARG cc_start: 0.5946 (ptt90) cc_final: 0.5469 (ttp-110) REVERT: B 217 LYS cc_start: 0.7372 (ttmt) cc_final: 0.7047 (tttp) REVERT: B 257 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7575 (mp-120) REVERT: B 278 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8159 (m) REVERT: B 298 MET cc_start: 0.9176 (mtm) cc_final: 0.8834 (mtt) REVERT: B 312 MET cc_start: 0.8429 (tpp) cc_final: 0.8132 (tpt) REVERT: B 372 ASP cc_start: 0.7572 (m-30) cc_final: 0.7146 (m-30) REVERT: B 411 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7828 (tp30) REVERT: B 416 TYR cc_start: 0.8177 (m-80) cc_final: 0.7350 (m-80) REVERT: B 421 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7429 (tt0) REVERT: B 458 GLN cc_start: 0.5627 (mt0) cc_final: 0.5365 (pm20) REVERT: B 510 ASN cc_start: 0.6934 (OUTLIER) cc_final: 0.6268 (m110) REVERT: C 125 ILE cc_start: 0.6629 (pt) cc_final: 0.6104 (pt) REVERT: C 252 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7557 (mt-10) REVERT: C 257 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7649 (mp10) REVERT: C 278 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.8092 (m) REVERT: C 298 MET cc_start: 0.9169 (mtm) cc_final: 0.8825 (mtt) REVERT: C 312 MET cc_start: 0.8481 (tpp) cc_final: 0.8185 (tpt) REVERT: C 411 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7759 (tp30) REVERT: C 458 GLN cc_start: 0.6127 (mt0) cc_final: 0.5912 (pm20) REVERT: C 510 ASN cc_start: 0.6895 (OUTLIER) cc_final: 0.6282 (m110) REVERT: A 125 ILE cc_start: 0.6567 (pt) cc_final: 0.5987 (pt) REVERT: A 257 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7505 (mp-120) REVERT: A 278 THR cc_start: 0.8423 (OUTLIER) cc_final: 0.8010 (m) REVERT: A 298 MET cc_start: 0.9156 (mtm) cc_final: 0.8920 (mtt) REVERT: A 312 MET cc_start: 0.8451 (tpp) cc_final: 0.8164 (tpt) REVERT: A 393 LYS cc_start: 0.7017 (mtmt) cc_final: 0.6812 (mmtt) REVERT: A 411 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7900 (tp30) REVERT: A 416 TYR cc_start: 0.8073 (m-80) cc_final: 0.7516 (m-80) REVERT: A 458 GLN cc_start: 0.5802 (mt0) cc_final: 0.5488 (pm20) REVERT: A 510 ASN cc_start: 0.6893 (OUTLIER) cc_final: 0.6242 (m110) REVERT: D 125 ILE cc_start: 0.6562 (pt) cc_final: 0.5769 (pt) REVERT: D 160 ASP cc_start: 0.4777 (m-30) cc_final: 0.4415 (t0) REVERT: D 206 ARG cc_start: 0.5946 (ptt90) cc_final: 0.5502 (ttp-110) REVERT: D 257 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7623 (mp-120) REVERT: D 278 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.8019 (m) REVERT: D 298 MET cc_start: 0.9169 (mtm) cc_final: 0.8861 (mtt) REVERT: D 312 MET cc_start: 0.8432 (tpp) cc_final: 0.8126 (tpt) REVERT: D 359 ARG cc_start: 0.6958 (tmt170) cc_final: 0.6627 (tmm160) REVERT: D 372 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7320 (m-30) REVERT: D 393 LYS cc_start: 0.6919 (mtmt) cc_final: 0.6703 (mmtt) REVERT: D 411 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7857 (tp30) REVERT: D 420 LYS cc_start: 0.7579 (mtmt) cc_final: 0.7352 (mmtm) REVERT: D 458 GLN cc_start: 0.5687 (mt0) cc_final: 0.5380 (pm20) REVERT: D 510 ASN cc_start: 0.6958 (OUTLIER) cc_final: 0.6285 (m110) outliers start: 172 outliers final: 25 residues processed: 469 average time/residue: 0.4887 time to fit residues: 254.6529 Evaluate side-chains 237 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 196 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 83 TRP Chi-restraints excluded: chain B residue 139 TYR Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 510 ASN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 83 TRP Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 510 ASN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 83 TRP Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 257 GLN Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 83 TRP Chi-restraints excluded: chain D residue 139 TYR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 257 GLN Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 510 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.0670 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 HIS B 254 ASN B 286 ASN B 311 ASN B 338 GLN B 490 ASN B 510 ASN B 511 ASN ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 ASN C 239 HIS C 254 ASN C 286 ASN C 338 GLN C 452 GLN C 474 GLN C 510 ASN A 209 ASN A 239 HIS A 254 ASN A 286 ASN A 325 ASN A 338 GLN A 427 ASN A 452 GLN A 474 GLN A 510 ASN D 209 ASN D 239 HIS D 254 ASN D 286 ASN D 474 GLN D 510 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.215046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.154327 restraints weight = 15231.407| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.90 r_work: 0.3597 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14980 Z= 0.147 Angle : 0.644 9.213 20376 Z= 0.338 Chirality : 0.041 0.197 2292 Planarity : 0.005 0.051 2556 Dihedral : 7.063 57.184 2065 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 5.53 % Allowed : 19.34 % Favored : 75.13 % 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 are not related in a simple way. whole: -0.73 (0.19), residues: 1788 helix: 0.20 (0.15), residues: 1088 sheet: -0.61 (0.50), residues: 84 loop : -1.61 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 194 TYR 0.016 0.002 TYR B 307 PHE 0.028 0.002 PHE B 433 TRP 0.015 0.002 TRP A 270 HIS 0.005 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (14980) covalent geometry : angle 0.64429 / 0.34 (20376) hydrogen bonds : bond 0.05552 / 3.68 ( 868) hydrogen bonds : angle 4.49629 / 3.25 ( 2502) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 226 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: B 130 PHE cc_start: 0.6550 (m-80) cc_final: 0.6274 (m-80) REVERT: B 146 LYS cc_start: 0.6357 (OUTLIER) cc_final: 0.5794 (tptm) REVERT: B 206 ARG cc_start: 0.5910 (ptt90) cc_final: 0.5524 (ttp-110) REVERT: B 217 LYS cc_start: 0.7316 (ttmt) cc_final: 0.6984 (tttp) REVERT: B 252 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7334 (mt-10) REVERT: B 278 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8189 (t) REVERT: B 344 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6900 (mm) REVERT: B 359 ARG cc_start: 0.7203 (tmt90) cc_final: 0.6683 (ttt-90) REVERT: B 372 ASP cc_start: 0.7764 (m-30) cc_final: 0.7464 (m-30) REVERT: B 389 GLU cc_start: 0.7155 (mp0) cc_final: 0.6855 (mp0) REVERT: B 416 TYR cc_start: 0.8270 (m-80) cc_final: 0.7577 (m-80) REVERT: B 421 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7666 (tt0) REVERT: B 442 ASP cc_start: 0.7438 (m-30) cc_final: 0.7139 (m-30) REVERT: B 458 GLN cc_start: 0.5806 (mt0) cc_final: 0.5162 (mp10) REVERT: B 510 ASN cc_start: 0.6659 (t0) cc_final: 0.6045 (m110) REVERT: C 130 PHE cc_start: 0.6582 (m-80) cc_final: 0.6307 (m-80) REVERT: C 139 TYR cc_start: 0.6027 (OUTLIER) cc_final: 0.5666 (m-80) REVERT: C 278 THR cc_start: 0.8663 (OUTLIER) cc_final: 0.8225 (t) REVERT: C 344 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6801 (mm) REVERT: C 405 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7915 (tp) REVERT: C 458 GLN cc_start: 0.6328 (mt0) cc_final: 0.5636 (mp10) REVERT: C 463 PHE cc_start: 0.4955 (t80) cc_final: 0.4466 (t80) REVERT: A 130 PHE cc_start: 0.6487 (m-80) cc_final: 0.6213 (m-80) REVERT: A 136 LYS cc_start: 0.6021 (OUTLIER) cc_final: 0.5328 (mttp) REVERT: A 278 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.7852 (m) REVERT: A 298 MET cc_start: 0.9106 (mtm) cc_final: 0.8903 (mtt) REVERT: A 344 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6861 (mm) REVERT: A 359 ARG cc_start: 0.7251 (tmt90) cc_final: 0.6788 (ttt-90) REVERT: A 416 TYR cc_start: 0.8038 (m-80) cc_final: 0.7739 (m-80) REVERT: A 442 ASP cc_start: 0.7393 (m-30) cc_final: 0.7118 (m-30) REVERT: A 458 GLN cc_start: 0.6046 (mt0) cc_final: 0.5378 (mp10) REVERT: D 130 PHE cc_start: 0.6515 (m-80) cc_final: 0.6236 (m-80) REVERT: D 160 ASP cc_start: 0.4291 (m-30) cc_final: 0.3854 (t0) REVERT: D 206 ARG cc_start: 0.5954 (ptt90) cc_final: 0.5537 (ttp-110) REVERT: D 278 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8193 (t) REVERT: D 298 MET cc_start: 0.9126 (mtm) cc_final: 0.8923 (mtm) REVERT: D 344 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6873 (mm) REVERT: D 347 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7830 (tp-100) REVERT: D 372 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7442 (m-30) REVERT: D 389 GLU cc_start: 0.7262 (mp0) cc_final: 0.6890 (mp0) REVERT: D 393 LYS cc_start: 0.6956 (mtmt) cc_final: 0.6535 (mmtt) REVERT: D 416 TYR cc_start: 0.8514 (m-80) cc_final: 0.7668 (m-80) REVERT: D 420 LYS cc_start: 0.7575 (mtmt) cc_final: 0.7363 (mmtm) REVERT: D 458 GLN cc_start: 0.5872 (mt0) cc_final: 0.5195 (mp10) outliers start: 87 outliers final: 29 residues processed: 298 average time/residue: 0.4407 time to fit residues: 147.3544 Evaluate side-chains 235 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 190 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 139 TYR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 139 TYR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 347 GLN Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 423 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 94 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 ASN C 340 ASN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 ASN D 239 HIS ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 511 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.212064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.150427 restraints weight = 15471.056| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.99 r_work: 0.3529 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14980 Z= 0.160 Angle : 0.629 16.389 20376 Z= 0.321 Chirality : 0.042 0.180 2292 Planarity : 0.004 0.047 2556 Dihedral : 5.573 55.324 2020 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 5.15 % Allowed : 19.59 % Favored : 75.25 % 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 are not related in a simple way. whole: 0.29 (0.20), residues: 1788 helix: 1.11 (0.15), residues: 1112 sheet: -0.30 (0.52), residues: 84 loop : -1.47 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 194 TYR 0.015 0.002 TYR D 269 PHE 0.025 0.002 PHE B 433 TRP 0.019 0.002 TRP A 270 HIS 0.007 0.001 HIS C 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (14980) covalent geometry : angle 0.62879 / 0.32 (20376) hydrogen bonds : bond 0.05503 / 3.65 ( 868) hydrogen bonds : angle 4.13338 / 2.97 ( 2502) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 215 time to evaluate : 0.453 Fit side-chains REVERT: B 130 PHE cc_start: 0.6543 (m-80) cc_final: 0.6336 (m-80) REVERT: B 190 TRP cc_start: 0.6538 (t-100) cc_final: 0.6184 (t-100) REVERT: B 191 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7673 (mtt-85) REVERT: B 206 ARG cc_start: 0.6227 (ptt90) cc_final: 0.5415 (tmm160) REVERT: B 359 ARG cc_start: 0.7254 (tmt90) cc_final: 0.6831 (ttt-90) REVERT: B 367 GLN cc_start: 0.7126 (tm-30) cc_final: 0.6699 (pp30) REVERT: B 372 ASP cc_start: 0.8048 (m-30) cc_final: 0.7629 (m-30) REVERT: B 416 TYR cc_start: 0.8378 (m-80) cc_final: 0.7642 (m-80) REVERT: B 442 ASP cc_start: 0.7544 (m-30) cc_final: 0.7231 (m-30) REVERT: B 458 GLN cc_start: 0.5936 (mt0) cc_final: 0.5285 (mp10) REVERT: B 510 ASN cc_start: 0.6706 (t0) cc_final: 0.6127 (m110) REVERT: C 118 ASN cc_start: 0.6898 (m110) cc_final: 0.6646 (p0) REVERT: C 130 PHE cc_start: 0.6416 (m-80) cc_final: 0.6178 (m-80) REVERT: C 159 PHE cc_start: 0.4579 (OUTLIER) cc_final: 0.3932 (m-80) REVERT: C 206 ARG cc_start: 0.5824 (ptp-170) cc_final: 0.5349 (ttp-170) REVERT: C 312 MET cc_start: 0.8169 (tpp) cc_final: 0.7685 (mmt) REVERT: C 344 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6849 (mm) REVERT: C 359 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6731 (ttt-90) REVERT: C 405 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8009 (tp) REVERT: C 458 GLN cc_start: 0.6289 (mt0) cc_final: 0.5551 (mp10) REVERT: C 463 PHE cc_start: 0.4975 (t80) cc_final: 0.4558 (t80) REVERT: C 510 ASN cc_start: 0.6575 (t0) cc_final: 0.6041 (m110) REVERT: A 130 PHE cc_start: 0.6543 (m-80) cc_final: 0.6328 (m-80) REVERT: A 190 TRP cc_start: 0.6393 (t-100) cc_final: 0.6046 (t-100) REVERT: A 312 MET cc_start: 0.8114 (tpp) cc_final: 0.7679 (mmt) REVERT: A 344 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6849 (mm) REVERT: A 359 ARG cc_start: 0.7259 (tmt90) cc_final: 0.6863 (ttt180) REVERT: A 416 TYR cc_start: 0.8256 (m-80) cc_final: 0.7587 (m-80) REVERT: A 442 ASP cc_start: 0.7575 (m-30) cc_final: 0.7316 (m-30) REVERT: A 458 GLN cc_start: 0.5923 (mt0) cc_final: 0.5166 (mp10) REVERT: A 510 ASN cc_start: 0.6538 (t0) cc_final: 0.5890 (m110) REVERT: D 160 ASP cc_start: 0.4905 (m-30) cc_final: 0.4320 (t0) REVERT: D 206 ARG cc_start: 0.5982 (ptt90) cc_final: 0.5330 (tmm160) REVERT: D 312 MET cc_start: 0.8139 (tpp) cc_final: 0.7648 (mmt) REVERT: D 344 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6816 (mm) REVERT: D 347 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7762 (tp-100) REVERT: D 372 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7543 (m-30) REVERT: D 393 LYS cc_start: 0.7072 (mtmt) cc_final: 0.6591 (mptt) REVERT: D 416 TYR cc_start: 0.8620 (m-80) cc_final: 0.7743 (m-80) REVERT: D 420 LYS cc_start: 0.7575 (mtmt) cc_final: 0.7340 (mmtm) REVERT: D 458 GLN cc_start: 0.5890 (mt0) cc_final: 0.5215 (mp10) REVERT: D 510 ASN cc_start: 0.6528 (t0) cc_final: 0.5853 (m110) outliers start: 81 outliers final: 27 residues processed: 281 average time/residue: 0.4333 time to fit residues: 137.4378 Evaluate side-chains 225 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 TYR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 191 ARG Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain D residue 139 TYR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 347 GLN Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 471 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 76 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 106 optimal weight: 0.0060 chunk 78 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 152 optimal weight: 0.3980 chunk 145 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 HIS B 340 ASN ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 HIS A 239 HIS ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS D 331 GLN ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.213900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.153372 restraints weight = 15338.578| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.14 r_work: 0.3542 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14980 Z= 0.138 Angle : 0.589 15.344 20376 Z= 0.300 Chirality : 0.041 0.170 2292 Planarity : 0.004 0.045 2556 Dihedral : 5.139 59.561 2004 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.82 % Allowed : 21.63 % Favored : 74.55 % 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 are not related in a simple way. whole: 0.82 (0.20), residues: 1788 helix: 1.56 (0.15), residues: 1112 sheet: -0.29 (0.52), residues: 88 loop : -1.31 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 194 TYR 0.018 0.002 TYR D 152 PHE 0.022 0.002 PHE B 433 TRP 0.017 0.002 TRP A 270 HIS 0.005 0.001 HIS B 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (14980) covalent geometry : angle 0.58924 / 0.30 (20376) hydrogen bonds : bond 0.04961 / 3.29 ( 868) hydrogen bonds : angle 3.90916 / 2.79 ( 2502) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 202 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 190 TRP cc_start: 0.6494 (t-100) cc_final: 0.6139 (t-100) REVERT: B 191 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7605 (mtt-85) REVERT: B 206 ARG cc_start: 0.6136 (ptt90) cc_final: 0.5364 (tmm160) REVERT: B 305 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8473 (mp) REVERT: B 312 MET cc_start: 0.8049 (tpp) cc_final: 0.7561 (mmt) REVERT: B 367 GLN cc_start: 0.6984 (tm-30) cc_final: 0.6480 (pp30) REVERT: B 372 ASP cc_start: 0.7991 (m-30) cc_final: 0.7558 (m-30) REVERT: B 416 TYR cc_start: 0.8386 (m-80) cc_final: 0.7602 (m-80) REVERT: B 421 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7669 (tt0) REVERT: B 442 ASP cc_start: 0.7505 (m-30) cc_final: 0.7192 (m-30) REVERT: B 458 GLN cc_start: 0.5854 (mt0) cc_final: 0.5167 (mp10) REVERT: B 510 ASN cc_start: 0.6631 (t0) cc_final: 0.6021 (m110) REVERT: C 206 ARG cc_start: 0.6017 (OUTLIER) cc_final: 0.5517 (ttp-170) REVERT: C 305 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8462 (mp) REVERT: C 312 MET cc_start: 0.8131 (tpp) cc_final: 0.7670 (mmt) REVERT: C 357 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.6422 (ttp80) REVERT: C 359 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6804 (ttt-90) REVERT: C 405 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7978 (tp) REVERT: C 458 GLN cc_start: 0.6263 (mt0) cc_final: 0.5534 (mp10) REVERT: C 463 PHE cc_start: 0.4889 (t80) cc_final: 0.4426 (t80) REVERT: C 510 ASN cc_start: 0.6526 (t0) cc_final: 0.5922 (m110) REVERT: A 190 TRP cc_start: 0.6381 (t-100) cc_final: 0.6061 (t-100) REVERT: A 367 GLN cc_start: 0.7048 (tm-30) cc_final: 0.6605 (pp30) REVERT: A 372 ASP cc_start: 0.7981 (m-30) cc_final: 0.7318 (m-30) REVERT: A 416 TYR cc_start: 0.8184 (m-80) cc_final: 0.7613 (m-80) REVERT: A 442 ASP cc_start: 0.7550 (m-30) cc_final: 0.7285 (m-30) REVERT: A 458 GLN cc_start: 0.5814 (mt0) cc_final: 0.5058 (mp10) REVERT: A 465 GLU cc_start: 0.8171 (pm20) cc_final: 0.7892 (pm20) REVERT: A 510 ASN cc_start: 0.6574 (t0) cc_final: 0.5924 (m110) REVERT: D 160 ASP cc_start: 0.4885 (m-30) cc_final: 0.4607 (t0) REVERT: D 206 ARG cc_start: 0.6185 (ptt90) cc_final: 0.5583 (tmm160) REVERT: D 305 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8439 (mp) REVERT: D 312 MET cc_start: 0.8120 (tpp) cc_final: 0.7665 (mmt) REVERT: D 372 ASP cc_start: 0.8059 (m-30) cc_final: 0.7554 (m-30) REVERT: D 393 LYS cc_start: 0.6947 (mtmt) cc_final: 0.6474 (mptt) REVERT: D 416 TYR cc_start: 0.8529 (m-80) cc_final: 0.7611 (m-80) REVERT: D 420 LYS cc_start: 0.7623 (mtmt) cc_final: 0.7294 (mmtm) REVERT: D 458 GLN cc_start: 0.5954 (mt0) cc_final: 0.5315 (mp10) REVERT: D 510 ASN cc_start: 0.6525 (t0) cc_final: 0.5817 (m110) outliers start: 60 outliers final: 23 residues processed: 248 average time/residue: 0.5082 time to fit residues: 140.8778 Evaluate side-chains 213 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 TYR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 191 ARG Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain D residue 139 TYR Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 471 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 HIS ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 ASN C 239 HIS ** C 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS D 331 GLN ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.212533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.149336 restraints weight = 15216.951| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.93 r_work: 0.3549 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14980 Z= 0.153 Angle : 0.601 15.564 20376 Z= 0.306 Chirality : 0.042 0.166 2292 Planarity : 0.004 0.044 2556 Dihedral : 4.974 51.011 1998 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.26 % Allowed : 22.65 % Favored : 73.09 % 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 are not related in a simple way. whole: 0.93 (0.20), residues: 1788 helix: 1.64 (0.15), residues: 1108 sheet: -0.09 (0.50), residues: 88 loop : -1.27 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 151 TYR 0.015 0.002 TYR D 269 PHE 0.021 0.002 PHE B 433 TRP 0.019 0.002 TRP A 270 HIS 0.005 0.001 HIS B 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (14980) covalent geometry : angle 0.60143 / 0.31 (20376) hydrogen bonds : bond 0.05089 / 3.37 ( 868) hydrogen bonds : angle 3.88523 / 2.77 ( 2502) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 192 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: B 190 TRP cc_start: 0.6507 (t-100) cc_final: 0.6124 (t-100) REVERT: B 191 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7550 (mtt-85) REVERT: B 206 ARG cc_start: 0.6098 (ptt90) cc_final: 0.5336 (tmm160) REVERT: B 305 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8386 (mp) REVERT: B 312 MET cc_start: 0.7986 (tpp) cc_final: 0.7458 (mmt) REVERT: B 367 GLN cc_start: 0.6915 (tm-30) cc_final: 0.6453 (pp30) REVERT: B 372 ASP cc_start: 0.7932 (m-30) cc_final: 0.7484 (m-30) REVERT: B 416 TYR cc_start: 0.8378 (m-80) cc_final: 0.7521 (m-80) REVERT: B 442 ASP cc_start: 0.7413 (m-30) cc_final: 0.7107 (m-30) REVERT: B 458 GLN cc_start: 0.5930 (mt0) cc_final: 0.5230 (mp10) REVERT: B 510 ASN cc_start: 0.6605 (t0) cc_final: 0.5995 (m110) REVERT: C 85 LEU cc_start: 0.6494 (OUTLIER) cc_final: 0.6260 (mm) REVERT: C 206 ARG cc_start: 0.6030 (OUTLIER) cc_final: 0.5538 (ttp-170) REVERT: C 305 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8382 (mp) REVERT: C 312 MET cc_start: 0.8096 (tpp) cc_final: 0.7607 (mmt) REVERT: C 357 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.6317 (ttp80) REVERT: C 359 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6856 (ttt-90) REVERT: C 363 GLU cc_start: 0.4082 (OUTLIER) cc_final: 0.2372 (tp30) REVERT: C 372 ASP cc_start: 0.8054 (m-30) cc_final: 0.7449 (m-30) REVERT: C 405 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7970 (tp) REVERT: C 416 TYR cc_start: 0.8200 (m-10) cc_final: 0.7563 (m-80) REVERT: C 458 GLN cc_start: 0.6359 (mt0) cc_final: 0.5621 (mp10) REVERT: C 463 PHE cc_start: 0.4922 (t80) cc_final: 0.4384 (t80) REVERT: C 465 GLU cc_start: 0.7667 (pm20) cc_final: 0.7380 (mp0) REVERT: C 510 ASN cc_start: 0.6582 (t0) cc_final: 0.5923 (m110) REVERT: A 85 LEU cc_start: 0.6420 (OUTLIER) cc_final: 0.6164 (mm) REVERT: A 190 TRP cc_start: 0.6401 (t-100) cc_final: 0.6078 (t-100) REVERT: A 295 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8531 (tp) REVERT: A 305 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8393 (mp) REVERT: A 312 MET cc_start: 0.8036 (tpp) cc_final: 0.7547 (mmt) REVERT: A 359 ARG cc_start: 0.7315 (tmt90) cc_final: 0.6887 (ttt-90) REVERT: A 367 GLN cc_start: 0.7003 (tm-30) cc_final: 0.6511 (pp30) REVERT: A 372 ASP cc_start: 0.8028 (m-30) cc_final: 0.7354 (m-30) REVERT: A 416 TYR cc_start: 0.8247 (m-80) cc_final: 0.7613 (m-80) REVERT: A 442 ASP cc_start: 0.7550 (m-30) cc_final: 0.7296 (m-30) REVERT: A 458 GLN cc_start: 0.5794 (mt0) cc_final: 0.5019 (mp10) REVERT: A 510 ASN cc_start: 0.6611 (t0) cc_final: 0.5902 (m110) REVERT: D 160 ASP cc_start: 0.4759 (m-30) cc_final: 0.4469 (t0) REVERT: D 206 ARG cc_start: 0.6166 (ptt90) cc_final: 0.5607 (tmm160) REVERT: D 305 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8377 (mp) REVERT: D 312 MET cc_start: 0.8052 (tpp) cc_final: 0.7555 (mmt) REVERT: D 372 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7417 (m-30) REVERT: D 420 LYS cc_start: 0.7566 (mtmt) cc_final: 0.7214 (mmtm) REVERT: D 458 GLN cc_start: 0.6007 (mt0) cc_final: 0.5366 (mp10) REVERT: D 510 ASN cc_start: 0.6595 (t0) cc_final: 0.5882 (m110) outliers start: 67 outliers final: 25 residues processed: 246 average time/residue: 0.4830 time to fit residues: 133.2046 Evaluate side-chains 215 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 TYR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 191 ARG Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain D residue 139 TYR Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 471 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 82 optimal weight: 0.0050 chunk 170 optimal weight: 0.0060 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.4810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 179 GLN B 239 HIS B 340 ASN B 452 GLN ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 HIS A 239 HIS ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS D 331 GLN ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.214563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.151564 restraints weight = 15207.185| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.94 r_work: 0.3543 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14980 Z= 0.122 Angle : 0.570 15.627 20376 Z= 0.288 Chirality : 0.040 0.153 2292 Planarity : 0.004 0.044 2556 Dihedral : 4.462 50.694 1995 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.24 % Allowed : 23.73 % Favored : 73.03 % 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 are not related in a simple way. whole: 1.22 (0.20), residues: 1788 helix: 1.83 (0.15), residues: 1112 sheet: 0.14 (0.50), residues: 88 loop : -1.08 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 151 TYR 0.017 0.001 TYR A 152 PHE 0.020 0.002 PHE B 433 TRP 0.015 0.001 TRP A 270 HIS 0.005 0.001 HIS B 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (14980) covalent geometry : angle 0.56954 / 0.29 (20376) hydrogen bonds : bond 0.04574 / 3.03 ( 868) hydrogen bonds : angle 3.75808 / 2.68 ( 2502) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 185 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: B 159 PHE cc_start: 0.4805 (OUTLIER) cc_final: 0.3638 (m-80) REVERT: B 190 TRP cc_start: 0.6410 (t-100) cc_final: 0.6081 (t-100) REVERT: B 305 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8396 (mp) REVERT: B 367 GLN cc_start: 0.6867 (tm-30) cc_final: 0.6300 (pp30) REVERT: B 372 ASP cc_start: 0.7822 (m-30) cc_final: 0.7366 (m-30) REVERT: B 416 TYR cc_start: 0.8353 (m-80) cc_final: 0.7529 (m-80) REVERT: B 442 ASP cc_start: 0.7309 (m-30) cc_final: 0.7021 (m-30) REVERT: B 458 GLN cc_start: 0.5903 (mt0) cc_final: 0.5127 (mp10) REVERT: B 510 ASN cc_start: 0.6517 (t0) cc_final: 0.5893 (m110) REVERT: C 85 LEU cc_start: 0.6405 (OUTLIER) cc_final: 0.6177 (mm) REVERT: C 206 ARG cc_start: 0.5979 (OUTLIER) cc_final: 0.5521 (ttp-170) REVERT: C 305 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8352 (mp) REVERT: C 357 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.6344 (ttp80) REVERT: C 359 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6703 (ttt-90) REVERT: C 372 ASP cc_start: 0.7935 (m-30) cc_final: 0.7330 (m-30) REVERT: C 405 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7871 (tp) REVERT: C 416 TYR cc_start: 0.8165 (m-10) cc_final: 0.7345 (m-80) REVERT: C 458 GLN cc_start: 0.6297 (mt0) cc_final: 0.5532 (mp10) REVERT: C 463 PHE cc_start: 0.4694 (t80) cc_final: 0.4228 (t80) REVERT: C 510 ASN cc_start: 0.6501 (t0) cc_final: 0.5814 (m110) REVERT: A 85 LEU cc_start: 0.6326 (OUTLIER) cc_final: 0.6098 (mm) REVERT: A 190 TRP cc_start: 0.6365 (t-100) cc_final: 0.6061 (t-100) REVERT: A 295 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8334 (tp) REVERT: A 305 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8391 (mp) REVERT: A 359 ARG cc_start: 0.7302 (tmt90) cc_final: 0.7001 (ttp80) REVERT: A 367 GLN cc_start: 0.6869 (tm-30) cc_final: 0.6334 (pp30) REVERT: A 372 ASP cc_start: 0.8005 (m-30) cc_final: 0.7364 (m-30) REVERT: A 416 TYR cc_start: 0.8136 (m-80) cc_final: 0.7469 (m-80) REVERT: A 442 ASP cc_start: 0.7490 (m-30) cc_final: 0.7236 (m-30) REVERT: A 458 GLN cc_start: 0.5700 (mt0) cc_final: 0.4863 (mp10) REVERT: A 510 ASN cc_start: 0.6516 (t0) cc_final: 0.5851 (m110) REVERT: D 85 LEU cc_start: 0.6360 (OUTLIER) cc_final: 0.6135 (mm) REVERT: D 159 PHE cc_start: 0.4953 (OUTLIER) cc_final: 0.3835 (m-80) REVERT: D 160 ASP cc_start: 0.4476 (m-30) cc_final: 0.4214 (t0) REVERT: D 206 ARG cc_start: 0.6149 (ptt90) cc_final: 0.5635 (tmm160) REVERT: D 305 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8365 (mp) REVERT: D 363 GLU cc_start: 0.3855 (OUTLIER) cc_final: 0.1787 (tp30) REVERT: D 372 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7433 (m-30) REVERT: D 420 LYS cc_start: 0.7577 (mtmt) cc_final: 0.7175 (mmtm) REVERT: D 458 GLN cc_start: 0.5879 (mt0) cc_final: 0.5219 (mp10) REVERT: D 510 ASN cc_start: 0.6516 (t0) cc_final: 0.5803 (m110) outliers start: 51 outliers final: 27 residues processed: 225 average time/residue: 0.4026 time to fit residues: 101.9383 Evaluate side-chains 215 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 TYR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 139 TYR Chi-restraints excluded: chain D residue 159 PHE Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 471 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 97 optimal weight: 0.3980 chunk 72 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 8 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 HIS ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 HIS C 340 ASN A 179 GLN A 239 HIS ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS D 331 GLN ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 511 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.213842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.150602 restraints weight = 15150.482| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.95 r_work: 0.3540 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14980 Z= 0.131 Angle : 0.571 14.179 20376 Z= 0.288 Chirality : 0.040 0.151 2292 Planarity : 0.004 0.045 2556 Dihedral : 4.479 51.318 1995 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.37 % Allowed : 23.92 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.20), residues: 1788 helix: 1.89 (0.15), residues: 1112 sheet: 0.16 (0.50), residues: 88 loop : -0.98 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 151 TYR 0.014 0.001 TYR D 152 PHE 0.019 0.002 PHE B 433 TRP 0.017 0.001 TRP A 270 HIS 0.005 0.001 HIS B 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (14980) covalent geometry : angle 0.57101 / 0.29 (20376) hydrogen bonds : bond 0.04692 / 3.10 ( 868) hydrogen bonds : angle 3.68626 / 2.62 ( 2502) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 179 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: B 159 PHE cc_start: 0.4692 (OUTLIER) cc_final: 0.3461 (m-80) REVERT: B 190 TRP cc_start: 0.6460 (t-100) cc_final: 0.6093 (t-100) REVERT: B 191 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7663 (mtt180) REVERT: B 305 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8377 (mp) REVERT: B 367 GLN cc_start: 0.6902 (tm-30) cc_final: 0.6296 (pp30) REVERT: B 372 ASP cc_start: 0.7836 (m-30) cc_final: 0.7365 (m-30) REVERT: B 416 TYR cc_start: 0.8351 (m-80) cc_final: 0.7504 (m-80) REVERT: B 442 ASP cc_start: 0.7225 (m-30) cc_final: 0.6972 (m-30) REVERT: B 458 GLN cc_start: 0.5857 (mt0) cc_final: 0.5179 (mp10) REVERT: B 510 ASN cc_start: 0.6544 (t0) cc_final: 0.5909 (m110) REVERT: C 85 LEU cc_start: 0.6464 (OUTLIER) cc_final: 0.6241 (mm) REVERT: C 206 ARG cc_start: 0.6047 (OUTLIER) cc_final: 0.5480 (ttp-170) REVERT: C 357 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.6379 (ttp80) REVERT: C 359 ARG cc_start: 0.7297 (tmt90) cc_final: 0.6865 (ttt-90) REVERT: C 372 ASP cc_start: 0.7950 (m-30) cc_final: 0.7376 (m-30) REVERT: C 405 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7908 (tp) REVERT: C 416 TYR cc_start: 0.8141 (m-10) cc_final: 0.7339 (m-80) REVERT: C 458 GLN cc_start: 0.6367 (mt0) cc_final: 0.5648 (mp10) REVERT: C 463 PHE cc_start: 0.4769 (t80) cc_final: 0.4312 (t80) REVERT: C 510 ASN cc_start: 0.6480 (t0) cc_final: 0.5799 (m110) REVERT: A 85 LEU cc_start: 0.6401 (OUTLIER) cc_final: 0.6195 (mm) REVERT: A 190 TRP cc_start: 0.6392 (t-100) cc_final: 0.6095 (t-100) REVERT: A 295 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8486 (tp) REVERT: A 305 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8398 (mp) REVERT: A 359 ARG cc_start: 0.7356 (tmt90) cc_final: 0.7070 (tmt90) REVERT: A 367 GLN cc_start: 0.6937 (tm-30) cc_final: 0.6376 (pp30) REVERT: A 372 ASP cc_start: 0.8036 (m-30) cc_final: 0.7429 (m-30) REVERT: A 416 TYR cc_start: 0.8154 (m-80) cc_final: 0.7493 (m-80) REVERT: A 442 ASP cc_start: 0.7490 (m-30) cc_final: 0.7249 (m-30) REVERT: A 510 ASN cc_start: 0.6548 (t0) cc_final: 0.5865 (m110) REVERT: D 85 LEU cc_start: 0.6439 (OUTLIER) cc_final: 0.6238 (mm) REVERT: D 159 PHE cc_start: 0.4958 (OUTLIER) cc_final: 0.3818 (m-80) REVERT: D 160 ASP cc_start: 0.4568 (m-30) cc_final: 0.4303 (t0) REVERT: D 206 ARG cc_start: 0.6199 (ptt90) cc_final: 0.5760 (tmm160) REVERT: D 363 GLU cc_start: 0.3751 (OUTLIER) cc_final: 0.1663 (tp30) REVERT: D 372 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7523 (m-30) REVERT: D 420 LYS cc_start: 0.7565 (mtmt) cc_final: 0.7166 (mmtm) REVERT: D 458 GLN cc_start: 0.5891 (mt0) cc_final: 0.5221 (mp10) REVERT: D 510 ASN cc_start: 0.6468 (t0) cc_final: 0.5786 (m110) outliers start: 53 outliers final: 26 residues processed: 223 average time/residue: 0.4601 time to fit residues: 115.2098 Evaluate side-chains 214 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 TYR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 191 ARG Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 139 TYR Chi-restraints excluded: chain D residue 159 PHE Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 471 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 78 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 79 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 60.878 > 50:) chunk 47 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 HIS ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 HIS A 239 HIS ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 GLN ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 511 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.212753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.152370 restraints weight = 15232.731| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.15 r_work: 0.3502 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14980 Z= 0.155 Angle : 0.599 17.316 20376 Z= 0.302 Chirality : 0.042 0.183 2292 Planarity : 0.004 0.045 2556 Dihedral : 4.589 53.685 1995 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.63 % Allowed : 24.11 % Favored : 72.26 % 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 are not related in a simple way. whole: 1.29 (0.20), residues: 1788 helix: 1.84 (0.15), residues: 1112 sheet: 0.06 (0.50), residues: 88 loop : -0.95 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 151 TYR 0.016 0.002 TYR D 152 PHE 0.020 0.002 PHE D 433 TRP 0.019 0.002 TRP A 270 HIS 0.004 0.001 HIS C 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (14980) covalent geometry : angle 0.59880 / 0.30 (20376) hydrogen bonds : bond 0.04978 / 3.29 ( 868) hydrogen bonds : angle 3.72852 / 2.65 ( 2502) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 176 time to evaluate : 0.398 Fit side-chains REVERT: B 159 PHE cc_start: 0.4642 (OUTLIER) cc_final: 0.3351 (m-80) REVERT: B 187 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7953 (mt) REVERT: B 190 TRP cc_start: 0.6554 (t-100) cc_final: 0.6214 (t-100) REVERT: B 191 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7821 (mtt180) REVERT: B 305 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8428 (mp) REVERT: B 312 MET cc_start: 0.8064 (tpp) cc_final: 0.7547 (mmt) REVERT: B 359 ARG cc_start: 0.7432 (tmt90) cc_final: 0.6920 (ttp80) REVERT: B 367 GLN cc_start: 0.6944 (tm-30) cc_final: 0.6355 (pp30) REVERT: B 372 ASP cc_start: 0.8011 (m-30) cc_final: 0.7550 (m-30) REVERT: B 442 ASP cc_start: 0.7377 (m-30) cc_final: 0.7109 (m-30) REVERT: B 458 GLN cc_start: 0.5977 (mt0) cc_final: 0.5236 (mp10) REVERT: B 470 CYS cc_start: 0.8225 (m) cc_final: 0.7813 (m) REVERT: B 509 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7921 (tpp) REVERT: B 510 ASN cc_start: 0.6680 (t0) cc_final: 0.5980 (m110) REVERT: C 85 LEU cc_start: 0.6617 (OUTLIER) cc_final: 0.6398 (mm) REVERT: C 206 ARG cc_start: 0.5991 (OUTLIER) cc_final: 0.5399 (ttp-170) REVERT: C 278 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8153 (t) REVERT: C 305 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8390 (mp) REVERT: C 312 MET cc_start: 0.8142 (tpp) cc_final: 0.7627 (mmt) REVERT: C 357 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.6370 (ttp80) REVERT: C 359 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6605 (ttp-170) REVERT: C 372 ASP cc_start: 0.8087 (m-30) cc_final: 0.7573 (m-30) REVERT: C 405 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8016 (tp) REVERT: C 416 TYR cc_start: 0.8249 (m-10) cc_final: 0.7490 (m-80) REVERT: C 458 GLN cc_start: 0.6363 (mt0) cc_final: 0.5605 (mp10) REVERT: C 463 PHE cc_start: 0.4962 (t80) cc_final: 0.4474 (t80) REVERT: C 510 ASN cc_start: 0.6559 (t0) cc_final: 0.5905 (m110) REVERT: A 85 LEU cc_start: 0.6495 (OUTLIER) cc_final: 0.6279 (mm) REVERT: A 159 PHE cc_start: 0.4629 (OUTLIER) cc_final: 0.3542 (m-80) REVERT: A 190 TRP cc_start: 0.6477 (t-100) cc_final: 0.6182 (t-100) REVERT: A 295 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8596 (tp) REVERT: A 305 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8442 (mp) REVERT: A 312 MET cc_start: 0.8080 (tpp) cc_final: 0.7580 (mmt) REVERT: A 367 GLN cc_start: 0.6966 (tm-30) cc_final: 0.6312 (pp30) REVERT: A 372 ASP cc_start: 0.8105 (m-30) cc_final: 0.7518 (m-30) REVERT: A 416 TYR cc_start: 0.8300 (m-80) cc_final: 0.7631 (m-80) REVERT: A 442 ASP cc_start: 0.7610 (m-30) cc_final: 0.7389 (m-30) REVERT: A 458 GLN cc_start: 0.5857 (mt0) cc_final: 0.5075 (mp10) REVERT: A 509 MET cc_start: 0.8133 (tpt) cc_final: 0.7907 (tpp) REVERT: A 510 ASN cc_start: 0.6647 (t0) cc_final: 0.5976 (m110) REVERT: D 159 PHE cc_start: 0.5010 (OUTLIER) cc_final: 0.3856 (m-80) REVERT: D 160 ASP cc_start: 0.4869 (m-30) cc_final: 0.4590 (t0) REVERT: D 206 ARG cc_start: 0.6199 (ptt90) cc_final: 0.5750 (tmm160) REVERT: D 305 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8406 (mp) REVERT: D 312 MET cc_start: 0.8125 (tpp) cc_final: 0.7615 (mmt) REVERT: D 363 GLU cc_start: 0.3989 (OUTLIER) cc_final: 0.1807 (tp30) REVERT: D 372 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7618 (m-30) REVERT: D 458 GLN cc_start: 0.6106 (mt0) cc_final: 0.5376 (mp10) REVERT: D 509 MET cc_start: 0.8156 (tpt) cc_final: 0.7914 (tpp) REVERT: D 510 ASN cc_start: 0.6610 (t0) cc_final: 0.5864 (m110) outliers start: 57 outliers final: 29 residues processed: 222 average time/residue: 0.4653 time to fit residues: 116.3387 Evaluate side-chains 221 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 172 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 TYR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 191 ARG Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain D residue 139 TYR Chi-restraints excluded: chain D residue 159 PHE Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 471 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 57 optimal weight: 0.0570 chunk 72 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 HIS ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 HIS A 239 HIS ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 GLN ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 511 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.214180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.150978 restraints weight = 15332.989| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.14 r_work: 0.3563 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14980 Z= 0.127 Angle : 0.572 16.396 20376 Z= 0.287 Chirality : 0.040 0.173 2292 Planarity : 0.004 0.045 2556 Dihedral : 4.470 53.772 1995 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.31 % Allowed : 25.00 % Favored : 71.69 % 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 are not related in a simple way. whole: 1.46 (0.20), residues: 1788 helix: 1.96 (0.15), residues: 1108 sheet: 0.11 (0.50), residues: 88 loop : -0.83 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 359 TYR 0.013 0.001 TYR D 152 PHE 0.019 0.001 PHE B 433 TRP 0.016 0.001 TRP A 270 HIS 0.004 0.001 HIS B 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (14980) covalent geometry : angle 0.57194 / 0.29 (20376) hydrogen bonds : bond 0.04535 / 3.00 ( 868) hydrogen bonds : angle 3.63995 / 2.59 ( 2502) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 178 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: B 159 PHE cc_start: 0.4667 (OUTLIER) cc_final: 0.3329 (m-80) REVERT: B 187 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7913 (mt) REVERT: B 190 TRP cc_start: 0.6504 (t-100) cc_final: 0.6205 (t-100) REVERT: B 206 ARG cc_start: 0.6297 (ptt90) cc_final: 0.5760 (tmm160) REVERT: B 245 MET cc_start: 0.7324 (mmm) cc_final: 0.6995 (mmm) REVERT: B 305 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8419 (mp) REVERT: B 359 ARG cc_start: 0.7434 (tmt90) cc_final: 0.6935 (ttp-170) REVERT: B 367 GLN cc_start: 0.6867 (tm-30) cc_final: 0.6325 (pp30) REVERT: B 372 ASP cc_start: 0.7927 (m-30) cc_final: 0.7464 (m-30) REVERT: B 442 ASP cc_start: 0.7238 (m-30) cc_final: 0.6990 (m-30) REVERT: B 458 GLN cc_start: 0.5852 (mt0) cc_final: 0.5214 (mp10) REVERT: B 509 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7936 (tpp) REVERT: B 510 ASN cc_start: 0.6664 (t0) cc_final: 0.5993 (m110) REVERT: C 85 LEU cc_start: 0.6513 (OUTLIER) cc_final: 0.6306 (mm) REVERT: C 206 ARG cc_start: 0.6002 (OUTLIER) cc_final: 0.5481 (ttp-170) REVERT: C 305 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8385 (mp) REVERT: C 357 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.6447 (ttp80) REVERT: C 372 ASP cc_start: 0.7998 (m-30) cc_final: 0.7495 (m-30) REVERT: C 405 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7939 (tp) REVERT: C 416 TYR cc_start: 0.8181 (m-10) cc_final: 0.7388 (m-80) REVERT: C 458 GLN cc_start: 0.6383 (mt0) cc_final: 0.5664 (mp10) REVERT: C 463 PHE cc_start: 0.4884 (t80) cc_final: 0.4433 (t80) REVERT: C 509 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7868 (tpp) REVERT: C 510 ASN cc_start: 0.6456 (t0) cc_final: 0.5823 (m110) REVERT: A 85 LEU cc_start: 0.6443 (OUTLIER) cc_final: 0.6224 (mm) REVERT: A 159 PHE cc_start: 0.4609 (OUTLIER) cc_final: 0.3490 (m-80) REVERT: A 190 TRP cc_start: 0.6396 (t-100) cc_final: 0.6187 (t-100) REVERT: A 295 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8397 (tp) REVERT: A 305 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8439 (mp) REVERT: A 367 GLN cc_start: 0.6992 (tm-30) cc_final: 0.6391 (pp30) REVERT: A 372 ASP cc_start: 0.8004 (m-30) cc_final: 0.7451 (m-30) REVERT: A 416 TYR cc_start: 0.8188 (m-80) cc_final: 0.7534 (m-80) REVERT: A 442 ASP cc_start: 0.7557 (m-30) cc_final: 0.7345 (m-30) REVERT: A 509 MET cc_start: 0.8099 (tpt) cc_final: 0.7871 (tpp) REVERT: A 510 ASN cc_start: 0.6586 (t0) cc_final: 0.5918 (m110) REVERT: D 160 ASP cc_start: 0.4573 (m-30) cc_final: 0.4365 (t0) REVERT: D 206 ARG cc_start: 0.6207 (ptt90) cc_final: 0.5817 (tmm160) REVERT: D 245 MET cc_start: 0.7294 (mmm) cc_final: 0.6956 (mmm) REVERT: D 305 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8411 (mp) REVERT: D 322 ARG cc_start: 0.5650 (OUTLIER) cc_final: 0.5189 (ttt180) REVERT: D 359 ARG cc_start: 0.7372 (tmm160) cc_final: 0.6875 (tmt-80) REVERT: D 363 GLU cc_start: 0.4067 (OUTLIER) cc_final: 0.1563 (tp30) REVERT: D 372 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7593 (m-30) REVERT: D 458 GLN cc_start: 0.6064 (mt0) cc_final: 0.5344 (mp10) REVERT: D 509 MET cc_start: 0.8104 (tpt) cc_final: 0.7875 (tpp) REVERT: D 510 ASN cc_start: 0.6541 (t0) cc_final: 0.5810 (m110) outliers start: 52 outliers final: 27 residues processed: 219 average time/residue: 0.4454 time to fit residues: 108.6551 Evaluate side-chains 213 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 TYR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain D residue 139 TYR Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 471 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 161 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 112 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 HIS ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 HIS A 239 HIS ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN D 331 GLN ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.213012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.149798 restraints weight = 15216.396| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.92 r_work: 0.3544 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14980 Z= 0.153 Angle : 0.598 15.681 20376 Z= 0.303 Chirality : 0.042 0.170 2292 Planarity : 0.004 0.048 2556 Dihedral : 4.589 55.262 1995 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.99 % Allowed : 25.45 % Favored : 71.56 % 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 are not related in a simple way. whole: 1.36 (0.20), residues: 1788 helix: 1.88 (0.15), residues: 1108 sheet: 0.10 (0.50), residues: 88 loop : -0.85 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 479 TYR 0.015 0.002 TYR D 152 PHE 0.020 0.002 PHE D 433 TRP 0.020 0.002 TRP D 190 HIS 0.004 0.001 HIS C 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (14980) covalent geometry : angle 0.59787 / 0.30 (20376) hydrogen bonds : bond 0.04901 / 3.24 ( 868) hydrogen bonds : angle 3.78141 / 2.68 ( 2502) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 174 time to evaluate : 0.359 Fit side-chains REVERT: B 159 PHE cc_start: 0.4659 (OUTLIER) cc_final: 0.3325 (m-80) REVERT: B 187 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7958 (mt) REVERT: B 190 TRP cc_start: 0.6551 (t-100) cc_final: 0.6240 (t-100) REVERT: B 305 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8390 (mp) REVERT: B 359 ARG cc_start: 0.7462 (tmt90) cc_final: 0.6922 (ttp-170) REVERT: B 367 GLN cc_start: 0.6894 (tm-30) cc_final: 0.6323 (pp30) REVERT: B 372 ASP cc_start: 0.7914 (m-30) cc_final: 0.7449 (m-30) REVERT: B 442 ASP cc_start: 0.7259 (m-30) cc_final: 0.6996 (m-30) REVERT: B 458 GLN cc_start: 0.5956 (mt0) cc_final: 0.5246 (mp10) REVERT: B 510 ASN cc_start: 0.6629 (t0) cc_final: 0.5995 (m110) REVERT: C 85 LEU cc_start: 0.6508 (OUTLIER) cc_final: 0.6302 (mm) REVERT: C 206 ARG cc_start: 0.5963 (OUTLIER) cc_final: 0.5401 (ttp-170) REVERT: C 278 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8105 (t) REVERT: C 305 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8352 (mp) REVERT: C 359 ARG cc_start: 0.7320 (tmt90) cc_final: 0.6960 (ttt-90) REVERT: C 372 ASP cc_start: 0.8007 (m-30) cc_final: 0.7497 (m-30) REVERT: C 405 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.8001 (tp) REVERT: C 416 TYR cc_start: 0.8244 (m-10) cc_final: 0.7414 (m-80) REVERT: C 458 GLN cc_start: 0.6282 (mt0) cc_final: 0.5558 (mp10) REVERT: C 463 PHE cc_start: 0.4870 (t80) cc_final: 0.4409 (t80) REVERT: C 509 MET cc_start: 0.8115 (tpt) cc_final: 0.7905 (tpp) REVERT: C 510 ASN cc_start: 0.6502 (t0) cc_final: 0.5840 (m110) REVERT: A 85 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.6211 (mm) REVERT: A 159 PHE cc_start: 0.4611 (OUTLIER) cc_final: 0.3491 (m-80) REVERT: A 190 TRP cc_start: 0.6421 (t-100) cc_final: 0.6201 (t-100) REVERT: A 295 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8537 (tp) REVERT: A 305 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8399 (mp) REVERT: A 359 ARG cc_start: 0.7331 (tmt90) cc_final: 0.7013 (tmt90) REVERT: A 367 GLN cc_start: 0.6996 (tm-30) cc_final: 0.6351 (pp30) REVERT: A 372 ASP cc_start: 0.8007 (m-30) cc_final: 0.7459 (m-30) REVERT: A 416 TYR cc_start: 0.8227 (m-80) cc_final: 0.7534 (m-80) REVERT: A 442 ASP cc_start: 0.7532 (m-30) cc_final: 0.7327 (m-30) REVERT: A 458 GLN cc_start: 0.5813 (mt0) cc_final: 0.5022 (mp10) REVERT: A 509 MET cc_start: 0.8102 (tpt) cc_final: 0.7869 (tpp) REVERT: A 510 ASN cc_start: 0.6508 (t0) cc_final: 0.5873 (m110) REVERT: D 160 ASP cc_start: 0.4752 (m-30) cc_final: 0.4532 (t0) REVERT: D 206 ARG cc_start: 0.6242 (ptt90) cc_final: 0.5830 (tmm160) REVERT: D 305 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8365 (mp) REVERT: D 322 ARG cc_start: 0.5696 (OUTLIER) cc_final: 0.5198 (ttt180) REVERT: D 359 ARG cc_start: 0.7400 (tmm160) cc_final: 0.7005 (tmt170) REVERT: D 363 GLU cc_start: 0.4165 (OUTLIER) cc_final: 0.1827 (tp30) REVERT: D 416 TYR cc_start: 0.8494 (m-80) cc_final: 0.7880 (m-80) REVERT: D 458 GLN cc_start: 0.6160 (mt0) cc_final: 0.5462 (mp10) REVERT: D 509 MET cc_start: 0.8128 (tpt) cc_final: 0.7879 (tpp) REVERT: D 510 ASN cc_start: 0.6573 (t0) cc_final: 0.5826 (m110) outliers start: 47 outliers final: 25 residues processed: 214 average time/residue: 0.4170 time to fit residues: 99.8807 Evaluate side-chains 212 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 TYR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain D residue 139 TYR Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 471 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 4 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 151 optimal weight: 0.8980 chunk 98 optimal weight: 0.0000 chunk 95 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 10 optimal weight: 0.0470 chunk 120 optimal weight: 0.5980 overall best weight: 0.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 HIS ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS D 331 GLN ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.215318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.152411 restraints weight = 15169.380| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.12 r_work: 0.3575 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14980 Z= 0.119 Angle : 0.569 15.620 20376 Z= 0.286 Chirality : 0.040 0.165 2292 Planarity : 0.004 0.046 2556 Dihedral : 4.405 54.253 1995 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.42 % Allowed : 25.89 % Favored : 71.69 % 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 are not related in a simple way. whole: 1.59 (0.20), residues: 1788 helix: 2.05 (0.15), residues: 1104 sheet: 0.24 (0.50), residues: 88 loop : -0.72 (0.28), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 359 TYR 0.013 0.001 TYR D 152 PHE 0.020 0.001 PHE B 433 TRP 0.021 0.001 TRP C 190 HIS 0.003 0.001 HIS C 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (14980) covalent geometry : angle 0.56892 / 0.29 (20376) hydrogen bonds : bond 0.04349 / 2.87 ( 868) hydrogen bonds : angle 3.67866 / 2.61 ( 2502) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6127.71 seconds wall clock time: 104 minutes 50.47 seconds (6290.47 seconds total)