Starting phenix.real_space_refine on Sun Aug 24 13:18:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q3n_18130/08_2025/8q3n_18130.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q3n_18130/08_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_18130/08_2025/8q3n_18130.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q3n_18130/08_2025/8q3n_18130.map" model { file = "/net/cci-nas-00/data/ceres_data/8q3n_18130/08_2025/8q3n_18130.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q3n_18130/08_2025/8q3n_18130.cif" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.87, per 1000 atoms: 0.24 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: 1.79 Conformation dependent library (CDL) restraints added in 814.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.81 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: 3.44 Time building geometry restraints manager: 2.36 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 1000) selection = (chain 'C' and resid 1 through 1000) selection = (chain 'D' and resid 1 through 1000) selection = (chain 'E' and resid 1 through 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: 4.220 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: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.680 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.630 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.013 0.000 ARG E 362 TYR 0.023 0.001 TYR E 197 PHE 0.009 0.001 PHE E 398 TRP 0.055 0.002 TRP E 381 HIS 0.008 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00349 (20214) covalent geometry : angle 0.64235 (27252) hydrogen bonds : bond 0.15462 ( 931) hydrogen bonds : angle 5.71770 ( 2718) 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 : 0.752 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: 0.6959 time to fit residues: 206.3213 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 : 0.609 ------------------------------------------------------------------------------- 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 216 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 30.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN B 275 ASN C 378 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 = 0.3836 r_free = 0.3836 target = 0.121695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.075077 restraints weight = 41560.216| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 4.21 r_work: 0.2771 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 20215 Z= 0.256 Angle : 0.649 8.898 27252 Z= 0.318 Chirality : 0.044 0.206 3096 Planarity : 0.004 0.058 3528 Dihedral : 10.519 179.851 2843 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.40 % Allowed : 14.62 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.17), residues: 2496 helix: 1.19 (0.16), residues: 1158 sheet: 0.33 (0.26), residues: 371 loop : 0.01 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 362 TYR 0.020 0.001 TYR F 72 PHE 0.017 0.001 PHE F 64 TRP 0.027 0.002 TRP E 381 HIS 0.005 0.001 HIS E 239 Details of bonding type rmsd covalent geometry : bond 0.00594 (20214) covalent geometry : angle 0.64905 (27252) hydrogen bonds : bond 0.04460 ( 931) hydrogen bonds : angle 4.57596 ( 2718) Misc. bond : bond 0.00024 ( 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 312 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 239 time to evaluate : 0.764 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: 0.7965 (ppp) cc_final: 0.7716 (pmm) REVERT: A 244 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: B 59 GLN cc_start: 0.8907 (pm20) cc_final: 0.8567 (pm20) REVERT: B 109 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8026 (ptt90) REVERT: B 326 LYS cc_start: 0.8694 (ptmm) cc_final: 0.8413 (pttt) REVERT: B 374 GLN cc_start: 0.8919 (tp40) cc_final: 0.8714 (tp40) REVERT: C 32 GLN cc_start: 0.9215 (mm-40) cc_final: 0.8945 (mp10) REVERT: C 322 ASP cc_start: 0.8214 (t0) cc_final: 0.7824 (t0) REVERT: C 374 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8224 (tm-30) REVERT: E 32 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8041 (mm-40) REVERT: E 172 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7928 (pt0) REVERT: E 244 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8421 (mp0) REVERT: F 21 MET cc_start: 0.4674 (tpt) cc_final: 0.4013 (tmm) REVERT: F 396 MET cc_start: 0.1673 (OUTLIER) cc_final: 0.0464 (mmm) outliers start: 73 outliers final: 32 residues processed: 289 average time/residue: 0.6185 time to fit residues: 199.2985 Evaluate side-chains 274 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 237 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 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 278 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 154 THR Chi-restraints excluded: chain D residue 157 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 32 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 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 147 MET Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 396 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 144 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 166 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 244 optimal weight: 8.9990 chunk 218 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 C 193 GLN D 193 GLN E 220 GLN E 388 HIS ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.122509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.076677 restraints weight = 41737.074| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.82 r_work: 0.2800 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1068 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= 0.171 Angle : 0.607 9.349 27252 Z= 0.294 Chirality : 0.043 0.175 3096 Planarity : 0.004 0.043 3528 Dihedral : 10.054 179.880 2821 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.79 % Allowed : 16.06 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.17), residues: 2496 helix: 1.22 (0.15), residues: 1159 sheet: 0.21 (0.26), residues: 381 loop : 0.05 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 362 TYR 0.017 0.001 TYR A 80 PHE 0.016 0.001 PHE F 64 TRP 0.030 0.001 TRP E 381 HIS 0.006 0.001 HIS F 256 Details of bonding type rmsd covalent geometry : bond 0.00395 (20214) covalent geometry : angle 0.60743 (27252) hydrogen bonds : bond 0.03752 ( 931) hydrogen bonds : angle 4.31685 ( 2718) Misc. bond : bond 0.00011 ( 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 316 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 256 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8128 (mmp) REVERT: A 193 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8657 (pm20) REVERT: A 220 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8101 (mp10) REVERT: A 244 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8072 (mp0) REVERT: B 59 GLN cc_start: 0.8906 (pm20) cc_final: 0.8582 (pm20) REVERT: B 244 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8622 (mm-30) REVERT: B 326 LYS cc_start: 0.8694 (ptmm) cc_final: 0.8310 (pttt) REVERT: B 362 ARG cc_start: 0.9184 (ttm110) cc_final: 0.8971 (mtp85) REVERT: B 374 GLN cc_start: 0.8900 (tp-100) cc_final: 0.8691 (tp40) REVERT: C 32 GLN cc_start: 0.9202 (mm-40) cc_final: 0.8938 (mp10) REVERT: C 322 ASP cc_start: 0.8270 (t0) cc_final: 0.7764 (t0) REVERT: C 374 GLN cc_start: 0.8611 (mm-40) cc_final: 0.8308 (tm-30) REVERT: D 374 GLN cc_start: 0.8189 (tp40) cc_final: 0.7792 (tm-30) REVERT: E 172 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7891 (pt0) REVERT: E 244 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8415 (mp0) REVERT: E 326 LYS cc_start: 0.9190 (mppt) cc_final: 0.8944 (mppt) REVERT: E 329 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8267 (mp0) REVERT: E 334 GLU cc_start: 0.8690 (mp0) cc_final: 0.8431 (mp0) REVERT: E 341 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.7824 (pp-130) REVERT: F 21 MET cc_start: 0.4600 (tpt) cc_final: 0.3952 (tmm) REVERT: F 73 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.5526 (pp) REVERT: F 111 PHE cc_start: 0.7063 (m-80) cc_final: 0.6737 (m-10) REVERT: F 300 PHE cc_start: 0.8181 (t80) cc_final: 0.7952 (t80) outliers start: 60 outliers final: 27 residues processed: 293 average time/residue: 0.7281 time to fit residues: 236.2035 Evaluate side-chains 268 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 233 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 220 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 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 260 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 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 5 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 245 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 242 optimal weight: 0.0020 chunk 184 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 241 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 189 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.122221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.076002 restraints weight = 41608.059| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 3.98 r_work: 0.2785 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20215 Z= 0.190 Angle : 0.620 9.291 27252 Z= 0.299 Chirality : 0.043 0.171 3096 Planarity : 0.004 0.047 3528 Dihedral : 9.694 177.435 2819 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.68 % Allowed : 15.50 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.17), residues: 2496 helix: 1.25 (0.15), residues: 1156 sheet: 0.13 (0.26), residues: 381 loop : 0.04 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 362 TYR 0.017 0.001 TYR E 197 PHE 0.015 0.001 PHE F 64 TRP 0.031 0.001 TRP E 381 HIS 0.006 0.001 HIS F 42 Details of bonding type rmsd covalent geometry : bond 0.00442 (20214) covalent geometry : angle 0.62018 (27252) hydrogen bonds : bond 0.03702 ( 931) hydrogen bonds : angle 4.25676 ( 2718) Misc. bond : bond 0.00015 ( 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 320 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 241 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8172 (mmp) REVERT: A 220 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8154 (mp10) REVERT: A 244 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8110 (mp0) REVERT: B 59 GLN cc_start: 0.8927 (pm20) cc_final: 0.8575 (pm20) REVERT: B 109 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8136 (ptt90) REVERT: B 244 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8625 (mm-30) REVERT: B 374 GLN cc_start: 0.8960 (tp-100) cc_final: 0.8747 (tp40) REVERT: C 32 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8946 (mp10) REVERT: C 322 ASP cc_start: 0.8410 (t0) cc_final: 0.7884 (t0) REVERT: C 374 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8081 (tm-30) REVERT: C 378 GLN cc_start: 0.9118 (mm-40) cc_final: 0.8660 (mm-40) REVERT: D 149 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7257 (mtm180) REVERT: D 374 GLN cc_start: 0.8359 (tp40) cc_final: 0.8095 (tp40) REVERT: E 32 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8119 (mm-40) REVERT: E 244 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8456 (mp0) REVERT: E 326 LYS cc_start: 0.9242 (mppt) cc_final: 0.8982 (mppt) REVERT: E 329 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8282 (mp0) REVERT: E 334 GLU cc_start: 0.8731 (mp0) cc_final: 0.8509 (mp0) REVERT: E 341 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.7919 (pp-130) REVERT: F 21 MET cc_start: 0.4594 (tpt) cc_final: 0.3979 (tmm) REVERT: F 36 PHE cc_start: 0.3139 (t80) cc_final: 0.2938 (t80) REVERT: F 49 ILE cc_start: 0.5113 (OUTLIER) cc_final: 0.4638 (pp) REVERT: F 73 LEU cc_start: 0.6335 (OUTLIER) cc_final: 0.5533 (pp) REVERT: F 111 PHE cc_start: 0.7161 (m-80) cc_final: 0.6771 (m-10) REVERT: F 224 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.8018 (pmtt) REVERT: F 263 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8445 (pp) REVERT: F 300 PHE cc_start: 0.8215 (t80) cc_final: 0.7955 (t80) outliers start: 79 outliers final: 33 residues processed: 295 average time/residue: 0.7416 time to fit residues: 243.7207 Evaluate side-chains 281 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 236 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 147 MET Chi-restraints excluded: chain A residue 220 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 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 278 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 149 ARG 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 113 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 241 GLN 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 E residue 416 MET 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 224 LYS 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 134 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 180 optimal weight: 2.9990 chunk 172 optimal weight: 0.2980 chunk 215 optimal weight: 50.0000 chunk 132 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN D 32 GLN D 193 GLN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3849 r_free = 0.3849 target = 0.122585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.076467 restraints weight = 41401.691| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.86 r_work: 0.2797 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20215 Z= 0.151 Angle : 0.617 9.092 27252 Z= 0.294 Chirality : 0.042 0.176 3096 Planarity : 0.004 0.045 3528 Dihedral : 9.309 174.452 2811 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.26 % Allowed : 16.81 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.17), residues: 2496 helix: 1.30 (0.15), residues: 1157 sheet: 0.10 (0.26), residues: 381 loop : 0.05 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 362 TYR 0.021 0.001 TYR A 80 PHE 0.014 0.001 PHE F 300 TRP 0.031 0.001 TRP E 381 HIS 0.005 0.001 HIS F 42 Details of bonding type rmsd covalent geometry : bond 0.00351 (20214) covalent geometry : angle 0.61706 (27252) hydrogen bonds : bond 0.03449 ( 931) hydrogen bonds : angle 4.17036 ( 2718) Misc. bond : bond 0.00002 ( 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 317 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 247 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.9588 (mp10) cc_final: 0.9328 (pm20) REVERT: A 147 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8162 (mmp) REVERT: A 220 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8088 (mp10) REVERT: A 244 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8123 (mp0) REVERT: B 59 GLN cc_start: 0.8929 (pm20) cc_final: 0.8579 (pm20) REVERT: B 109 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7968 (ptt90) REVERT: B 244 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8631 (mm-30) REVERT: C 32 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8953 (mp10) REVERT: C 322 ASP cc_start: 0.8411 (t0) cc_final: 0.7894 (t0) REVERT: C 374 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8025 (tm-30) REVERT: C 378 GLN cc_start: 0.9126 (mm-40) cc_final: 0.8666 (mm-40) REVERT: D 149 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7253 (mtm180) REVERT: D 374 GLN cc_start: 0.8356 (tp40) cc_final: 0.8038 (tp40) REVERT: E 32 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8132 (mm-40) REVERT: E 244 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8514 (mm-30) REVERT: E 326 LYS cc_start: 0.9255 (mppt) cc_final: 0.8991 (mppt) REVERT: E 329 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8296 (mp0) REVERT: E 334 GLU cc_start: 0.8755 (mp0) cc_final: 0.8475 (mp0) REVERT: E 341 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.7788 (pp-130) REVERT: E 390 MET cc_start: 0.8715 (ptt) cc_final: 0.8486 (ptt) REVERT: F 21 MET cc_start: 0.4518 (tpt) cc_final: 0.3902 (tmm) REVERT: F 36 PHE cc_start: 0.3130 (t80) cc_final: 0.2908 (t80) REVERT: F 49 ILE cc_start: 0.4845 (OUTLIER) cc_final: 0.4408 (pp) REVERT: F 73 LEU cc_start: 0.6523 (OUTLIER) cc_final: 0.5708 (pp) REVERT: F 111 PHE cc_start: 0.7109 (m-80) cc_final: 0.6696 (m-10) REVERT: F 300 PHE cc_start: 0.8218 (t80) cc_final: 0.7677 (m-80) REVERT: F 396 MET cc_start: 0.2027 (mpt) cc_final: 0.0587 (tpt) outliers start: 70 outliers final: 36 residues processed: 294 average time/residue: 0.6041 time to fit residues: 197.0170 Evaluate side-chains 282 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 236 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 220 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 113 LEU 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 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 149 ARG 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 113 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 241 GLN 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 E residue 416 MET 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 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 185 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 218 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 203 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 195 optimal weight: 1.9990 chunk 23 optimal weight: 0.0020 chunk 8 optimal weight: 0.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN B 275 ASN D 193 GLN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 GLN E 388 HIS ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.123051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.077259 restraints weight = 41714.349| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.77 r_work: 0.2813 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20215 Z= 0.129 Angle : 0.620 8.954 27252 Z= 0.295 Chirality : 0.042 0.187 3096 Planarity : 0.004 0.047 3528 Dihedral : 9.158 174.317 2811 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.07 % Allowed : 17.64 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.17), residues: 2496 helix: 1.39 (0.16), residues: 1157 sheet: -0.12 (0.25), residues: 389 loop : 0.07 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 362 TYR 0.019 0.001 TYR E 197 PHE 0.014 0.001 PHE F 300 TRP 0.031 0.001 TRP E 381 HIS 0.006 0.001 HIS F 42 Details of bonding type rmsd covalent geometry : bond 0.00298 (20214) covalent geometry : angle 0.61990 (27252) hydrogen bonds : bond 0.03253 ( 931) hydrogen bonds : angle 4.10977 ( 2718) Misc. bond : bond 0.00014 ( 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 309 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 243 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8175 (mmp) REVERT: A 244 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8113 (mp0) REVERT: B 41 GLN cc_start: 0.9065 (tp-100) cc_final: 0.8715 (tp40) REVERT: B 59 GLN cc_start: 0.8914 (pm20) cc_final: 0.8566 (pm20) REVERT: B 109 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7925 (ptt90) REVERT: B 157 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8726 (mp) REVERT: B 244 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8626 (mm-30) REVERT: C 32 GLN cc_start: 0.9198 (mm-40) cc_final: 0.8947 (mp10) REVERT: C 322 ASP cc_start: 0.8435 (t0) cc_final: 0.7893 (t0) REVERT: C 374 GLN cc_start: 0.8701 (mm-40) cc_final: 0.8471 (mm-40) REVERT: C 378 GLN cc_start: 0.9140 (mm-40) cc_final: 0.8914 (mm-40) REVERT: D 149 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7217 (mtm180) REVERT: D 374 GLN cc_start: 0.8349 (tp40) cc_final: 0.7996 (tp40) REVERT: E 32 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8118 (mm-40) REVERT: E 244 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8486 (mm-30) REVERT: E 326 LYS cc_start: 0.9292 (mppt) cc_final: 0.9046 (mppt) REVERT: E 329 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8316 (mp0) REVERT: E 341 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.7802 (pp-130) REVERT: F 1 MET cc_start: 0.4235 (OUTLIER) cc_final: 0.2537 (pmm) REVERT: F 21 MET cc_start: 0.4513 (tpt) cc_final: 0.3886 (tmm) REVERT: F 36 PHE cc_start: 0.3270 (t80) cc_final: 0.3052 (t80) REVERT: F 49 ILE cc_start: 0.4762 (OUTLIER) cc_final: 0.4520 (pp) REVERT: F 73 LEU cc_start: 0.6595 (OUTLIER) cc_final: 0.5749 (pp) REVERT: F 111 PHE cc_start: 0.7118 (m-80) cc_final: 0.6729 (m-10) REVERT: F 300 PHE cc_start: 0.8228 (t80) cc_final: 0.7617 (m-80) outliers start: 66 outliers final: 34 residues processed: 283 average time/residue: 0.7241 time to fit residues: 227.7973 Evaluate side-chains 287 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 242 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 147 MET 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 113 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 157 LEU 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 149 ARG Chi-restraints excluded: chain D residue 157 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 158 THR Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 241 GLN 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 49 ILE Chi-restraints excluded: chain F residue 50 PHE 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 224 LYS 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 172 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 242 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 173 optimal weight: 0.8980 chunk 245 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 HIS ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.122425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.075507 restraints weight = 41808.423| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 4.05 r_work: 0.2777 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20215 Z= 0.209 Angle : 0.654 9.067 27252 Z= 0.314 Chirality : 0.043 0.207 3096 Planarity : 0.004 0.050 3528 Dihedral : 9.158 174.970 2811 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.93 % Allowed : 18.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.17), residues: 2496 helix: 1.32 (0.15), residues: 1153 sheet: 0.11 (0.26), residues: 372 loop : 0.04 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 362 TYR 0.020 0.001 TYR E 197 PHE 0.013 0.001 PHE F 300 TRP 0.031 0.001 TRP E 381 HIS 0.005 0.001 HIS F 42 Details of bonding type rmsd covalent geometry : bond 0.00490 (20214) covalent geometry : angle 0.65440 (27252) hydrogen bonds : bond 0.03696 ( 931) hydrogen bonds : angle 4.20004 ( 2718) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 243 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.9595 (mp10) cc_final: 0.9298 (pm20) REVERT: A 147 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8168 (mmp) REVERT: A 193 GLN cc_start: 0.9164 (pt0) cc_final: 0.8696 (pm20) REVERT: A 220 GLN cc_start: 0.8693 (mt0) cc_final: 0.8093 (mp10) REVERT: A 244 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: A 333 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8291 (tm-30) REVERT: B 41 GLN cc_start: 0.9091 (tp-100) cc_final: 0.8763 (tp40) REVERT: B 59 GLN cc_start: 0.8906 (pm20) cc_final: 0.8570 (pm20) REVERT: B 157 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8789 (mp) REVERT: B 244 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8605 (mm-30) REVERT: B 362 ARG cc_start: 0.9177 (ttm110) cc_final: 0.8743 (mtm-85) REVERT: C 32 GLN cc_start: 0.9211 (mm-40) cc_final: 0.8952 (mp10) REVERT: C 322 ASP cc_start: 0.8536 (t0) cc_final: 0.8008 (t0) REVERT: C 374 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8421 (mm-40) REVERT: C 378 GLN cc_start: 0.9122 (mm-40) cc_final: 0.8891 (mm-40) REVERT: D 149 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7220 (mtm180) REVERT: D 374 GLN cc_start: 0.8438 (tp40) cc_final: 0.7897 (tp40) REVERT: D 378 GLN cc_start: 0.8871 (mt0) cc_final: 0.8582 (mt0) REVERT: E 32 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8093 (mm-40) REVERT: E 41 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8095 (tm-30) REVERT: E 244 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8488 (mm-30) REVERT: E 326 LYS cc_start: 0.9289 (mppt) cc_final: 0.9052 (mppt) REVERT: E 329 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8264 (mp0) REVERT: E 341 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7739 (pp-130) REVERT: F 1 MET cc_start: 0.4572 (OUTLIER) cc_final: 0.2937 (pmm) REVERT: F 21 MET cc_start: 0.4607 (tpt) cc_final: 0.4026 (tmm) REVERT: F 73 LEU cc_start: 0.6394 (OUTLIER) cc_final: 0.5648 (pp) REVERT: F 396 MET cc_start: 0.2002 (mpt) cc_final: 0.0515 (tpt) outliers start: 63 outliers final: 35 residues processed: 286 average time/residue: 0.7796 time to fit residues: 247.3861 Evaluate side-chains 290 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 245 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 147 MET 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 113 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 157 LEU 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 278 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 149 ARG Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 157 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 158 THR Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 241 GLN 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 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 151 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 235 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 117 optimal weight: 0.0170 chunk 107 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 216 optimal weight: 30.0000 chunk 169 optimal weight: 6.9990 chunk 233 optimal weight: 6.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- 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 42 HIS D 193 GLN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3856 r_free = 0.3856 target = 0.122909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.076878 restraints weight = 41786.771| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.85 r_work: 0.2806 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20215 Z= 0.141 Angle : 0.649 10.396 27252 Z= 0.310 Chirality : 0.042 0.224 3096 Planarity : 0.004 0.054 3528 Dihedral : 8.762 157.615 2811 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.03 % Allowed : 18.72 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.17), residues: 2496 helix: 1.39 (0.16), residues: 1150 sheet: 0.10 (0.26), residues: 375 loop : 0.04 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 362 TYR 0.020 0.001 TYR E 197 PHE 0.014 0.001 PHE F 300 TRP 0.032 0.001 TRP E 381 HIS 0.005 0.001 HIS F 42 Details of bonding type rmsd covalent geometry : bond 0.00329 (20214) covalent geometry : angle 0.64935 (27252) hydrogen bonds : bond 0.03273 ( 931) hydrogen bonds : angle 4.11156 ( 2718) Misc. bond : bond 0.00013 ( 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 313 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 248 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.9588 (mp10) cc_final: 0.9273 (pm20) REVERT: A 147 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8159 (mmp) REVERT: A 193 GLN cc_start: 0.9148 (pt0) cc_final: 0.8687 (pm20) REVERT: A 220 GLN cc_start: 0.8672 (mt0) cc_final: 0.8059 (mp10) REVERT: A 244 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8049 (mp0) REVERT: B 41 GLN cc_start: 0.9110 (tp-100) cc_final: 0.8761 (tp40) REVERT: B 59 GLN cc_start: 0.8918 (pm20) cc_final: 0.8540 (pm20) REVERT: B 244 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8632 (mm-30) REVERT: C 32 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8933 (mp10) REVERT: C 322 ASP cc_start: 0.8550 (t0) cc_final: 0.8012 (t0) REVERT: C 374 GLN cc_start: 0.8697 (mm-40) cc_final: 0.8383 (mm-40) REVERT: C 378 GLN cc_start: 0.9111 (mm-40) cc_final: 0.8888 (mm-40) REVERT: D 149 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7195 (mtm180) REVERT: D 374 GLN cc_start: 0.8395 (tp40) cc_final: 0.7834 (tp40) REVERT: D 378 GLN cc_start: 0.8848 (mt0) cc_final: 0.8547 (mt0) REVERT: E 32 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8066 (mm-40) REVERT: E 244 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8464 (mm-30) REVERT: E 326 LYS cc_start: 0.9275 (mppt) cc_final: 0.9055 (mppt) REVERT: E 329 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8266 (mp0) REVERT: E 341 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.7844 (pp-130) REVERT: F 1 MET cc_start: 0.4456 (OUTLIER) cc_final: 0.2820 (pmm) REVERT: F 21 MET cc_start: 0.4474 (tpt) cc_final: 0.3876 (tmm) REVERT: F 36 PHE cc_start: 0.3545 (t80) cc_final: 0.3336 (t80) REVERT: F 73 LEU cc_start: 0.6621 (OUTLIER) cc_final: 0.5776 (pp) REVERT: F 111 PHE cc_start: 0.6872 (m-80) cc_final: 0.6572 (m-10) REVERT: F 300 PHE cc_start: 0.8161 (t80) cc_final: 0.7579 (m-80) outliers start: 65 outliers final: 37 residues processed: 291 average time/residue: 0.7441 time to fit residues: 240.8650 Evaluate side-chains 275 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 230 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 93 THR Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 153 SER 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 113 LEU 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 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 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 149 ARG Chi-restraints excluded: chain D residue 157 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 158 THR Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 241 GLN 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 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 185 optimal weight: 0.6980 chunk 38 optimal weight: 0.0980 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 91 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 205 optimal weight: 50.0000 chunk 190 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN C 25 ASN D 32 GLN D 193 GLN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3857 r_free = 0.3857 target = 0.123000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.077213 restraints weight = 41548.089| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.92 r_work: 0.2809 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1574 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= 0.139 Angle : 0.653 11.676 27252 Z= 0.311 Chirality : 0.042 0.236 3096 Planarity : 0.004 0.057 3528 Dihedral : 8.424 160.088 2811 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.37 % Allowed : 19.46 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.17), residues: 2496 helix: 1.41 (0.16), residues: 1150 sheet: 0.12 (0.26), residues: 372 loop : 0.06 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 362 TYR 0.021 0.001 TYR E 197 PHE 0.013 0.001 PHE F 300 TRP 0.032 0.001 TRP E 381 HIS 0.005 0.001 HIS F 42 Details of bonding type rmsd covalent geometry : bond 0.00326 (20214) covalent geometry : angle 0.65294 (27252) hydrogen bonds : bond 0.03213 ( 931) hydrogen bonds : angle 4.10150 ( 2718) Misc. bond : bond 0.00013 ( 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 288 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 237 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8182 (mmp) REVERT: A 244 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: B 41 GLN cc_start: 0.9118 (tp-100) cc_final: 0.8762 (tp40) REVERT: B 59 GLN cc_start: 0.8913 (pm20) cc_final: 0.8528 (pm20) REVERT: B 244 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8601 (mm-30) REVERT: C 32 GLN cc_start: 0.9199 (mm-40) cc_final: 0.8938 (mp10) REVERT: C 186 MET cc_start: 0.9252 (mtp) cc_final: 0.8969 (mtm) REVERT: C 322 ASP cc_start: 0.8536 (t0) cc_final: 0.7999 (t0) REVERT: C 374 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8379 (mm-40) REVERT: C 378 GLN cc_start: 0.9114 (mm-40) cc_final: 0.8903 (mm-40) REVERT: C 417 LYS cc_start: 0.9222 (ttpp) cc_final: 0.8997 (ttmm) REVERT: D 149 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7166 (mtm180) REVERT: D 374 GLN cc_start: 0.8431 (tp40) cc_final: 0.7856 (tp40) REVERT: D 378 GLN cc_start: 0.8873 (mt0) cc_final: 0.8569 (mt0) REVERT: E 32 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8102 (mm-40) REVERT: E 244 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8459 (mm-30) REVERT: E 326 LYS cc_start: 0.9294 (mppt) cc_final: 0.9068 (mppt) REVERT: E 329 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8285 (mp0) REVERT: E 341 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.7853 (pp-130) REVERT: F 1 MET cc_start: 0.4448 (OUTLIER) cc_final: 0.2820 (pmm) REVERT: F 21 MET cc_start: 0.4576 (tpt) cc_final: 0.3953 (tmm) REVERT: F 73 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.5780 (pp) outliers start: 51 outliers final: 32 residues processed: 276 average time/residue: 0.6882 time to fit residues: 211.4281 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 : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 153 SER 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 113 LEU 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 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 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 149 ARG Chi-restraints excluded: chain D residue 157 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 158 THR Chi-restraints excluded: chain E residue 241 GLN 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 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 169 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 231 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.2980 chunk 3 optimal weight: 6.9990 chunk 166 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN C 25 ASN D 193 GLN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.123052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.076958 restraints weight = 41655.426| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.89 r_work: 0.2808 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1598 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= 0.147 Angle : 0.669 12.300 27252 Z= 0.319 Chirality : 0.042 0.244 3096 Planarity : 0.004 0.056 3528 Dihedral : 8.059 162.252 2809 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.28 % Allowed : 19.83 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.17), residues: 2496 helix: 1.39 (0.16), residues: 1150 sheet: 0.17 (0.26), residues: 364 loop : 0.03 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 362 TYR 0.026 0.001 TYR A 80 PHE 0.013 0.001 PHE F 300 TRP 0.032 0.001 TRP E 381 HIS 0.004 0.001 HIS F 42 Details of bonding type rmsd covalent geometry : bond 0.00346 (20214) covalent geometry : angle 0.66946 (27252) hydrogen bonds : bond 0.03257 ( 931) hydrogen bonds : angle 4.10784 ( 2718) Misc. bond : bond 0.00013 ( 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 300 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 251 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.9579 (mp10) cc_final: 0.9259 (pm20) REVERT: A 147 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8188 (mmp) REVERT: A 193 GLN cc_start: 0.9164 (pt0) cc_final: 0.8744 (pm20) REVERT: A 220 GLN cc_start: 0.8703 (mt0) cc_final: 0.8088 (mp10) REVERT: A 244 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: B 41 GLN cc_start: 0.9128 (tp-100) cc_final: 0.8741 (tp40) REVERT: B 59 GLN cc_start: 0.8927 (pm20) cc_final: 0.8534 (pm20) REVERT: B 244 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8597 (mm-30) REVERT: B 362 ARG cc_start: 0.9209 (ttm110) cc_final: 0.8794 (mtm-85) REVERT: C 32 GLN cc_start: 0.9201 (mm-40) cc_final: 0.8938 (mp10) REVERT: C 186 MET cc_start: 0.9246 (mtp) cc_final: 0.8979 (mtm) REVERT: C 322 ASP cc_start: 0.8573 (t0) cc_final: 0.8045 (t0) REVERT: C 374 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8442 (mm-40) REVERT: C 378 GLN cc_start: 0.9127 (mm-40) cc_final: 0.8915 (mm-40) REVERT: C 417 LYS cc_start: 0.9240 (ttpp) cc_final: 0.9023 (ttmm) REVERT: D 149 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7153 (mtm180) REVERT: D 374 GLN cc_start: 0.8447 (tp40) cc_final: 0.7863 (tp40) REVERT: D 378 GLN cc_start: 0.8878 (mt0) cc_final: 0.8572 (mt0) REVERT: D 417 LYS cc_start: 0.9396 (ttpp) cc_final: 0.9051 (tmmm) REVERT: E 32 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8087 (mm-40) REVERT: E 244 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8455 (mm-30) REVERT: E 326 LYS cc_start: 0.9300 (mppt) cc_final: 0.9047 (mppt) REVERT: E 329 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8273 (mp0) REVERT: E 341 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7830 (pp-130) REVERT: F 1 MET cc_start: 0.4461 (OUTLIER) cc_final: 0.2882 (pmm) REVERT: F 21 MET cc_start: 0.4539 (tpt) cc_final: 0.3923 (tmm) REVERT: F 25 ASN cc_start: -0.0682 (t0) cc_final: -0.1425 (t0) REVERT: F 36 PHE cc_start: 0.3573 (t80) cc_final: 0.3358 (t80) REVERT: F 73 LEU cc_start: 0.6625 (OUTLIER) cc_final: 0.5815 (pp) REVERT: F 111 PHE cc_start: 0.6838 (m-80) cc_final: 0.6560 (m-10) REVERT: F 300 PHE cc_start: 0.8192 (t80) cc_final: 0.7656 (m-80) outliers start: 49 outliers final: 36 residues processed: 287 average time/residue: 0.6395 time to fit residues: 203.6095 Evaluate side-chains 282 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 238 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 93 THR Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 153 SER 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 116 VAL 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 277 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 149 ARG Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 162 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 158 THR Chi-restraints excluded: chain E residue 241 GLN 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 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 17 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 191 optimal weight: 0.0060 chunk 97 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 219 optimal weight: 50.0000 chunk 245 optimal weight: 0.0980 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 172 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 = 0.3869 r_free = 0.3869 target = 0.123698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.077671 restraints weight = 41771.445| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.95 r_work: 0.2828 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1673 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= 0.122 Angle : 0.666 12.346 27252 Z= 0.316 Chirality : 0.042 0.254 3096 Planarity : 0.004 0.058 3528 Dihedral : 7.746 164.166 2809 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.05 % Allowed : 20.16 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.17), residues: 2496 helix: 1.43 (0.16), residues: 1150 sheet: -0.05 (0.26), residues: 372 loop : 0.05 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 362 TYR 0.020 0.001 TYR E 197 PHE 0.013 0.001 PHE F 300 TRP 0.032 0.001 TRP E 381 HIS 0.004 0.000 HIS F 42 Details of bonding type rmsd covalent geometry : bond 0.00284 (20214) covalent geometry : angle 0.66607 (27252) hydrogen bonds : bond 0.03016 ( 931) hydrogen bonds : angle 4.06728 ( 2718) Misc. bond : bond 0.00016 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9477.73 seconds wall clock time: 161 minutes 35.25 seconds (9695.25 seconds total)