Starting phenix.real_space_refine on Tue Jun 17 15:50:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q3n_18130/06_2025/8q3n_18130.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q3n_18130/06_2025/8q3n_18130.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q3n_18130/06_2025/8q3n_18130.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q3n_18130/06_2025/8q3n_18130.map" model { file = "/net/cci-nas-00/data/ceres_data/8q3n_18130/06_2025/8q3n_18130.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q3n_18130/06_2025/8q3n_18130.cif" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 102 5.16 5 C 12486 2.51 5 N 3540 2.21 5 O 3768 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19912 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "B" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "C" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "D" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "E" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "F" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.66, per 1000 atoms: 0.69 Number of scatterers: 19912 At special positions: 0 Unit cell: (116.48, 134.784, 144.768, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 102 16.00 P 12 15.00 Mg 4 11.99 O 3768 8.00 N 3540 7.00 C 12486 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.17 Conformation dependent library (CDL) restraints added in 2.6 seconds 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4668 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 20 sheets defined 49.6% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 10 through 22 Processing helix chain 'A' and resid 30 through 46 Processing helix chain 'A' and resid 82 through 89 Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 153 through 166 removed outlier: 4.041A pdb=" N THR A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 199 Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 235 through 255 removed outlier: 3.538A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 285 through 289 removed outlier: 4.002A pdb=" N VAL A 289 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.567A pdb=" N GLU A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.298A pdb=" N LEU A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 388 Processing helix chain 'A' and resid 391 through 405 Processing helix chain 'A' and resid 408 through 418 Processing helix chain 'B' and resid 2 through 9 removed outlier: 3.619A pdb=" N THR B 9 " --> pdb=" O GLU B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 21 Processing helix chain 'B' and resid 30 through 44 Processing helix chain 'B' and resid 82 through 89 Processing helix chain 'B' and resid 123 through 128 removed outlier: 3.796A pdb=" N ARG B 128 " --> pdb=" O PRO B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 155 through 166 removed outlier: 3.955A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 Processing helix chain 'B' and resid 212 through 223 Processing helix chain 'B' and resid 235 through 255 removed outlier: 3.550A pdb=" N HIS B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 290 through 302 removed outlier: 4.214A pdb=" N ARG B 296 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Proline residue: B 297 - end of helix Processing helix chain 'B' and resid 325 through 335 removed outlier: 3.567A pdb=" N GLU B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 352 Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.083A pdb=" N LEU B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 388 Processing helix chain 'B' and resid 391 through 405 removed outlier: 3.778A pdb=" N MET B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 417 Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 10 through 22 Processing helix chain 'C' and resid 30 through 46 removed outlier: 3.714A pdb=" N SER C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY C 46 " --> pdb=" O HIS C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 Processing helix chain 'C' and resid 123 through 128 removed outlier: 3.584A pdb=" N ARG C 128 " --> pdb=" O PRO C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 155 through 166 removed outlier: 4.021A pdb=" N ALA C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 199 Processing helix chain 'C' and resid 212 through 223 Processing helix chain 'C' and resid 235 through 255 Processing helix chain 'C' and resid 266 through 278 Processing helix chain 'C' and resid 291 through 302 removed outlier: 4.228A pdb=" N ARG C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) Proline residue: C 297 - end of helix Processing helix chain 'C' and resid 325 through 335 Processing helix chain 'C' and resid 346 through 352 Processing helix chain 'C' and resid 367 through 372 removed outlier: 4.159A pdb=" N LEU C 371 " --> pdb=" O LYS C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 388 Processing helix chain 'C' and resid 391 through 404 Processing helix chain 'C' and resid 408 through 417 Processing helix chain 'D' and resid 2 through 7 Processing helix chain 'D' and resid 10 through 22 Processing helix chain 'D' and resid 30 through 46 removed outlier: 3.544A pdb=" N GLY D 46 " --> pdb=" O HIS D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 82 through 89 Processing helix chain 'D' and resid 123 through 128 removed outlier: 3.677A pdb=" N ARG D 128 " --> pdb=" O PRO D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 154 through 166 removed outlier: 4.273A pdb=" N THR D 158 " --> pdb=" O THR D 154 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 Processing helix chain 'D' and resid 212 through 223 Processing helix chain 'D' and resid 235 through 255 removed outlier: 3.525A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 278 Processing helix chain 'D' and resid 290 through 303 removed outlier: 4.160A pdb=" N ARG D 296 " --> pdb=" O ASN D 292 " (cutoff:3.500A) Proline residue: D 297 - end of helix Processing helix chain 'D' and resid 325 through 335 Processing helix chain 'D' and resid 346 through 352 Processing helix chain 'D' and resid 367 through 372 removed outlier: 4.224A pdb=" N LEU D 371 " --> pdb=" O LYS D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 388 Processing helix chain 'D' and resid 391 through 405 removed outlier: 3.870A pdb=" N MET D 405 " --> pdb=" O ASN D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 417 Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 10 through 22 Processing helix chain 'E' and resid 30 through 44 Processing helix chain 'E' and resid 82 through 89 removed outlier: 3.625A pdb=" N ILE E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 128 Processing helix chain 'E' and resid 153 through 166 Processing helix chain 'E' and resid 183 through 199 Processing helix chain 'E' and resid 212 through 223 Processing helix chain 'E' and resid 235 through 255 Processing helix chain 'E' and resid 266 through 278 Processing helix chain 'E' and resid 290 through 302 removed outlier: 4.105A pdb=" N ARG E 296 " --> pdb=" O ASN E 292 " (cutoff:3.500A) Proline residue: E 297 - end of helix Processing helix chain 'E' and resid 325 through 334 removed outlier: 3.646A pdb=" N GLU E 329 " --> pdb=" O SER E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 352 Processing helix chain 'E' and resid 367 through 371 removed outlier: 3.684A pdb=" N LEU E 370 " --> pdb=" O LYS E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 388 removed outlier: 3.695A pdb=" N LEU E 377 " --> pdb=" O THR E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 405 removed outlier: 3.896A pdb=" N MET E 405 " --> pdb=" O ASN E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 418 Processing helix chain 'F' and resid 2 through 9 removed outlier: 3.507A pdb=" N THR F 9 " --> pdb=" O GLU F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 22 Processing helix chain 'F' and resid 31 through 44 Processing helix chain 'F' and resid 82 through 89 removed outlier: 4.007A pdb=" N ILE F 86 " --> pdb=" O SER F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 127 Processing helix chain 'F' and resid 132 through 136 Processing helix chain 'F' and resid 153 through 166 removed outlier: 4.168A pdb=" N LEU F 162 " --> pdb=" O THR F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 199 removed outlier: 3.999A pdb=" N LEU F 187 " --> pdb=" O GLY F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 223 Processing helix chain 'F' and resid 235 through 256 removed outlier: 3.913A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 278 Processing helix chain 'F' and resid 290 through 302 removed outlier: 3.796A pdb=" N LEU F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG F 296 " --> pdb=" O ASN F 292 " (cutoff:3.500A) Proline residue: F 297 - end of helix Processing helix chain 'F' and resid 326 through 335 Processing helix chain 'F' and resid 346 through 351 Processing helix chain 'F' and resid 373 through 388 Processing helix chain 'F' and resid 391 through 406 Processing helix chain 'F' and resid 408 through 418 removed outlier: 3.625A pdb=" N ARG F 418 " --> pdb=" O GLU F 414 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 57 removed outlier: 3.733A pdb=" N ILE A 79 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N TYR A 80 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N LYS A 115 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU A 114 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ARG A 102 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL A 116 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LYS A 100 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ILE A 49 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.563A pdb=" N ASN A 306 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 318 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL A 203 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU A 263 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N MET A 205 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU A 204 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL A 228 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N VAL A 206 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N SER A 230 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU A 208 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.563A pdb=" N ASN A 306 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLY A 174 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ALA A 319 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE A 176 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ARG A 173 " --> pdb=" O MET A 341 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LEU A 343 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 175 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 49 through 57 removed outlier: 3.855A pdb=" N ILE B 79 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LYS B 100 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N VAL B 116 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N SER B 98 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLU B 118 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR B 96 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE B 49 " --> pdb=" O ILE B 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 138 through 139 removed outlier: 6.494A pdb=" N VAL B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ILE B 316 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE B 262 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N THR B 318 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU B 264 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 9.469A pdb=" N LEU B 320 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL B 203 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LEU B 263 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N MET B 205 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 138 through 139 removed outlier: 6.475A pdb=" N GLY B 174 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ALA B 319 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE B 176 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 49 through 57 removed outlier: 3.844A pdb=" N ILE C 79 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LYS C 100 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N VAL C 116 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N SER C 98 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLU C 118 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR C 96 " --> pdb=" O GLU C 118 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE C 49 " --> pdb=" O ILE C 101 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.502A pdb=" N ASN C 306 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL C 260 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILE C 316 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE C 262 " --> pdb=" O ILE C 316 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N THR C 318 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU C 264 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N LEU C 320 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL C 203 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU C 263 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N MET C 205 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.502A pdb=" N ASN C 306 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLY C 174 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ALA C 319 " --> pdb=" O GLY C 174 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE C 176 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU C 175 " --> pdb=" O LEU C 343 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU C 345 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C 177 " --> pdb=" O LEU C 345 " (cutoff:3.500A) removed outlier: 9.869A pdb=" N GLU C 342 " --> pdb=" O ASN C 361 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N ASN C 361 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N HIS C 344 " --> pdb=" O ASP C 359 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 284 through 285 removed outlier: 3.770A pdb=" N VAL C 289 " --> pdb=" O LEU C 285 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 49 through 57 removed outlier: 3.806A pdb=" N ILE D 79 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LYS D 100 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL D 116 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N SER D 98 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU D 118 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR D 96 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE D 49 " --> pdb=" O ILE D 101 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 138 through 139 removed outlier: 3.565A pdb=" N ASN D 306 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL D 260 " --> pdb=" O THR D 314 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ILE D 316 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE D 262 " --> pdb=" O ILE D 316 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N THR D 318 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU D 264 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N LEU D 320 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL D 203 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU D 263 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N MET D 205 " --> pdb=" O LEU D 263 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 138 through 139 removed outlier: 3.565A pdb=" N ASN D 306 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY D 174 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA D 319 " --> pdb=" O GLY D 174 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE D 176 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU D 175 " --> pdb=" O LEU D 343 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU D 345 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL D 177 " --> pdb=" O LEU D 345 " (cutoff:3.500A) removed outlier: 10.011A pdb=" N GLU D 342 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N ASN D 361 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N HIS D 344 " --> pdb=" O ASP D 359 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 49 through 57 removed outlier: 3.761A pdb=" N ILE E 79 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS E 100 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N VAL E 116 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N SER E 98 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU E 118 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR E 96 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE E 49 " --> pdb=" O ILE E 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 138 through 139 removed outlier: 3.616A pdb=" N ASN E 306 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL E 260 " --> pdb=" O THR E 314 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE E 316 " --> pdb=" O VAL E 260 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE E 262 " --> pdb=" O ILE E 316 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N THR E 318 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU E 264 " --> pdb=" O THR E 318 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N LEU E 320 " --> pdb=" O LEU E 264 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU E 204 " --> pdb=" O GLU E 226 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N VAL E 228 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL E 206 " --> pdb=" O VAL E 228 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N SER E 230 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU E 208 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 138 through 139 removed outlier: 3.616A pdb=" N ASN E 306 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU E 342 " --> pdb=" O GLY E 364 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 144 through 145 removed outlier: 4.229A pdb=" N ILE E 168 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 49 through 57 removed outlier: 8.765A pdb=" N TYR F 80 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA F 112 " --> pdb=" O ARG F 102 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE F 49 " --> pdb=" O ILE F 101 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 138 through 139 removed outlier: 3.983A pdb=" N ASN F 306 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR F 314 " --> pdb=" O VAL F 260 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL F 203 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU F 204 " --> pdb=" O GLU F 226 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N VAL F 228 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N VAL F 206 " --> pdb=" O VAL F 228 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 138 through 139 removed outlier: 3.983A pdb=" N ASN F 306 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY F 174 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ALA F 319 " --> pdb=" O GLY F 174 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE F 176 " --> pdb=" O ALA F 319 " (cutoff:3.500A) 950 hydrogen bonds defined for protein. 2718 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.17 Time building geometry restraints manager: 6.08 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: 6759 1.34 - 1.46: 3970 1.46 - 1.58: 9268 1.58 - 1.70: 19 1.70 - 1.82: 198 Bond restraints: 20214 Sorted by residual: bond pdb=" CB PRO F 167 " pdb=" CG PRO F 167 " ideal model delta sigma weight residual 1.492 1.589 -0.097 5.00e-02 4.00e+02 3.77e+00 bond pdb=" CB LYS F 257 " pdb=" CG LYS F 257 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.65e+00 bond pdb=" CB ASP C 322 " pdb=" CG ASP C 322 " ideal model delta sigma weight residual 1.516 1.548 -0.032 2.50e-02 1.60e+03 1.62e+00 bond pdb=" CB LYS A 348 " pdb=" CG LYS A 348 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.52e+00 bond pdb=" CG PRO F 167 " pdb=" CD PRO F 167 " ideal model delta sigma weight residual 1.503 1.462 0.041 3.40e-02 8.65e+02 1.45e+00 ... (remaining 20209 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 26859 2.41 - 4.82: 309 4.82 - 7.23: 69 7.23 - 9.65: 12 9.65 - 12.06: 3 Bond angle restraints: 27252 Sorted by residual: angle pdb=" CA PRO F 167 " pdb=" N PRO F 167 " pdb=" CD PRO F 167 " ideal model delta sigma weight residual 112.00 104.97 7.03 1.40e+00 5.10e-01 2.52e+01 angle pdb=" C LYS F 379 " pdb=" N MET F 380 " pdb=" CA MET F 380 " ideal model delta sigma weight residual 121.58 112.00 9.58 1.95e+00 2.63e-01 2.41e+01 angle pdb=" CA MET F 380 " pdb=" CB MET F 380 " pdb=" CG MET F 380 " ideal model delta sigma weight residual 114.10 123.23 -9.13 2.00e+00 2.50e-01 2.08e+01 angle pdb=" N MET F 380 " pdb=" CA MET F 380 " pdb=" CB MET F 380 " ideal model delta sigma weight residual 110.41 117.79 -7.38 1.68e+00 3.54e-01 1.93e+01 angle pdb=" CB MET D 416 " pdb=" CG MET D 416 " pdb=" SD MET D 416 " ideal model delta sigma weight residual 112.70 124.76 -12.06 3.00e+00 1.11e-01 1.62e+01 ... (remaining 27247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 12189 35.65 - 71.30: 302 71.30 - 106.94: 15 106.94 - 142.59: 5 142.59 - 178.24: 5 Dihedral angle restraints: 12516 sinusoidal: 5304 harmonic: 7212 Sorted by residual: dihedral pdb=" O2A ADP D1000 " pdb=" O3A ADP D1000 " pdb=" PA ADP D1000 " pdb=" PB ADP D1000 " ideal model delta sinusoidal sigma weight residual -60.00 118.24 -178.24 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP C1000 " pdb=" O3A ADP C1000 " pdb=" PA ADP C1000 " pdb=" PB ADP C1000 " ideal model delta sinusoidal sigma weight residual -60.00 115.43 -175.43 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP D1000 " pdb=" O5' ADP D1000 " pdb=" PA ADP D1000 " pdb=" O2A ADP D1000 " ideal model delta sinusoidal sigma weight residual 300.00 129.32 170.68 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 12513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2528 0.052 - 0.103: 466 0.103 - 0.154: 100 0.154 - 0.206: 1 0.206 - 0.257: 1 Chirality restraints: 3096 Sorted by residual: chirality pdb=" CA MET F 380 " pdb=" N MET F 380 " pdb=" C MET F 380 " pdb=" CB MET F 380 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CG LEU F 188 " pdb=" CB LEU F 188 " pdb=" CD1 LEU F 188 " pdb=" CD2 LEU F 188 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.87e-01 chirality pdb=" CA ASP B 322 " pdb=" N ASP B 322 " pdb=" C ASP B 322 " pdb=" CB ASP B 322 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 3093 not shown) Planarity restraints: 3528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER F 166 " 0.078 5.00e-02 4.00e+02 1.14e-01 2.10e+01 pdb=" N PRO F 167 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO F 167 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO F 167 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 381 " -0.022 2.00e-02 2.50e+03 2.04e-02 1.04e+01 pdb=" CG TRP E 381 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP E 381 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP E 381 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 381 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 381 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 381 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 381 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 381 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP E 381 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 322 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.08e+00 pdb=" C ASP C 322 " -0.039 2.00e-02 2.50e+03 pdb=" O ASP C 322 " 0.015 2.00e-02 2.50e+03 pdb=" N THR C 323 " 0.013 2.00e-02 2.50e+03 ... (remaining 3525 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 232 2.57 - 3.15: 16155 3.15 - 3.74: 31886 3.74 - 4.32: 43263 4.32 - 4.90: 72543 Nonbonded interactions: 164079 Sorted by model distance: nonbonded pdb=" O2B ADP C1000 " pdb="MG MG C1001 " model vdw 1.991 2.170 nonbonded pdb=" O2B ADP D1000 " pdb="MG MG D1001 " model vdw 1.996 2.170 nonbonded pdb=" O1B ADP B1000 " pdb="MG MG B1001 " model vdw 2.017 2.170 nonbonded pdb=" O3B ADP E1000 " pdb="MG MG E1001 " model vdw 2.038 2.170 nonbonded pdb=" OG1 THR C 185 " pdb="MG MG C1001 " model vdw 2.052 2.170 ... (remaining 164074 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 1 through 418 or resid 1000)) selection = (chain 'C' and (resid 1 through 418 or resid 1000)) selection = (chain 'D' and (resid 1 through 418 or resid 1000)) selection = (chain 'E' and (resid 1 through 418 or resid 1000)) selection = chain 'F' } 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: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 49.430 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 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 : 0.003 0.097 20215 Z= 0.149 Angle : 0.642 12.058 27252 Z= 0.310 Chirality : 0.041 0.257 3096 Planarity : 0.004 0.114 3528 Dihedral : 16.080 178.238 7848 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.54 % Allowed : 17.36 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.17), residues: 2496 helix: 1.30 (0.16), residues: 1148 sheet: 0.58 (0.27), residues: 367 loop : -0.02 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP E 381 HIS 0.008 0.001 HIS A 42 PHE 0.009 0.001 PHE E 398 TYR 0.023 0.001 TYR E 197 ARG 0.013 0.000 ARG E 362 Details of bonding type rmsd hydrogen bonds : bond 0.15462 ( 931) hydrogen bonds : angle 5.71770 ( 2718) covalent geometry : bond 0.00349 (20214) covalent geometry : angle 0.64235 (27252) Misc. bond : bond 0.00043 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 241 time to evaluate : 2.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 GLN cc_start: 0.8798 (pm20) cc_final: 0.8447 (pm20) REVERT: C 374 GLN cc_start: 0.8313 (mm-40) cc_final: 0.7980 (tm-30) REVERT: C 378 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8540 (mm-40) REVERT: E 21 MET cc_start: 0.7838 (tmt) cc_final: 0.7359 (ttt) REVERT: E 41 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8198 (tm-30) REVERT: F 1 MET cc_start: 0.1851 (pmm) cc_final: 0.0364 (ptp) REVERT: F 21 MET cc_start: 0.4325 (tpt) cc_final: 0.3066 (tmm) REVERT: F 36 PHE cc_start: 0.4259 (t80) cc_final: 0.3882 (t80) REVERT: F 120 ASN cc_start: 0.1079 (m110) cc_final: 0.0834 (m-40) REVERT: F 396 MET cc_start: 0.2199 (mpt) cc_final: 0.0653 (tpt) outliers start: 33 outliers final: 27 residues processed: 267 average time/residue: 1.7387 time to fit residues: 517.5835 Evaluate side-chains 254 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 225 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 73 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 7.9990 chunk 186 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 192 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN C 378 GLN D 85 GLN D 193 GLN E 220 GLN E 388 HIS F 193 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.123875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.076996 restraints weight = 41000.603| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 4.21 r_work: 0.2825 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20215 Z= 0.136 Angle : 0.605 8.338 27252 Z= 0.294 Chirality : 0.042 0.208 3096 Planarity : 0.004 0.056 3528 Dihedral : 10.340 179.115 2843 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.07 % Allowed : 14.71 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.17), residues: 2496 helix: 1.31 (0.16), residues: 1154 sheet: 0.31 (0.26), residues: 378 loop : 0.10 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 381 HIS 0.004 0.001 HIS E 388 PHE 0.014 0.001 PHE F 64 TYR 0.017 0.001 TYR F 72 ARG 0.006 0.000 ARG E 362 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 931) hydrogen bonds : angle 4.41878 ( 2718) covalent geometry : bond 0.00310 (20214) covalent geometry : angle 0.60474 (27252) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 247 time to evaluate : 2.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 GLN cc_start: 0.8912 (pm20) cc_final: 0.8562 (pm20) REVERT: B 155 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8579 (pm20) REVERT: B 326 LYS cc_start: 0.8639 (ptmm) cc_final: 0.8374 (pttt) REVERT: C 32 GLN cc_start: 0.9209 (mm-40) cc_final: 0.8944 (mp10) REVERT: C 186 MET cc_start: 0.9255 (mtp) cc_final: 0.8969 (mtm) REVERT: C 322 ASP cc_start: 0.8047 (t0) cc_final: 0.7627 (t0) REVERT: C 374 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8158 (tm-30) REVERT: E 32 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8055 (mm-40) REVERT: E 172 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7872 (pt0) REVERT: E 244 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8438 (mp0) REVERT: E 326 LYS cc_start: 0.9141 (mppt) cc_final: 0.8910 (mppt) REVERT: E 329 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8224 (mp0) REVERT: E 347 ARG cc_start: 0.8168 (tpm170) cc_final: 0.7913 (tpt170) REVERT: E 400 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.9079 (mm) REVERT: F 21 MET cc_start: 0.4715 (tpt) cc_final: 0.4114 (tmm) REVERT: F 36 PHE cc_start: 0.3741 (t80) cc_final: 0.3520 (t80) REVERT: F 73 LEU cc_start: 0.5919 (OUTLIER) cc_final: 0.5130 (pp) outliers start: 66 outliers final: 24 residues processed: 289 average time/residue: 2.0000 time to fit residues: 644.8398 Evaluate side-chains 270 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 240 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 172 GLN Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 381 TRP Chi-restraints excluded: chain E residue 400 ILE Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain F residue 64 PHE Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 318 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 27 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 211 optimal weight: 30.0000 chunk 145 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 104 optimal weight: 0.3980 chunk 144 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 219 optimal weight: 20.0000 chunk 159 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN B 193 GLN B 275 ASN D 193 GLN E 220 GLN E 388 HIS ** F 256 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 = 0.3860 r_free = 0.3860 target = 0.123295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.076362 restraints weight = 40978.130| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.81 r_work: 0.2814 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20215 Z= 0.163 Angle : 0.600 9.115 27252 Z= 0.290 Chirality : 0.042 0.176 3096 Planarity : 0.004 0.048 3528 Dihedral : 9.711 177.151 2814 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.12 % Allowed : 15.27 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.17), residues: 2496 helix: 1.30 (0.16), residues: 1163 sheet: 0.22 (0.26), residues: 378 loop : 0.09 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 381 HIS 0.005 0.001 HIS F 256 PHE 0.016 0.001 PHE F 64 TYR 0.017 0.001 TYR A 80 ARG 0.008 0.000 ARG E 362 Details of bonding type rmsd hydrogen bonds : bond 0.03663 ( 931) hydrogen bonds : angle 4.27658 ( 2718) covalent geometry : bond 0.00378 (20214) covalent geometry : angle 0.60000 (27252) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 253 time to evaluate : 2.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8658 (pm20) REVERT: A 220 GLN cc_start: 0.8689 (mt0) cc_final: 0.8123 (mp10) REVERT: A 244 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8093 (mp0) REVERT: B 59 GLN cc_start: 0.8902 (pm20) cc_final: 0.8570 (pm20) REVERT: B 109 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7985 (ptt90) REVERT: B 244 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8592 (mm-30) REVERT: B 362 ARG cc_start: 0.9136 (ttm110) cc_final: 0.8932 (mtp85) REVERT: C 32 GLN cc_start: 0.9190 (mm-40) cc_final: 0.8923 (mp10) REVERT: C 322 ASP cc_start: 0.8131 (t0) cc_final: 0.7602 (t0) REVERT: C 326 LYS cc_start: 0.8710 (mppt) cc_final: 0.8469 (mmmm) REVERT: C 374 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8288 (tm-30) REVERT: D 374 GLN cc_start: 0.8158 (tp40) cc_final: 0.7821 (tm-30) REVERT: E 172 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7886 (pt0) REVERT: E 244 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8424 (mp0) REVERT: E 326 LYS cc_start: 0.9161 (mppt) cc_final: 0.8916 (mppt) REVERT: E 329 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8243 (mp0) REVERT: E 334 GLU cc_start: 0.8634 (mp0) cc_final: 0.8365 (mp0) REVERT: E 341 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7635 (pp-130) REVERT: F 21 MET cc_start: 0.4595 (tpt) cc_final: 0.3946 (tmm) REVERT: F 73 LEU cc_start: 0.6238 (OUTLIER) cc_final: 0.5401 (pp) REVERT: F 300 PHE cc_start: 0.8015 (t80) cc_final: 0.7803 (t80) outliers start: 67 outliers final: 28 residues processed: 296 average time/residue: 2.0262 time to fit residues: 670.1441 Evaluate side-chains 266 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 231 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 172 GLN Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 381 TRP Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain F residue 64 PHE Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 318 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 0.9980 chunk 134 optimal weight: 0.5980 chunk 45 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 233 optimal weight: 0.3980 chunk 231 optimal weight: 7.9990 chunk 126 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 chunk 92 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 193 GLN D 193 GLN E 220 GLN E 388 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.123829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.078183 restraints weight = 41452.264| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.96 r_work: 0.2841 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20215 Z= 0.114 Angle : 0.599 9.295 27252 Z= 0.286 Chirality : 0.042 0.188 3096 Planarity : 0.003 0.044 3528 Dihedral : 9.465 174.597 2814 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.07 % Allowed : 16.15 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.17), residues: 2496 helix: 1.39 (0.16), residues: 1161 sheet: -0.04 (0.25), residues: 389 loop : 0.12 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 381 HIS 0.005 0.001 HIS F 42 PHE 0.014 0.001 PHE F 64 TYR 0.017 0.001 TYR E 197 ARG 0.008 0.000 ARG E 362 Details of bonding type rmsd hydrogen bonds : bond 0.03194 ( 931) hydrogen bonds : angle 4.13881 ( 2718) covalent geometry : bond 0.00258 (20214) covalent geometry : angle 0.59858 (27252) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 244 time to evaluate : 2.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8150 (mp0) REVERT: B 59 GLN cc_start: 0.8907 (pm20) cc_final: 0.8568 (pm20) REVERT: B 109 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7913 (ptt90) REVERT: B 155 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8564 (pm20) REVERT: B 244 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8624 (mm-30) REVERT: B 362 ARG cc_start: 0.9179 (ttm110) cc_final: 0.8971 (mtp85) REVERT: B 374 GLN cc_start: 0.8805 (tp40) cc_final: 0.8597 (tp40) REVERT: C 32 GLN cc_start: 0.9190 (mm-40) cc_final: 0.8940 (mp10) REVERT: C 186 MET cc_start: 0.9228 (mtp) cc_final: 0.8967 (mtm) REVERT: C 322 ASP cc_start: 0.8185 (t0) cc_final: 0.7582 (t0) REVERT: C 326 LYS cc_start: 0.8656 (mppt) cc_final: 0.8404 (mmmm) REVERT: C 374 GLN cc_start: 0.8548 (mm-40) cc_final: 0.7894 (tm-30) REVERT: C 378 GLN cc_start: 0.9072 (mm-40) cc_final: 0.8597 (mm-40) REVERT: C 417 LYS cc_start: 0.9215 (ttpp) cc_final: 0.8983 (ttmm) REVERT: D 374 GLN cc_start: 0.8172 (tp40) cc_final: 0.7779 (tm-30) REVERT: E 32 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8071 (mm-40) REVERT: E 172 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7873 (pt0) REVERT: E 244 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8424 (mm-30) REVERT: E 326 LYS cc_start: 0.9226 (mppt) cc_final: 0.8960 (mppt) REVERT: E 329 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8269 (mp0) REVERT: E 334 GLU cc_start: 0.8652 (mp0) cc_final: 0.8142 (mp0) REVERT: E 341 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7702 (pp-130) REVERT: F 21 MET cc_start: 0.4604 (tpt) cc_final: 0.3994 (tmm) REVERT: F 36 PHE cc_start: 0.3401 (t80) cc_final: 0.3167 (t80) REVERT: F 49 ILE cc_start: 0.3845 (OUTLIER) cc_final: 0.3470 (pp) REVERT: F 73 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.5560 (pp) REVERT: F 111 PHE cc_start: 0.7252 (m-10) cc_final: 0.6872 (m-10) REVERT: F 263 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8439 (pp) REVERT: F 300 PHE cc_start: 0.8034 (t80) cc_final: 0.7779 (t80) outliers start: 66 outliers final: 27 residues processed: 287 average time/residue: 2.8056 time to fit residues: 903.0438 Evaluate side-chains 279 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 242 time to evaluate : 2.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 172 GLN Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 381 TRP Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 64 PHE Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 318 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 16 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 168 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 201 optimal weight: 10.0000 chunk 142 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN B 275 ASN D 32 GLN D 193 GLN E 220 GLN E 388 HIS ** F 256 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 = 0.3870 r_free = 0.3870 target = 0.123730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.077973 restraints weight = 41829.374| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.66 r_work: 0.2833 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20215 Z= 0.123 Angle : 0.601 8.721 27252 Z= 0.285 Chirality : 0.042 0.181 3096 Planarity : 0.003 0.043 3528 Dihedral : 9.183 171.315 2808 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.89 % Allowed : 17.18 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.17), residues: 2496 helix: 1.41 (0.16), residues: 1161 sheet: 0.20 (0.26), residues: 378 loop : 0.11 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 381 HIS 0.006 0.001 HIS F 42 PHE 0.014 0.001 PHE F 300 TYR 0.020 0.001 TYR A 80 ARG 0.009 0.000 ARG E 362 Details of bonding type rmsd hydrogen bonds : bond 0.03135 ( 931) hydrogen bonds : angle 4.09938 ( 2718) covalent geometry : bond 0.00281 (20214) covalent geometry : angle 0.60054 (27252) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 250 time to evaluate : 3.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.9528 (mp10) cc_final: 0.9272 (pm20) REVERT: A 220 GLN cc_start: 0.8660 (mt0) cc_final: 0.8066 (mp10) REVERT: A 244 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: A 326 LYS cc_start: 0.8129 (ptmt) cc_final: 0.7918 (ptmt) REVERT: A 405 MET cc_start: 0.8961 (mtt) cc_final: 0.8451 (mpp) REVERT: B 59 GLN cc_start: 0.8895 (pm20) cc_final: 0.8558 (pm20) REVERT: B 109 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7898 (ptt90) REVERT: B 155 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8571 (pm20) REVERT: B 244 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8625 (mm-30) REVERT: B 362 ARG cc_start: 0.9147 (ttm110) cc_final: 0.8944 (mtp85) REVERT: B 374 GLN cc_start: 0.8817 (tp40) cc_final: 0.8595 (tp40) REVERT: C 32 GLN cc_start: 0.9178 (mm-40) cc_final: 0.8925 (mp10) REVERT: C 186 MET cc_start: 0.9199 (mtp) cc_final: 0.8924 (mtm) REVERT: C 322 ASP cc_start: 0.8215 (t0) cc_final: 0.7614 (t0) REVERT: C 326 LYS cc_start: 0.8638 (mppt) cc_final: 0.8385 (mmmm) REVERT: C 374 GLN cc_start: 0.8586 (mm-40) cc_final: 0.7923 (tm-30) REVERT: C 378 GLN cc_start: 0.9087 (mm-40) cc_final: 0.8591 (mm-40) REVERT: C 417 LYS cc_start: 0.9220 (ttpp) cc_final: 0.8989 (ttmm) REVERT: D 374 GLN cc_start: 0.8244 (tp40) cc_final: 0.7782 (tm-30) REVERT: E 244 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8422 (mm-30) REVERT: E 326 LYS cc_start: 0.9207 (mppt) cc_final: 0.8952 (mppt) REVERT: E 329 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8244 (mp0) REVERT: E 334 GLU cc_start: 0.8682 (mp0) cc_final: 0.8153 (mp0) REVERT: E 341 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.7838 (pp-130) REVERT: F 1 MET cc_start: 0.4151 (OUTLIER) cc_final: 0.2493 (pmm) REVERT: F 21 MET cc_start: 0.4458 (tpt) cc_final: 0.3828 (tmm) REVERT: F 73 LEU cc_start: 0.6481 (OUTLIER) cc_final: 0.5609 (pp) REVERT: F 111 PHE cc_start: 0.7238 (m-10) cc_final: 0.6969 (m-10) REVERT: F 300 PHE cc_start: 0.8109 (t80) cc_final: 0.7827 (t80) outliers start: 62 outliers final: 31 residues processed: 294 average time/residue: 1.9383 time to fit residues: 635.3342 Evaluate side-chains 278 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 240 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 381 TRP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 64 PHE Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 318 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 171 optimal weight: 4.9990 chunk 235 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 212 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN B 193 GLN D 42 HIS D 193 GLN E 220 GLN E 388 HIS ** F 256 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 = 0.3869 r_free = 0.3869 target = 0.123584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.078352 restraints weight = 41652.298| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.53 r_work: 0.2830 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20215 Z= 0.137 Angle : 0.622 8.760 27252 Z= 0.295 Chirality : 0.042 0.188 3096 Planarity : 0.003 0.046 3528 Dihedral : 9.088 172.116 2808 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.61 % Allowed : 17.60 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.17), residues: 2496 helix: 1.44 (0.16), residues: 1157 sheet: 0.20 (0.26), residues: 378 loop : 0.08 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 381 HIS 0.003 0.001 HIS E 388 PHE 0.013 0.001 PHE F 300 TYR 0.019 0.001 TYR E 197 ARG 0.011 0.000 ARG E 362 Details of bonding type rmsd hydrogen bonds : bond 0.03177 ( 931) hydrogen bonds : angle 4.09266 ( 2718) covalent geometry : bond 0.00319 (20214) covalent geometry : angle 0.62152 (27252) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 246 time to evaluate : 2.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8075 (mp0) REVERT: A 326 LYS cc_start: 0.8199 (ptmt) cc_final: 0.7990 (ptmt) REVERT: A 405 MET cc_start: 0.8988 (mtt) cc_final: 0.8488 (mpp) REVERT: B 59 GLN cc_start: 0.8896 (pm20) cc_final: 0.8546 (pm20) REVERT: B 109 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7888 (ptt90) REVERT: B 155 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8590 (pm20) REVERT: B 244 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8608 (mm-30) REVERT: B 362 ARG cc_start: 0.9137 (ttm110) cc_final: 0.8919 (mtp85) REVERT: B 374 GLN cc_start: 0.8820 (tp-100) cc_final: 0.8595 (tp40) REVERT: C 32 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8959 (mp10) REVERT: C 186 MET cc_start: 0.9212 (mtp) cc_final: 0.8935 (mtm) REVERT: C 322 ASP cc_start: 0.8271 (t0) cc_final: 0.7677 (t0) REVERT: C 326 LYS cc_start: 0.8640 (mppt) cc_final: 0.8380 (mmmm) REVERT: C 374 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8046 (tm-30) REVERT: C 378 GLN cc_start: 0.9118 (mm-40) cc_final: 0.8672 (mm-40) REVERT: C 417 LYS cc_start: 0.9224 (ttpp) cc_final: 0.8989 (ttmm) REVERT: D 30 ARG cc_start: 0.7995 (mtm-85) cc_final: 0.7680 (mtp-110) REVERT: D 374 GLN cc_start: 0.8268 (tp40) cc_final: 0.7929 (tp40) REVERT: E 32 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8054 (mm-40) REVERT: E 244 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8464 (mm-30) REVERT: E 326 LYS cc_start: 0.9239 (mppt) cc_final: 0.8979 (mppt) REVERT: E 329 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8276 (mp0) REVERT: E 341 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.7915 (pp-130) REVERT: F 1 MET cc_start: 0.3480 (OUTLIER) cc_final: 0.1785 (pmm) REVERT: F 21 MET cc_start: 0.4490 (tpt) cc_final: 0.3834 (tmm) REVERT: F 73 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.5710 (pp) REVERT: F 111 PHE cc_start: 0.7427 (m-10) cc_final: 0.7120 (m-10) REVERT: F 300 PHE cc_start: 0.8146 (t80) cc_final: 0.7492 (m-80) REVERT: F 396 MET cc_start: 0.1838 (mpt) cc_final: 0.0356 (tpt) outliers start: 56 outliers final: 30 residues processed: 284 average time/residue: 1.5174 time to fit residues: 479.7161 Evaluate side-chains 282 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 244 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 381 TRP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 318 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 17 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 203 optimal weight: 0.6980 chunk 232 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 242 optimal weight: 9.9990 chunk 201 optimal weight: 2.9990 chunk 92 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN D 193 GLN E 220 GLN E 388 HIS ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.123970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.077827 restraints weight = 41707.708| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.87 r_work: 0.2837 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20215 Z= 0.131 Angle : 0.627 9.094 27252 Z= 0.299 Chirality : 0.042 0.205 3096 Planarity : 0.003 0.050 3528 Dihedral : 8.929 178.239 2806 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.47 % Allowed : 18.11 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.17), residues: 2496 helix: 1.44 (0.16), residues: 1158 sheet: 0.24 (0.26), residues: 372 loop : 0.07 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 381 HIS 0.003 0.001 HIS E 388 PHE 0.026 0.001 PHE F 64 TYR 0.020 0.001 TYR E 197 ARG 0.012 0.000 ARG E 362 Details of bonding type rmsd hydrogen bonds : bond 0.03114 ( 931) hydrogen bonds : angle 4.06671 ( 2718) covalent geometry : bond 0.00304 (20214) covalent geometry : angle 0.62723 (27252) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 253 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.9561 (mp10) cc_final: 0.9337 (pm20) REVERT: A 220 GLN cc_start: 0.8721 (mt0) cc_final: 0.8134 (mp10) REVERT: A 244 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8111 (mp0) REVERT: B 41 GLN cc_start: 0.9071 (tp-100) cc_final: 0.8711 (tp40) REVERT: B 59 GLN cc_start: 0.8905 (pm20) cc_final: 0.8552 (pm20) REVERT: B 109 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7877 (ptt90) REVERT: B 155 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8607 (pm20) REVERT: B 244 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8653 (mm-30) REVERT: B 374 GLN cc_start: 0.8847 (tp-100) cc_final: 0.8635 (tp40) REVERT: C 32 GLN cc_start: 0.9210 (mm-40) cc_final: 0.8959 (mp10) REVERT: C 186 MET cc_start: 0.9215 (mtp) cc_final: 0.8943 (mtm) REVERT: C 322 ASP cc_start: 0.8337 (t0) cc_final: 0.7770 (t0) REVERT: C 326 LYS cc_start: 0.8648 (mppt) cc_final: 0.8385 (mmmm) REVERT: C 374 GLN cc_start: 0.8615 (mm-40) cc_final: 0.7982 (tm-30) REVERT: C 378 GLN cc_start: 0.9123 (mm-40) cc_final: 0.8675 (mm-40) REVERT: C 417 LYS cc_start: 0.9227 (ttpp) cc_final: 0.8995 (ttmm) REVERT: D 374 GLN cc_start: 0.8317 (tp40) cc_final: 0.7957 (tp40) REVERT: E 32 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8085 (mm-40) REVERT: E 244 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8455 (mm-30) REVERT: E 326 LYS cc_start: 0.9273 (mppt) cc_final: 0.9012 (mppt) REVERT: E 329 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8308 (mp0) REVERT: E 341 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7950 (pp-130) REVERT: F 1 MET cc_start: 0.3867 (OUTLIER) cc_final: 0.2289 (pmm) REVERT: F 21 MET cc_start: 0.4629 (tpt) cc_final: 0.4020 (tmm) REVERT: F 73 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.5770 (pp) REVERT: F 300 PHE cc_start: 0.8073 (t80) cc_final: 0.7503 (m-80) outliers start: 53 outliers final: 35 residues processed: 290 average time/residue: 1.4994 time to fit residues: 484.1104 Evaluate side-chains 284 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 241 time to evaluate : 2.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 381 TRP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 318 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 165 optimal weight: 0.8980 chunk 66 optimal weight: 0.0970 chunk 17 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 133 optimal weight: 0.4980 chunk 69 optimal weight: 3.9990 chunk 111 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN C 41 GLN D 193 GLN E 220 GLN E 388 HIS ** F 256 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 = 0.3884 r_free = 0.3884 target = 0.124607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.077311 restraints weight = 41943.049| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 4.10 r_work: 0.2842 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20215 Z= 0.117 Angle : 0.641 10.401 27252 Z= 0.305 Chirality : 0.042 0.215 3096 Planarity : 0.003 0.053 3528 Dihedral : 8.536 159.935 2806 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.19 % Allowed : 19.13 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.17), residues: 2496 helix: 1.46 (0.16), residues: 1157 sheet: 0.19 (0.26), residues: 372 loop : 0.08 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 381 HIS 0.003 0.000 HIS F 256 PHE 0.025 0.001 PHE F 64 TYR 0.021 0.001 TYR E 197 ARG 0.012 0.000 ARG E 362 Details of bonding type rmsd hydrogen bonds : bond 0.02943 ( 931) hydrogen bonds : angle 4.04976 ( 2718) covalent geometry : bond 0.00270 (20214) covalent geometry : angle 0.64083 (27252) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 253 time to evaluate : 2.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.9559 (mp10) cc_final: 0.9278 (pm20) REVERT: A 220 GLN cc_start: 0.8668 (mt0) cc_final: 0.8071 (mp10) REVERT: A 244 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: B 41 GLN cc_start: 0.9093 (tp-100) cc_final: 0.8724 (tp40) REVERT: B 59 GLN cc_start: 0.8904 (pm20) cc_final: 0.8515 (pm20) REVERT: B 155 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8619 (pm20) REVERT: B 244 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8610 (mm-30) REVERT: B 374 GLN cc_start: 0.8799 (tp-100) cc_final: 0.8593 (tp40) REVERT: C 32 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8938 (mp10) REVERT: C 186 MET cc_start: 0.9223 (mtp) cc_final: 0.8919 (mtm) REVERT: C 322 ASP cc_start: 0.8376 (t0) cc_final: 0.7804 (t0) REVERT: C 326 LYS cc_start: 0.8632 (mppt) cc_final: 0.8357 (mmmm) REVERT: C 417 LYS cc_start: 0.9231 (ttpp) cc_final: 0.9005 (ttmm) REVERT: E 21 MET cc_start: 0.8590 (ttt) cc_final: 0.8189 (ttt) REVERT: E 32 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8043 (mm-40) REVERT: E 41 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8127 (tm-30) REVERT: E 244 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8445 (mm-30) REVERT: E 326 LYS cc_start: 0.9266 (mppt) cc_final: 0.9012 (mppt) REVERT: E 329 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8273 (mp0) REVERT: E 341 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7921 (pp-130) REVERT: F 1 MET cc_start: 0.4277 (OUTLIER) cc_final: 0.2936 (pmm) REVERT: F 21 MET cc_start: 0.4684 (tpt) cc_final: 0.4066 (tmm) REVERT: F 25 ASN cc_start: -0.1891 (t0) cc_final: -0.2123 (t0) REVERT: F 73 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.5765 (pp) REVERT: F 300 PHE cc_start: 0.8065 (t80) cc_final: 0.7512 (m-80) REVERT: F 396 MET cc_start: 0.1832 (mpt) cc_final: 0.0363 (tpt) outliers start: 47 outliers final: 26 residues processed: 286 average time/residue: 1.5104 time to fit residues: 480.5331 Evaluate side-chains 279 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 245 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 381 TRP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 318 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 224 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 154 optimal weight: 0.8980 chunk 172 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN C 25 ASN D 32 GLN D 193 GLN D 378 GLN E 388 HIS ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 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 = 0.3872 r_free = 0.3872 target = 0.123893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.077034 restraints weight = 41577.939| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 4.14 r_work: 0.2833 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20215 Z= 0.134 Angle : 0.646 10.883 27252 Z= 0.308 Chirality : 0.042 0.216 3096 Planarity : 0.004 0.057 3528 Dihedral : 8.275 162.180 2804 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.05 % Allowed : 19.69 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.17), residues: 2496 helix: 1.44 (0.16), residues: 1157 sheet: 0.15 (0.26), residues: 366 loop : 0.09 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 381 HIS 0.003 0.001 HIS E 388 PHE 0.022 0.001 PHE F 64 TYR 0.022 0.001 TYR E 197 ARG 0.013 0.000 ARG E 362 Details of bonding type rmsd hydrogen bonds : bond 0.03043 ( 931) hydrogen bonds : angle 4.06820 ( 2718) covalent geometry : bond 0.00314 (20214) covalent geometry : angle 0.64622 (27252) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 252 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 GLN cc_start: 0.9342 (mt0) cc_final: 0.8691 (mt0) REVERT: A 193 GLN cc_start: 0.9165 (pt0) cc_final: 0.8643 (pm20) REVERT: A 220 GLN cc_start: 0.8675 (mt0) cc_final: 0.8082 (mp10) REVERT: A 244 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8098 (mp0) REVERT: A 341 MET cc_start: 0.8992 (ttp) cc_final: 0.8452 (tmm) REVERT: A 353 ARG cc_start: 0.8806 (tpp-160) cc_final: 0.8479 (mmm-85) REVERT: B 41 GLN cc_start: 0.9102 (tp-100) cc_final: 0.8727 (tp40) REVERT: B 59 GLN cc_start: 0.8905 (pm20) cc_final: 0.8512 (pm20) REVERT: B 109 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7867 (ptt90) REVERT: B 155 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8611 (pm20) REVERT: B 244 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8593 (mm-30) REVERT: B 374 GLN cc_start: 0.8830 (tp-100) cc_final: 0.8625 (tp40) REVERT: C 32 GLN cc_start: 0.9186 (mm-40) cc_final: 0.8922 (mp10) REVERT: C 186 MET cc_start: 0.9234 (mtp) cc_final: 0.8921 (mtm) REVERT: C 322 ASP cc_start: 0.8387 (t0) cc_final: 0.7815 (t0) REVERT: C 326 LYS cc_start: 0.8643 (mppt) cc_final: 0.8367 (mmmm) REVERT: C 417 LYS cc_start: 0.9241 (ttpp) cc_final: 0.9014 (ttmm) REVERT: D 32 GLN cc_start: 0.9006 (mp10) cc_final: 0.8797 (mp10) REVERT: D 374 GLN cc_start: 0.8500 (mm-40) cc_final: 0.8057 (tp40) REVERT: E 32 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8023 (mm-40) REVERT: E 244 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8441 (mm-30) REVERT: E 326 LYS cc_start: 0.9270 (mppt) cc_final: 0.9033 (mppt) REVERT: E 329 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8269 (mp0) REVERT: E 334 GLU cc_start: 0.8763 (mp0) cc_final: 0.8508 (mp0) REVERT: F 1 MET cc_start: 0.4324 (OUTLIER) cc_final: 0.3111 (pmm) REVERT: F 21 MET cc_start: 0.4616 (tpt) cc_final: 0.3973 (tmm) REVERT: F 25 ASN cc_start: -0.1919 (t0) cc_final: -0.2201 (t0) REVERT: F 73 LEU cc_start: 0.6635 (OUTLIER) cc_final: 0.5914 (pp) REVERT: F 300 PHE cc_start: 0.8080 (t80) cc_final: 0.7518 (m-80) REVERT: F 396 MET cc_start: 0.1845 (mpt) cc_final: 0.0271 (tpt) outliers start: 44 outliers final: 29 residues processed: 282 average time/residue: 1.5071 time to fit residues: 472.9588 Evaluate side-chains 282 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 246 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 381 TRP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 318 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 170 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 228 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 186 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN C 25 ASN C 374 GLN C 378 GLN D 193 GLN D 378 GLN E 193 GLN E 220 GLN E 388 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.122918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.077027 restraints weight = 41730.338| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.64 r_work: 0.2806 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20215 Z= 0.178 Angle : 0.677 12.398 27252 Z= 0.324 Chirality : 0.043 0.235 3096 Planarity : 0.004 0.060 3528 Dihedral : 8.187 163.402 2804 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.05 % Allowed : 19.83 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.17), residues: 2496 helix: 1.36 (0.16), residues: 1156 sheet: 0.15 (0.26), residues: 366 loop : 0.08 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 381 HIS 0.003 0.001 HIS E 239 PHE 0.031 0.001 PHE F 64 TYR 0.021 0.001 TYR E 197 ARG 0.013 0.000 ARG E 362 Details of bonding type rmsd hydrogen bonds : bond 0.03455 ( 931) hydrogen bonds : angle 4.16989 ( 2718) covalent geometry : bond 0.00419 (20214) covalent geometry : angle 0.67653 (27252) Misc. bond : bond 0.00011 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 248 time to evaluate : 2.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.9187 (pt0) cc_final: 0.8760 (pm20) REVERT: A 220 GLN cc_start: 0.8728 (mt0) cc_final: 0.8146 (mp10) REVERT: A 244 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8144 (mp0) REVERT: A 341 MET cc_start: 0.9018 (ttp) cc_final: 0.8512 (tmm) REVERT: A 390 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8415 (ptt) REVERT: B 41 GLN cc_start: 0.9105 (tp-100) cc_final: 0.8748 (tm-30) REVERT: B 59 GLN cc_start: 0.8931 (pm20) cc_final: 0.8539 (pm20) REVERT: B 109 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7884 (ptt90) REVERT: B 244 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8638 (mm-30) REVERT: C 32 GLN cc_start: 0.9207 (mm-40) cc_final: 0.8937 (mp10) REVERT: C 322 ASP cc_start: 0.8514 (t0) cc_final: 0.7964 (t0) REVERT: C 326 LYS cc_start: 0.8671 (mppt) cc_final: 0.8385 (mmmm) REVERT: C 374 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7995 (tp-100) REVERT: C 417 LYS cc_start: 0.9250 (ttpp) cc_final: 0.9016 (ttmm) REVERT: D 374 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8000 (tp40) REVERT: E 32 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8059 (mm-40) REVERT: E 41 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8191 (tm-30) REVERT: E 244 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8487 (mm-30) REVERT: E 326 LYS cc_start: 0.9296 (mppt) cc_final: 0.9071 (mppt) REVERT: E 329 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8310 (mp0) REVERT: E 334 GLU cc_start: 0.8829 (mp0) cc_final: 0.8593 (mp0) REVERT: F 1 MET cc_start: 0.3739 (OUTLIER) cc_final: 0.2378 (pmm) REVERT: F 21 MET cc_start: 0.4518 (tpt) cc_final: 0.3892 (tmm) REVERT: F 25 ASN cc_start: -0.2002 (t0) cc_final: -0.2311 (t0) REVERT: F 73 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6396 (pp) REVERT: F 300 PHE cc_start: 0.8199 (t80) cc_final: 0.7650 (m-80) REVERT: F 396 MET cc_start: 0.1978 (mpt) cc_final: 0.0505 (tpt) outliers start: 44 outliers final: 29 residues processed: 277 average time/residue: 1.5325 time to fit residues: 476.1903 Evaluate side-chains 280 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 242 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 381 TRP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 318 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 146 optimal weight: 0.0670 chunk 5 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN ** B 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN C 378 GLN D 193 GLN D 378 GLN E 193 GLN E 220 GLN E 388 HIS ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 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 = 0.3854 r_free = 0.3854 target = 0.122869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.076744 restraints weight = 41807.291| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.86 r_work: 0.2808 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 20215 Z= 0.188 Angle : 0.831 59.193 27252 Z= 0.437 Chirality : 0.042 0.211 3096 Planarity : 0.004 0.057 3528 Dihedral : 8.182 163.365 2804 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.86 % Allowed : 20.02 % Favored : 78.12 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.17), residues: 2496 helix: 1.36 (0.16), residues: 1156 sheet: 0.15 (0.26), residues: 366 loop : 0.09 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 381 HIS 0.004 0.001 HIS E 239 PHE 0.020 0.001 PHE F 64 TYR 0.020 0.001 TYR E 197 ARG 0.012 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.03430 ( 931) hydrogen bonds : angle 4.17216 ( 2718) covalent geometry : bond 0.00425 (20214) covalent geometry : angle 0.83098 (27252) Misc. bond : bond 0.00010 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20591.56 seconds wall clock time: 361 minutes 38.91 seconds (21698.91 seconds total)