Starting phenix.real_space_refine on Tue May 20 15:22:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q3n_18130/05_2025/8q3n_18130.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q3n_18130/05_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_18130/05_2025/8q3n_18130.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q3n_18130/05_2025/8q3n_18130.map" model { file = "/net/cci-nas-00/data/ceres_data/8q3n_18130/05_2025/8q3n_18130.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q3n_18130/05_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-5687/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: 13.69, 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: 5.37 Conformation dependent library (CDL) restraints added in 2.9 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: 2.90 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: 7.04 Time building geometry restraints manager: 6.19 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: 5.950 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: 0.140 Set scattering table: 0.210 Process input model: 48.800 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.840 ------------------------------------------------------------------------------- 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 : 2.852 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: 1.5027 time to fit residues: 447.6754 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 : 2.332 ------------------------------------------------------------------------------- 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 = 0.123877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.076380 restraints weight = 41001.563| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 4.67 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 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 8.337 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 4.41876 ( 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 : 2.295 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: 0.8789 (pm20) cc_final: 0.8456 (pm20) REVERT: B 155 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8407 (pm20) REVERT: B 326 LYS cc_start: 0.8476 (ptmm) cc_final: 0.8201 (pttt) REVERT: C 32 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8699 (mp10) REVERT: C 186 MET cc_start: 0.8892 (mtp) cc_final: 0.8609 (mtm) REVERT: C 322 ASP cc_start: 0.7610 (t0) cc_final: 0.7209 (t0) REVERT: C 374 GLN cc_start: 0.8137 (mm-40) cc_final: 0.7738 (tm-30) REVERT: E 32 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.7870 (mm-40) REVERT: E 172 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7780 (pt0) REVERT: E 244 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8073 (mp0) REVERT: E 326 LYS cc_start: 0.9095 (mppt) cc_final: 0.8866 (mppt) REVERT: E 329 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8202 (mp0) REVERT: E 334 GLU cc_start: 0.8333 (mp0) cc_final: 0.8099 (mp0) REVERT: E 347 ARG cc_start: 0.8109 (tpm170) cc_final: 0.7866 (tpt170) REVERT: F 21 MET cc_start: 0.4843 (tpt) cc_final: 0.4273 (tmm) REVERT: F 36 PHE cc_start: 0.3728 (t80) cc_final: 0.3522 (t80) REVERT: F 73 LEU cc_start: 0.5708 (OUTLIER) cc_final: 0.5032 (pp) outliers start: 66 outliers final: 24 residues processed: 289 average time/residue: 1.4049 time to fit residues: 453.9591 Evaluate side-chains 270 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 241 time to evaluate : 2.206 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 104 optimal weight: 0.6980 chunk 144 optimal weight: 0.7980 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: 1.0382 ------------------------------------------------------------------------------- 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 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 = 0.3865 r_free = 0.3865 target = 0.123596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.077569 restraints weight = 40896.820| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 4.13 r_work: 0.2825 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1042 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= 0.146 Angle : 0.594 9.147 27252 Z= 0.286 Chirality : 0.042 0.173 3096 Planarity : 0.004 0.048 3528 Dihedral : 9.702 177.018 2814 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.07 % Allowed : 15.32 % 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: 0.96 (0.17), residues: 2496 helix: 1.32 (0.16), residues: 1163 sheet: 0.24 (0.26), residues: 378 loop : 0.10 (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 300 TYR 0.018 0.001 TYR A 80 ARG 0.008 0.000 ARG E 362 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 931) hydrogen bonds : angle 4.26404 ( 2718) covalent geometry : bond 0.00336 (20214) covalent geometry : angle 0.59403 (27252) Misc. bond : bond 0.00012 ( 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: 66 poor density : 254 time to evaluate : 2.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8662 (pm20) REVERT: A 220 GLN cc_start: 0.8652 (mt0) cc_final: 0.8092 (mp10) REVERT: A 244 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8051 (mp0) REVERT: B 59 GLN cc_start: 0.8930 (pm20) cc_final: 0.8589 (pm20) REVERT: B 109 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7983 (ptt90) REVERT: B 244 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8599 (mm-30) REVERT: B 362 ARG cc_start: 0.9145 (ttm110) cc_final: 0.8942 (mtp85) REVERT: C 32 GLN cc_start: 0.9188 (mm-40) cc_final: 0.8929 (mp10) REVERT: C 186 MET cc_start: 0.9247 (mtp) cc_final: 0.8965 (mtm) REVERT: C 322 ASP cc_start: 0.8095 (t0) cc_final: 0.7566 (t0) REVERT: C 326 LYS cc_start: 0.8651 (mppt) cc_final: 0.8407 (mmmm) REVERT: C 374 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8302 (tm-30) REVERT: D 374 GLN cc_start: 0.8123 (tp40) cc_final: 0.7812 (tm-30) REVERT: E 172 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7796 (pt0) REVERT: E 244 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8408 (mp0) REVERT: E 326 LYS cc_start: 0.9133 (mppt) cc_final: 0.8906 (mppt) REVERT: E 329 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8224 (mp0) REVERT: E 334 GLU cc_start: 0.8659 (mp0) cc_final: 0.8436 (mp0) REVERT: E 341 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7494 (pp-130) REVERT: F 21 MET cc_start: 0.4658 (tpt) cc_final: 0.4039 (tmm) REVERT: F 73 LEU cc_start: 0.6079 (OUTLIER) cc_final: 0.5311 (pp) outliers start: 66 outliers final: 28 residues processed: 296 average time/residue: 1.4495 time to fit residues: 478.3046 Evaluate side-chains 267 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 232 time to evaluate : 2.208 ------------------------------------------------------------------------------- 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: 0.9990 chunk 134 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 233 optimal weight: 0.0030 chunk 231 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 chunk 92 optimal weight: 0.0770 overall best weight: 0.5750 ------------------------------------------------------------------------------- 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 32 GLN D 193 GLN E 220 GLN E 388 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.123903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.077767 restraints weight = 41479.569| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 4.14 r_work: 0.2835 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1177 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= 0.115 Angle : 0.598 8.822 27252 Z= 0.285 Chirality : 0.042 0.186 3096 Planarity : 0.003 0.045 3528 Dihedral : 9.476 174.242 2814 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.12 % Allowed : 16.11 % 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: 1.38 (0.16), residues: 1161 sheet: -0.01 (0.25), residues: 386 loop : 0.11 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 381 HIS 0.005 0.001 HIS F 42 PHE 0.015 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 0.03203 ( 931) hydrogen bonds : angle 4.14021 ( 2718) covalent geometry : bond 0.00261 (20214) covalent geometry : angle 0.59779 (27252) Misc. bond : bond 0.00014 ( 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 312 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 245 time to evaluate : 2.600 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: 0.8371 (OUTLIER) cc_final: 0.8138 (mp0) REVERT: B 59 GLN cc_start: 0.8902 (pm20) cc_final: 0.8556 (pm20) REVERT: B 109 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7913 (ptt90) REVERT: B 155 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8572 (pm20) REVERT: B 244 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8625 (mm-30) REVERT: B 362 ARG cc_start: 0.9177 (ttm110) cc_final: 0.8968 (mtp85) REVERT: B 374 GLN cc_start: 0.8797 (tp40) cc_final: 0.8589 (tp40) REVERT: C 32 GLN cc_start: 0.9191 (mm-40) cc_final: 0.8941 (mp10) REVERT: C 186 MET cc_start: 0.9227 (mtp) cc_final: 0.8965 (mtm) REVERT: C 322 ASP cc_start: 0.8166 (t0) cc_final: 0.7570 (t0) REVERT: C 326 LYS cc_start: 0.8645 (mppt) cc_final: 0.8395 (mmmm) REVERT: C 374 GLN cc_start: 0.8531 (mm-40) cc_final: 0.7907 (tm-30) REVERT: C 378 GLN cc_start: 0.9077 (mm-40) cc_final: 0.8613 (mm-40) REVERT: C 417 LYS cc_start: 0.9212 (ttpp) cc_final: 0.8978 (ttmm) REVERT: D 374 GLN cc_start: 0.8151 (tp40) cc_final: 0.7766 (tm-30) REVERT: E 32 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8047 (mm-40) REVERT: E 172 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7858 (pt0) REVERT: E 244 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8399 (mp0) REVERT: E 326 LYS cc_start: 0.9217 (mppt) cc_final: 0.8958 (mppt) REVERT: E 329 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8268 (mp0) REVERT: E 334 GLU cc_start: 0.8695 (mp0) cc_final: 0.8448 (mp0) REVERT: E 341 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7686 (pp-130) REVERT: F 21 MET cc_start: 0.4671 (tpt) cc_final: 0.4066 (tmm) REVERT: F 36 PHE cc_start: 0.3286 (t80) cc_final: 0.3074 (t80) REVERT: F 49 ILE cc_start: 0.4112 (OUTLIER) cc_final: 0.3710 (pp) REVERT: F 73 LEU cc_start: 0.6190 (OUTLIER) cc_final: 0.5468 (pp) REVERT: F 111 PHE cc_start: 0.7221 (m-10) cc_final: 0.6835 (m-10) REVERT: F 263 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8383 (pp) outliers start: 67 outliers final: 28 residues processed: 286 average time/residue: 1.4705 time to fit residues: 469.0318 Evaluate side-chains 279 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 241 time to evaluate : 2.323 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 27 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 124 optimal weight: 0.8980 chunk 168 optimal weight: 0.7980 chunk 155 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 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 D 42 HIS 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 = 0.3873 r_free = 0.3873 target = 0.123861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.078063 restraints weight = 41827.996| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.68 r_work: 0.2835 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1284 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 : 0.602 8.722 27252 Z= 0.286 Chirality : 0.042 0.182 3096 Planarity : 0.003 0.043 3528 Dihedral : 9.202 170.859 2808 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.89 % Allowed : 16.99 % Favored : 80.12 % 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: 1.01 (0.17), residues: 2496 helix: 1.40 (0.16), residues: 1161 sheet: 0.20 (0.26), residues: 378 loop : 0.10 (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 0.021 0.001 PHE F 300 TYR 0.019 0.001 TYR A 80 ARG 0.008 0.000 ARG E 362 Details of bonding type rmsd hydrogen bonds : bond 0.03146 ( 931) hydrogen bonds : angle 4.10047 ( 2718) covalent geometry : bond 0.00282 (20214) covalent geometry : angle 0.60205 (27252) Misc. bond : bond 0.00014 ( 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 : 2.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8158 (ppp) cc_final: 0.7921 (pmm) REVERT: A 85 GLN cc_start: 0.9543 (mp10) cc_final: 0.9279 (pm20) REVERT: A 220 GLN cc_start: 0.8695 (mt0) cc_final: 0.8116 (mp10) REVERT: A 244 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8076 (mp0) REVERT: A 326 LYS cc_start: 0.8200 (ptmt) cc_final: 0.7978 (ptmt) REVERT: A 405 MET cc_start: 0.9009 (mtt) cc_final: 0.8514 (mpp) REVERT: B 59 GLN cc_start: 0.8896 (pm20) cc_final: 0.8560 (pm20) REVERT: B 109 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7885 (ptt90) REVERT: B 155 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8569 (pm20) REVERT: B 244 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8626 (mm-30) REVERT: B 362 ARG cc_start: 0.9167 (ttm110) cc_final: 0.8955 (mtp85) REVERT: B 374 GLN cc_start: 0.8811 (tp40) cc_final: 0.8585 (tp40) REVERT: C 32 GLN cc_start: 0.9188 (mm-40) cc_final: 0.8935 (mp10) REVERT: C 186 MET cc_start: 0.9212 (mtp) cc_final: 0.8938 (mtm) REVERT: C 322 ASP cc_start: 0.8208 (t0) cc_final: 0.7608 (t0) REVERT: C 326 LYS cc_start: 0.8640 (mppt) cc_final: 0.8390 (mmmm) REVERT: C 374 GLN cc_start: 0.8552 (mm-40) cc_final: 0.7892 (tm-30) REVERT: C 378 GLN cc_start: 0.9093 (mm-40) cc_final: 0.8623 (mm-40) REVERT: C 417 LYS cc_start: 0.9216 (ttpp) cc_final: 0.8984 (ttmm) REVERT: D 374 GLN cc_start: 0.8223 (tp40) cc_final: 0.7779 (tm-30) REVERT: E 244 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8415 (mm-30) REVERT: E 326 LYS cc_start: 0.9243 (mppt) cc_final: 0.8971 (mppt) REVERT: E 329 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8294 (mp0) REVERT: E 334 GLU cc_start: 0.8706 (mp0) cc_final: 0.8491 (mp0) REVERT: E 341 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7849 (pp-130) REVERT: F 1 MET cc_start: 0.3955 (OUTLIER) cc_final: 0.2237 (pmm) REVERT: F 21 MET cc_start: 0.4511 (tpt) cc_final: 0.3861 (tmm) REVERT: F 73 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.5679 (pp) REVERT: F 111 PHE cc_start: 0.7274 (m-10) cc_final: 0.6988 (m-10) outliers start: 62 outliers final: 31 residues processed: 294 average time/residue: 1.4301 time to fit residues: 470.1912 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 : 2.534 ------------------------------------------------------------------------------- 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: 30.0000 chunk 127 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 212 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 179 optimal weight: 0.0470 chunk 138 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 overall best weight: 1.1684 ------------------------------------------------------------------------------- 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 C 25 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.123329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.077628 restraints weight = 41786.790| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.55 r_work: 0.2823 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20215 Z= 0.157 Angle : 0.623 8.658 27252 Z= 0.297 Chirality : 0.042 0.190 3096 Planarity : 0.004 0.046 3528 Dihedral : 9.139 171.370 2808 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.75 % Allowed : 17.46 % 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: 0.99 (0.17), residues: 2496 helix: 1.41 (0.16), residues: 1157 sheet: 0.20 (0.26), residues: 378 loop : 0.07 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 381 HIS 0.003 0.001 HIS E 388 PHE 0.013 0.001 PHE F 64 TYR 0.020 0.001 TYR E 197 ARG 0.010 0.000 ARG E 362 Details of bonding type rmsd hydrogen bonds : bond 0.03324 ( 931) hydrogen bonds : angle 4.12846 ( 2718) covalent geometry : bond 0.00366 (20214) covalent geometry : angle 0.62289 (27252) Misc. bond : bond 0.00002 ( 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 303 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 244 time to evaluate : 2.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: A 326 LYS cc_start: 0.8203 (ptmt) cc_final: 0.7987 (ptmt) REVERT: A 405 MET cc_start: 0.8966 (mtt) cc_final: 0.8466 (mpp) REVERT: B 59 GLN cc_start: 0.8876 (pm20) cc_final: 0.8535 (pm20) REVERT: B 109 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7946 (ptt90) REVERT: B 155 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8593 (pm20) REVERT: B 244 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8637 (mm-30) REVERT: B 326 LYS cc_start: 0.8451 (pptt) cc_final: 0.8238 (pptt) REVERT: B 362 ARG cc_start: 0.9159 (ttm110) cc_final: 0.8935 (mtp85) REVERT: C 32 GLN cc_start: 0.9188 (mm-40) cc_final: 0.8948 (mp10) REVERT: C 322 ASP cc_start: 0.8290 (t0) cc_final: 0.7699 (t0) REVERT: C 326 LYS cc_start: 0.8659 (mppt) cc_final: 0.8396 (mmmm) REVERT: C 374 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8047 (tm-30) REVERT: C 378 GLN cc_start: 0.9107 (mm-40) cc_final: 0.8663 (mm-40) REVERT: C 417 LYS cc_start: 0.9227 (ttpp) cc_final: 0.8991 (ttmm) REVERT: D 374 GLN cc_start: 0.8278 (tp40) cc_final: 0.7945 (tp40) REVERT: E 32 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8015 (mm-40) REVERT: E 244 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8420 (mm-30) REVERT: E 326 LYS cc_start: 0.9233 (mppt) cc_final: 0.8977 (mppt) REVERT: E 329 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8265 (mp0) REVERT: E 334 GLU cc_start: 0.8756 (mp0) cc_final: 0.8517 (mp0) REVERT: E 341 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.7886 (pp-130) REVERT: F 1 MET cc_start: 0.3647 (OUTLIER) cc_final: 0.2006 (pmm) REVERT: F 21 MET cc_start: 0.4531 (tpt) cc_final: 0.3892 (tmm) REVERT: F 73 LEU cc_start: 0.6575 (OUTLIER) cc_final: 0.5657 (pp) REVERT: F 111 PHE cc_start: 0.7359 (m-10) cc_final: 0.6977 (m-10) REVERT: F 300 PHE cc_start: 0.7231 (t80) cc_final: 0.6501 (m-80) REVERT: F 396 MET cc_start: 0.1951 (mpt) cc_final: 0.0449 (tpt) outliers start: 59 outliers final: 31 residues processed: 284 average time/residue: 1.4756 time to fit residues: 467.0574 Evaluate side-chains 283 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 244 time to evaluate : 2.309 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 175 optimal weight: 1.9990 chunk 203 optimal weight: 0.8980 chunk 232 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 242 optimal weight: 8.9990 chunk 201 optimal weight: 3.9990 chunk 92 optimal weight: 0.0980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN C 25 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.123897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.077728 restraints weight = 41733.433| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.93 r_work: 0.2830 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20215 Z= 0.128 Angle : 0.630 9.291 27252 Z= 0.300 Chirality : 0.042 0.208 3096 Planarity : 0.003 0.050 3528 Dihedral : 8.946 178.698 2806 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.37 % Allowed : 17.88 % Favored : 79.75 % 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: 0.22 (0.26), residues: 372 loop : 0.06 (0.20), residues: 967 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 0.020 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 0.03127 ( 931) hydrogen bonds : angle 4.06440 ( 2718) covalent geometry : bond 0.00297 (20214) covalent geometry : angle 0.63015 (27252) Misc. bond : bond 0.00011 ( 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 303 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 252 time to evaluate : 2.371 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: 0.9566 (mp10) cc_final: 0.9339 (pm20) REVERT: A 220 GLN cc_start: 0.8718 (mt0) cc_final: 0.8138 (mp10) REVERT: A 244 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8108 (mp0) REVERT: A 333 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8386 (tm-30) REVERT: B 41 GLN cc_start: 0.9070 (tp-100) cc_final: 0.8712 (tp40) REVERT: B 59 GLN cc_start: 0.8907 (pm20) cc_final: 0.8553 (pm20) REVERT: B 109 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7914 (ptt90) REVERT: B 155 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8605 (pm20) REVERT: B 244 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8644 (mm-30) REVERT: B 362 ARG cc_start: 0.9179 (ttm110) cc_final: 0.8971 (mtp85) REVERT: C 32 GLN cc_start: 0.9213 (mm-40) cc_final: 0.8961 (mp10) REVERT: C 186 MET cc_start: 0.9220 (mtp) cc_final: 0.8948 (mtm) REVERT: C 322 ASP cc_start: 0.8351 (t0) cc_final: 0.7781 (t0) REVERT: C 326 LYS cc_start: 0.8654 (mppt) cc_final: 0.8386 (mmmm) REVERT: C 374 GLN cc_start: 0.8618 (mm-40) cc_final: 0.7964 (tm-30) REVERT: C 378 GLN cc_start: 0.9136 (mm-40) cc_final: 0.8683 (mm-40) REVERT: C 417 LYS cc_start: 0.9229 (ttpp) cc_final: 0.8997 (ttmm) REVERT: D 374 GLN cc_start: 0.8320 (tp40) cc_final: 0.7976 (tp40) REVERT: E 32 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8041 (mm-40) REVERT: E 244 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8445 (mm-30) REVERT: E 326 LYS cc_start: 0.9273 (mppt) cc_final: 0.9014 (mppt) REVERT: E 329 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8317 (mp0) REVERT: E 334 GLU cc_start: 0.8777 (mp0) cc_final: 0.8551 (mp0) REVERT: E 341 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7911 (pp-130) REVERT: F 1 MET cc_start: 0.3960 (OUTLIER) cc_final: 0.2368 (pmm) REVERT: F 21 MET cc_start: 0.4652 (tpt) cc_final: 0.4043 (tmm) REVERT: F 73 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.5703 (pp) REVERT: F 111 PHE cc_start: 0.7399 (m-10) cc_final: 0.7119 (m-10) REVERT: F 300 PHE cc_start: 0.7243 (t80) cc_final: 0.6667 (m-80) outliers start: 51 outliers final: 32 residues processed: 286 average time/residue: 1.4816 time to fit residues: 472.3131 Evaluate side-chains 284 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 244 time to evaluate : 2.139 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 66 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 133 optimal weight: 0.7980 chunk 69 optimal weight: 0.0470 chunk 111 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 41 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.124306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.078203 restraints weight = 41808.690| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 4.04 r_work: 0.2845 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20215 Z= 0.117 Angle : 0.641 10.344 27252 Z= 0.305 Chirality : 0.042 0.214 3096 Planarity : 0.003 0.053 3528 Dihedral : 8.544 160.547 2804 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.19 % Allowed : 18.85 % Favored : 78.96 % 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: 1.45 (0.16), residues: 1157 sheet: 0.19 (0.26), residues: 372 loop : 0.09 (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 42 PHE 0.029 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 0.02969 ( 931) hydrogen bonds : angle 4.04563 ( 2718) covalent geometry : bond 0.00269 (20214) covalent geometry : angle 0.64117 (27252) Misc. bond : bond 0.00017 ( 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 304 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 257 time to evaluate : 2.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.9562 (mp10) cc_final: 0.9289 (pm20) REVERT: A 220 GLN cc_start: 0.8692 (mt0) cc_final: 0.8098 (mp10) REVERT: A 244 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: B 41 GLN cc_start: 0.9098 (tp-100) cc_final: 0.8737 (tp40) REVERT: B 59 GLN cc_start: 0.8893 (pm20) cc_final: 0.8504 (pm20) REVERT: B 155 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8607 (pm20) REVERT: B 244 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8601 (mm-30) REVERT: C 32 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8940 (mp10) REVERT: C 186 MET cc_start: 0.9228 (mtp) cc_final: 0.8948 (mtm) REVERT: C 322 ASP cc_start: 0.8327 (t0) cc_final: 0.7764 (t0) REVERT: C 326 LYS cc_start: 0.8623 (mppt) cc_final: 0.8353 (mmmm) REVERT: C 417 LYS cc_start: 0.9226 (ttpp) cc_final: 0.8998 (ttmm) REVERT: D 327 MET cc_start: 0.8772 (ttm) cc_final: 0.8559 (ttp) REVERT: D 374 GLN cc_start: 0.8288 (tp40) cc_final: 0.7896 (tp40) REVERT: E 21 MET cc_start: 0.8600 (ttt) cc_final: 0.8215 (ttt) REVERT: E 32 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8045 (mm-40) REVERT: E 41 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8167 (tm-30) REVERT: E 244 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8453 (mm-30) REVERT: E 326 LYS cc_start: 0.9266 (mppt) cc_final: 0.9031 (mppt) REVERT: E 329 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8275 (mp0) REVERT: E 341 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7877 (pp-130) REVERT: F 1 MET cc_start: 0.4243 (OUTLIER) cc_final: 0.2889 (pmm) REVERT: F 21 MET cc_start: 0.4718 (tpt) cc_final: 0.4107 (tmm) REVERT: F 73 LEU cc_start: 0.6604 (OUTLIER) cc_final: 0.5856 (pp) REVERT: F 111 PHE cc_start: 0.7378 (m-10) cc_final: 0.7161 (m-10) REVERT: F 300 PHE cc_start: 0.7383 (t80) cc_final: 0.6834 (m-80) REVERT: F 396 MET cc_start: 0.1890 (mpt) cc_final: 0.0376 (tpt) outliers start: 47 outliers final: 27 residues processed: 289 average time/residue: 1.4821 time to fit residues: 476.4912 Evaluate side-chains 274 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 239 time to evaluate : 2.353 ------------------------------------------------------------------------------- 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 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 224 optimal weight: 9.9990 chunk 55 optimal weight: 0.0970 chunk 1 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 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 = 0.3873 r_free = 0.3873 target = 0.124003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.077909 restraints weight = 41561.869| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.72 r_work: 0.2840 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1605 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= 0.130 Angle : 0.657 10.921 27252 Z= 0.313 Chirality : 0.042 0.216 3096 Planarity : 0.004 0.058 3528 Dihedral : 8.277 162.428 2804 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.19 % Allowed : 19.27 % Favored : 78.54 % 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: 1.43 (0.16), residues: 1157 sheet: 0.16 (0.26), residues: 372 loop : 0.10 (0.20), residues: 967 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 0.009 0.001 PHE E 398 TYR 0.022 0.001 TYR E 197 ARG 0.014 0.000 ARG E 362 Details of bonding type rmsd hydrogen bonds : bond 0.03023 ( 931) hydrogen bonds : angle 4.05987 ( 2718) covalent geometry : bond 0.00305 (20214) covalent geometry : angle 0.65679 (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 295 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 248 time to evaluate : 2.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8096 (mp0) REVERT: A 341 MET cc_start: 0.8982 (ttp) cc_final: 0.8418 (tmm) REVERT: B 41 GLN cc_start: 0.9101 (tp-100) cc_final: 0.8729 (tp40) REVERT: B 59 GLN cc_start: 0.8872 (pm20) cc_final: 0.8492 (pm20) REVERT: B 109 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7893 (ptt90) REVERT: B 155 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8616 (pm20) REVERT: B 244 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8597 (mm-30) REVERT: C 32 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8928 (mp10) REVERT: C 186 MET cc_start: 0.9232 (mtp) cc_final: 0.8933 (mtm) REVERT: C 322 ASP cc_start: 0.8413 (t0) cc_final: 0.7840 (t0) REVERT: C 326 LYS cc_start: 0.8631 (mppt) cc_final: 0.8352 (mmmm) REVERT: C 417 LYS cc_start: 0.9238 (ttpp) cc_final: 0.9014 (ttmm) REVERT: D 327 MET cc_start: 0.8769 (ttm) cc_final: 0.8553 (ttp) REVERT: D 374 GLN cc_start: 0.8309 (tp40) cc_final: 0.7926 (tp40) REVERT: E 32 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8021 (mm-40) REVERT: E 244 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8443 (mm-30) REVERT: E 326 LYS cc_start: 0.9272 (mppt) cc_final: 0.9059 (mppt) REVERT: E 329 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8269 (mp0) REVERT: E 334 GLU cc_start: 0.8792 (mp0) cc_final: 0.8527 (mp0) REVERT: F 1 MET cc_start: 0.3822 (OUTLIER) cc_final: 0.2482 (pmm) REVERT: F 21 MET cc_start: 0.4583 (tpt) cc_final: 0.3958 (tmm) REVERT: F 73 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6047 (pp) REVERT: F 111 PHE cc_start: 0.7494 (m-10) cc_final: 0.7231 (m-10) REVERT: F 300 PHE cc_start: 0.7547 (t80) cc_final: 0.6965 (m-80) REVERT: F 396 MET cc_start: 0.1955 (mpt) cc_final: 0.0424 (tpt) outliers start: 47 outliers final: 30 residues processed: 281 average time/residue: 1.4566 time to fit residues: 457.2974 Evaluate side-chains 285 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 248 time to evaluate : 2.139 ------------------------------------------------------------------------------- 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 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 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 381 TRP Chi-restraints excluded: chain F residue 1 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 2 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 228 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 186 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 32 GLN D 193 GLN E 193 GLN E 220 GLN E 388 HIS ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.122347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.076225 restraints weight = 41762.851| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.69 r_work: 0.2790 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 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 : 0.005 0.043 20215 Z= 0.215 Angle : 0.697 12.310 27252 Z= 0.334 Chirality : 0.044 0.236 3096 Planarity : 0.004 0.061 3528 Dihedral : 8.320 162.797 2804 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.00 % Allowed : 19.69 % Favored : 78.31 % 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: 0.91 (0.17), residues: 2496 helix: 1.34 (0.16), residues: 1149 sheet: 0.14 (0.26), residues: 366 loop : 0.05 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 381 HIS 0.004 0.001 HIS D 295 PHE 0.018 0.001 PHE F 64 TYR 0.022 0.002 TYR E 197 ARG 0.013 0.000 ARG E 362 Details of bonding type rmsd hydrogen bonds : bond 0.03744 ( 931) hydrogen bonds : angle 4.23333 ( 2718) covalent geometry : bond 0.00503 (20214) covalent geometry : angle 0.69661 (27252) Misc. bond : bond 0.00008 ( 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 289 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 246 time to evaluate : 2.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8715 (mt0) cc_final: 0.8143 (mp10) REVERT: A 244 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8111 (mp0) REVERT: A 341 MET cc_start: 0.9029 (ttp) cc_final: 0.8512 (tmm) REVERT: B 41 GLN cc_start: 0.9098 (tp-100) cc_final: 0.8793 (tp40) REVERT: B 59 GLN cc_start: 0.8874 (pm20) cc_final: 0.8477 (pm20) REVERT: B 109 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7907 (ptt90) REVERT: B 244 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8640 (mm-30) REVERT: C 32 GLN cc_start: 0.9199 (mm-40) cc_final: 0.8934 (mp10) REVERT: C 322 ASP cc_start: 0.8584 (t0) cc_final: 0.8049 (t0) REVERT: C 326 LYS cc_start: 0.8693 (mppt) cc_final: 0.8395 (mmmm) REVERT: C 374 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8006 (tp-100) REVERT: C 417 LYS cc_start: 0.9228 (ttpp) cc_final: 0.8995 (ttmm) REVERT: D 327 MET cc_start: 0.8842 (ttm) cc_final: 0.8624 (ttp) REVERT: D 374 GLN cc_start: 0.8446 (tp40) cc_final: 0.8048 (tp40) REVERT: E 32 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8041 (mm-40) REVERT: E 41 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8164 (tm-30) REVERT: E 244 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8449 (mm-30) REVERT: F 1 MET cc_start: 0.3863 (OUTLIER) cc_final: 0.2540 (pmm) REVERT: F 21 MET cc_start: 0.4597 (tpt) cc_final: 0.3910 (tmm) REVERT: F 73 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6124 (pp) REVERT: F 111 PHE cc_start: 0.7495 (m-10) cc_final: 0.7258 (m-10) REVERT: F 300 PHE cc_start: 0.7582 (t80) cc_final: 0.7000 (m-80) REVERT: F 396 MET cc_start: 0.1977 (mpt) cc_final: 0.0462 (tpt) outliers start: 43 outliers final: 29 residues processed: 274 average time/residue: 1.4770 time to fit residues: 450.9820 Evaluate side-chains 269 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 233 time to evaluate : 2.323 ------------------------------------------------------------------------------- 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 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 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 93 THR 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 6 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 174 optimal weight: 0.0980 chunk 146 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** A 241 GLN B 193 GLN C 25 ASN C 193 GLN C 378 GLN D 193 GLN E 42 HIS E 193 GLN E 388 HIS ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.122439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.076400 restraints weight = 41893.153| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.65 r_work: 0.2794 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 20215 Z= 0.203 Angle : 0.840 59.199 27252 Z= 0.440 Chirality : 0.043 0.304 3096 Planarity : 0.004 0.058 3528 Dihedral : 8.316 162.731 2804 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.86 % Allowed : 19.88 % Favored : 78.26 % 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: 0.91 (0.17), residues: 2496 helix: 1.32 (0.16), residues: 1153 sheet: 0.13 (0.26), residues: 366 loop : 0.06 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 381 HIS 0.007 0.001 HIS C 239 PHE 0.014 0.001 PHE F 64 TYR 0.020 0.001 TYR E 197 ARG 0.013 0.000 ARG B 272 Details of bonding type rmsd hydrogen bonds : bond 0.03686 ( 931) hydrogen bonds : angle 4.23527 ( 2718) covalent geometry : bond 0.00470 (20214) covalent geometry : angle 0.84024 (27252) Misc. bond : bond 0.00009 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17962.68 seconds wall clock time: 310 minutes 18.97 seconds (18618.97 seconds total)