Starting phenix.real_space_refine on Mon Jul 22 22:44:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3n_18130/07_2024/8q3n_18130_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3n_18130/07_2024/8q3n_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3n_18130/07_2024/8q3n_18130.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3n_18130/07_2024/8q3n_18130.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3n_18130/07_2024/8q3n_18130_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3n_18130/07_2024/8q3n_18130_neut.cif" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 102 5.16 5 C 12486 2.51 5 N 3540 2.21 5 O 3768 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 52": "OD1" <-> "OD2" Residue "A ASP 60": "OD1" <-> "OD2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "B GLU 13": "OE1" <-> "OE2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 244": "OE1" <-> "OE2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 5": "OE1" <-> "OE2" Residue "C ASP 52": "OD1" <-> "OD2" Residue "C GLU 106": "OE1" <-> "OE2" Residue "C TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 322": "OD1" <-> "OD2" Residue "C GLU 334": "OE1" <-> "OE2" Residue "D PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 210": "OD1" <-> "OD2" Residue "D PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 333": "OE1" <-> "OE2" Residue "E TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 328": "OD1" <-> "OD2" Residue "E GLU 334": "OE1" <-> "OE2" Residue "E GLU 351": "OE1" <-> "OE2" Residue "F PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 19912 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "B" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "C" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "D" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "E" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "F" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.45, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 7.42 Conformation dependent library (CDL) restraints added in 3.6 seconds 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4668 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 20 sheets defined 49.6% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 10 through 22 Processing helix chain 'A' and resid 30 through 46 Processing helix chain 'A' and resid 82 through 89 Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 153 through 166 removed outlier: 4.041A pdb=" N THR A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 199 Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 235 through 255 removed outlier: 3.538A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 285 through 289 removed outlier: 4.002A pdb=" N VAL A 289 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.567A pdb=" N GLU A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.298A pdb=" N LEU A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 388 Processing helix chain 'A' and resid 391 through 405 Processing helix chain 'A' and resid 408 through 418 Processing helix chain 'B' and resid 2 through 9 removed outlier: 3.619A pdb=" N THR B 9 " --> pdb=" O GLU B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 21 Processing helix chain 'B' and resid 30 through 44 Processing helix chain 'B' and resid 82 through 89 Processing helix chain 'B' and resid 123 through 128 removed outlier: 3.796A pdb=" N ARG B 128 " --> pdb=" O PRO B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 155 through 166 removed outlier: 3.955A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 Processing helix chain 'B' and resid 212 through 223 Processing helix chain 'B' and resid 235 through 255 removed outlier: 3.550A pdb=" N HIS B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 290 through 302 removed outlier: 4.214A pdb=" N ARG B 296 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Proline residue: B 297 - end of helix Processing helix chain 'B' and resid 325 through 335 removed outlier: 3.567A pdb=" N GLU B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 352 Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.083A pdb=" N LEU B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 388 Processing helix chain 'B' and resid 391 through 405 removed outlier: 3.778A pdb=" N MET B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 417 Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 10 through 22 Processing helix chain 'C' and resid 30 through 46 removed outlier: 3.714A pdb=" N SER C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY C 46 " --> pdb=" O HIS C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 Processing helix chain 'C' and resid 123 through 128 removed outlier: 3.584A pdb=" N ARG C 128 " --> pdb=" O PRO C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 155 through 166 removed outlier: 4.021A pdb=" N ALA C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 199 Processing helix chain 'C' and resid 212 through 223 Processing helix chain 'C' and resid 235 through 255 Processing helix chain 'C' and resid 266 through 278 Processing helix chain 'C' and resid 291 through 302 removed outlier: 4.228A pdb=" N ARG C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) Proline residue: C 297 - end of helix Processing helix chain 'C' and resid 325 through 335 Processing helix chain 'C' and resid 346 through 352 Processing helix chain 'C' and resid 367 through 372 removed outlier: 4.159A pdb=" N LEU C 371 " --> pdb=" O LYS C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 388 Processing helix chain 'C' and resid 391 through 404 Processing helix chain 'C' and resid 408 through 417 Processing helix chain 'D' and resid 2 through 7 Processing helix chain 'D' and resid 10 through 22 Processing helix chain 'D' and resid 30 through 46 removed outlier: 3.544A pdb=" N GLY D 46 " --> pdb=" O HIS D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 82 through 89 Processing helix chain 'D' and resid 123 through 128 removed outlier: 3.677A pdb=" N ARG D 128 " --> pdb=" O PRO D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 154 through 166 removed outlier: 4.273A pdb=" N THR D 158 " --> pdb=" O THR D 154 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 Processing helix chain 'D' and resid 212 through 223 Processing helix chain 'D' and resid 235 through 255 removed outlier: 3.525A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 278 Processing helix chain 'D' and resid 290 through 303 removed outlier: 4.160A pdb=" N ARG D 296 " --> pdb=" O ASN D 292 " (cutoff:3.500A) Proline residue: D 297 - end of helix Processing helix chain 'D' and resid 325 through 335 Processing helix chain 'D' and resid 346 through 352 Processing helix chain 'D' and resid 367 through 372 removed outlier: 4.224A pdb=" N LEU D 371 " --> pdb=" O LYS D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 388 Processing helix chain 'D' and resid 391 through 405 removed outlier: 3.870A pdb=" N MET D 405 " --> pdb=" O ASN D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 417 Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 10 through 22 Processing helix chain 'E' and resid 30 through 44 Processing helix chain 'E' and resid 82 through 89 removed outlier: 3.625A pdb=" N ILE E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 128 Processing helix chain 'E' and resid 153 through 166 Processing helix chain 'E' and resid 183 through 199 Processing helix chain 'E' and resid 212 through 223 Processing helix chain 'E' and resid 235 through 255 Processing helix chain 'E' and resid 266 through 278 Processing helix chain 'E' and resid 290 through 302 removed outlier: 4.105A pdb=" N ARG E 296 " --> pdb=" O ASN E 292 " (cutoff:3.500A) Proline residue: E 297 - end of helix Processing helix chain 'E' and resid 325 through 334 removed outlier: 3.646A pdb=" N GLU E 329 " --> pdb=" O SER E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 352 Processing helix chain 'E' and resid 367 through 371 removed outlier: 3.684A pdb=" N LEU E 370 " --> pdb=" O LYS E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 388 removed outlier: 3.695A pdb=" N LEU E 377 " --> pdb=" O THR E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 405 removed outlier: 3.896A pdb=" N MET E 405 " --> pdb=" O ASN E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 418 Processing helix chain 'F' and resid 2 through 9 removed outlier: 3.507A pdb=" N THR F 9 " --> pdb=" O GLU F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 22 Processing helix chain 'F' and resid 31 through 44 Processing helix chain 'F' and resid 82 through 89 removed outlier: 4.007A pdb=" N ILE F 86 " --> pdb=" O SER F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 127 Processing helix chain 'F' and resid 132 through 136 Processing helix chain 'F' and resid 153 through 166 removed outlier: 4.168A pdb=" N LEU F 162 " --> pdb=" O THR F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 199 removed outlier: 3.999A pdb=" N LEU F 187 " --> pdb=" O GLY F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 223 Processing helix chain 'F' and resid 235 through 256 removed outlier: 3.913A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 278 Processing helix chain 'F' and resid 290 through 302 removed outlier: 3.796A pdb=" N LEU F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG F 296 " --> pdb=" O ASN F 292 " (cutoff:3.500A) Proline residue: F 297 - end of helix Processing helix chain 'F' and resid 326 through 335 Processing helix chain 'F' and resid 346 through 351 Processing helix chain 'F' and resid 373 through 388 Processing helix chain 'F' and resid 391 through 406 Processing helix chain 'F' and resid 408 through 418 removed outlier: 3.625A pdb=" N ARG F 418 " --> pdb=" O GLU F 414 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 57 removed outlier: 3.733A pdb=" N ILE A 79 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N TYR A 80 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N LYS A 115 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU A 114 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ARG A 102 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL A 116 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LYS A 100 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ILE A 49 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.563A pdb=" N ASN A 306 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 318 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL A 203 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU A 263 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N MET A 205 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU A 204 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL A 228 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N VAL A 206 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N SER A 230 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU A 208 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.563A pdb=" N ASN A 306 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLY A 174 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ALA A 319 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE A 176 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ARG A 173 " --> pdb=" O MET A 341 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LEU A 343 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 175 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 49 through 57 removed outlier: 3.855A pdb=" N ILE B 79 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LYS B 100 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N VAL B 116 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N SER B 98 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLU B 118 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR B 96 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE B 49 " --> pdb=" O ILE B 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 138 through 139 removed outlier: 6.494A pdb=" N VAL B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ILE B 316 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE B 262 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N THR B 318 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU B 264 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 9.469A pdb=" N LEU B 320 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL B 203 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LEU B 263 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N MET B 205 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 138 through 139 removed outlier: 6.475A pdb=" N GLY B 174 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ALA B 319 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE B 176 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 49 through 57 removed outlier: 3.844A pdb=" N ILE C 79 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LYS C 100 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N VAL C 116 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N SER C 98 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLU C 118 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR C 96 " --> pdb=" O GLU C 118 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE C 49 " --> pdb=" O ILE C 101 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.502A pdb=" N ASN C 306 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL C 260 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILE C 316 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE C 262 " --> pdb=" O ILE C 316 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N THR C 318 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU C 264 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N LEU C 320 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL C 203 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU C 263 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N MET C 205 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.502A pdb=" N ASN C 306 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLY C 174 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ALA C 319 " --> pdb=" O GLY C 174 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE C 176 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU C 175 " --> pdb=" O LEU C 343 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU C 345 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C 177 " --> pdb=" O LEU C 345 " (cutoff:3.500A) removed outlier: 9.869A pdb=" N GLU C 342 " --> pdb=" O ASN C 361 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N ASN C 361 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N HIS C 344 " --> pdb=" O ASP C 359 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 284 through 285 removed outlier: 3.770A pdb=" N VAL C 289 " --> pdb=" O LEU C 285 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 49 through 57 removed outlier: 3.806A pdb=" N ILE D 79 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LYS D 100 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL D 116 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N SER D 98 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU D 118 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR D 96 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE D 49 " --> pdb=" O ILE D 101 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 138 through 139 removed outlier: 3.565A pdb=" N ASN D 306 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL D 260 " --> pdb=" O THR D 314 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ILE D 316 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE D 262 " --> pdb=" O ILE D 316 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N THR D 318 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU D 264 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N LEU D 320 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL D 203 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU D 263 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N MET D 205 " --> pdb=" O LEU D 263 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 138 through 139 removed outlier: 3.565A pdb=" N ASN D 306 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY D 174 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA D 319 " --> pdb=" O GLY D 174 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE D 176 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU D 175 " --> pdb=" O LEU D 343 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU D 345 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL D 177 " --> pdb=" O LEU D 345 " (cutoff:3.500A) removed outlier: 10.011A pdb=" N GLU D 342 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N ASN D 361 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N HIS D 344 " --> pdb=" O ASP D 359 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 49 through 57 removed outlier: 3.761A pdb=" N ILE E 79 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS E 100 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N VAL E 116 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N SER E 98 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU E 118 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR E 96 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE E 49 " --> pdb=" O ILE E 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 138 through 139 removed outlier: 3.616A pdb=" N ASN E 306 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL E 260 " --> pdb=" O THR E 314 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE E 316 " --> pdb=" O VAL E 260 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE E 262 " --> pdb=" O ILE E 316 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N THR E 318 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU E 264 " --> pdb=" O THR E 318 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N LEU E 320 " --> pdb=" O LEU E 264 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU E 204 " --> pdb=" O GLU E 226 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N VAL E 228 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL E 206 " --> pdb=" O VAL E 228 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N SER E 230 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU E 208 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 138 through 139 removed outlier: 3.616A pdb=" N ASN E 306 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU E 342 " --> pdb=" O GLY E 364 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 144 through 145 removed outlier: 4.229A pdb=" N ILE E 168 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 49 through 57 removed outlier: 8.765A pdb=" N TYR F 80 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA F 112 " --> pdb=" O ARG F 102 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE F 49 " --> pdb=" O ILE F 101 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 138 through 139 removed outlier: 3.983A pdb=" N ASN F 306 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR F 314 " --> pdb=" O VAL F 260 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL F 203 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU F 204 " --> pdb=" O GLU F 226 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N VAL F 228 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N VAL F 206 " --> pdb=" O VAL F 228 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 138 through 139 removed outlier: 3.983A pdb=" N ASN F 306 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY F 174 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ALA F 319 " --> pdb=" O GLY F 174 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE F 176 " --> pdb=" O ALA F 319 " (cutoff:3.500A) 950 hydrogen bonds defined for protein. 2718 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.54 Time building geometry restraints manager: 8.18 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: 94.97 - 103.19: 199 103.19 - 111.40: 9081 111.40 - 119.62: 8437 119.62 - 127.83: 9418 127.83 - 136.05: 117 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 1 through 418 or resid 1000)) selection = (chain 'C' and (resid 1 through 418 or resid 1000)) selection = (chain 'D' and (resid 1 through 418 or resid 1000)) selection = (chain 'E' and (resid 1 through 418 or resid 1000)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.790 Check model and map are aligned: 0.160 Set scattering table: 0.170 Process input model: 54.930 Find NCS groups from input model: 1.920 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.720 ------------------------------------------------------------------------------- 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 20214 Z= 0.232 Angle : 0.642 12.058 27252 Z= 0.310 Chirality : 0.041 0.257 3096 Planarity : 0.004 0.114 3528 Dihedral : 16.080 178.238 7848 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.54 % Allowed : 17.36 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.17), residues: 2496 helix: 1.30 (0.16), residues: 1148 sheet: 0.58 (0.27), residues: 367 loop : -0.02 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP E 381 HIS 0.008 0.001 HIS A 42 PHE 0.009 0.001 PHE E 398 TYR 0.023 0.001 TYR E 197 ARG 0.013 0.000 ARG E 362 *********************** 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 fitting. rotamer outliers: 33 poor density : 241 time to evaluate : 2.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 GLN cc_start: 0.8798 (pm20) cc_final: 0.8447 (pm20) REVERT: C 374 GLN cc_start: 0.8313 (mm-40) cc_final: 0.7980 (tm-30) REVERT: C 378 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8540 (mm-40) REVERT: E 21 MET cc_start: 0.7838 (tmt) cc_final: 0.7359 (ttt) REVERT: E 41 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8198 (tm-30) REVERT: F 1 MET cc_start: 0.1851 (pmm) cc_final: 0.0364 (ptp) REVERT: F 21 MET cc_start: 0.4325 (tpt) cc_final: 0.3066 (tmm) REVERT: F 36 PHE cc_start: 0.4259 (t80) cc_final: 0.3882 (t80) REVERT: F 120 ASN cc_start: 0.1079 (m110) cc_final: 0.0834 (m-40) REVERT: F 396 MET cc_start: 0.2199 (mpt) cc_final: 0.0653 (tpt) outliers start: 33 outliers final: 27 residues processed: 267 average time/residue: 1.4377 time to fit residues: 428.3158 Evaluate side-chains 254 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 225 time to evaluate : 2.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 73 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 63 optimal weight: 0.0980 chunk 125 optimal weight: 0.1980 chunk 99 optimal weight: 1.9990 chunk 192 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 378 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN D 193 GLN ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 GLN E 388 HIS F 193 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.0646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20214 Z= 0.186 Angle : 0.578 8.546 27252 Z= 0.279 Chirality : 0.041 0.210 3096 Planarity : 0.004 0.057 3528 Dihedral : 10.214 177.743 2843 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.98 % Allowed : 15.22 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.17), residues: 2496 helix: 1.41 (0.16), residues: 1160 sheet: 0.54 (0.26), residues: 365 loop : 0.06 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 381 HIS 0.005 0.001 HIS E 388 PHE 0.015 0.001 PHE F 64 TYR 0.019 0.001 TYR F 72 ARG 0.006 0.000 ARG E 362 *********************** 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 305 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 241 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7898 (ppp) cc_final: 0.7588 (pmm) REVERT: A 193 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8672 (pm20) REVERT: A 396 MET cc_start: 0.9589 (tpt) cc_final: 0.9387 (tpp) REVERT: B 59 GLN cc_start: 0.8788 (pm20) cc_final: 0.8393 (pm20) REVERT: B 326 LYS cc_start: 0.8594 (ptmm) cc_final: 0.8323 (pttt) REVERT: C 32 GLN cc_start: 0.9108 (mm-40) cc_final: 0.8844 (mp10) REVERT: C 322 ASP cc_start: 0.7870 (t0) cc_final: 0.7469 (t0) REVERT: F 1 MET cc_start: 0.2046 (pmm) cc_final: 0.0543 (ptp) REVERT: F 21 MET cc_start: 0.4596 (tpt) cc_final: 0.3448 (tmm) REVERT: F 36 PHE cc_start: 0.4191 (t80) cc_final: 0.3814 (t80) REVERT: F 73 LEU cc_start: 0.6687 (OUTLIER) cc_final: 0.5344 (pp) REVERT: F 329 GLU cc_start: 0.7866 (pp20) cc_final: 0.7619 (pp20) REVERT: F 396 MET cc_start: 0.2130 (OUTLIER) cc_final: 0.0671 (mmm) outliers start: 64 outliers final: 28 residues processed: 281 average time/residue: 1.4480 time to fit residues: 454.3465 Evaluate side-chains 269 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 238 time to evaluate : 2.178 ------------------------------------------------------------------------------- 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 185 THR Chi-restraints excluded: chain A residue 193 GLN 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 233 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain E residue 116 VAL 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 124 optimal weight: 0.6980 chunk 69 optimal weight: 0.0670 chunk 185 optimal weight: 0.0030 chunk 152 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 223 optimal weight: 7.9990 chunk 241 optimal weight: 20.0000 chunk 199 optimal weight: 2.9990 chunk 221 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 overall best weight: 0.5130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN B 193 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 GLN E 388 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20214 Z= 0.155 Angle : 0.561 8.676 27252 Z= 0.267 Chirality : 0.041 0.179 3096 Planarity : 0.003 0.050 3528 Dihedral : 9.519 178.957 2818 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.51 % Allowed : 16.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.17), residues: 2496 helix: 1.50 (0.16), residues: 1162 sheet: 0.48 (0.26), residues: 372 loop : 0.08 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 381 HIS 0.005 0.001 HIS F 256 PHE 0.015 0.001 PHE F 64 TYR 0.018 0.001 TYR A 80 ARG 0.008 0.000 ARG E 362 *********************** 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 310 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 256 time to evaluate : 2.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8695 (pm20) REVERT: A 220 GLN cc_start: 0.8763 (mt0) cc_final: 0.8269 (mp10) REVERT: A 244 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8247 (mp0) REVERT: B 59 GLN cc_start: 0.8786 (pm20) cc_final: 0.8353 (pm20) REVERT: B 155 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8430 (pm20) REVERT: B 244 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8472 (mm-30) REVERT: B 326 LYS cc_start: 0.8588 (ptmm) cc_final: 0.8321 (pttt) REVERT: B 374 GLN cc_start: 0.8693 (tp40) cc_final: 0.8456 (tp40) REVERT: C 32 GLN cc_start: 0.9093 (mm-40) cc_final: 0.8843 (mp10) REVERT: C 186 MET cc_start: 0.9211 (mtp) cc_final: 0.8912 (mtm) REVERT: C 322 ASP cc_start: 0.7910 (t0) cc_final: 0.7371 (t0) REVERT: C 326 LYS cc_start: 0.8637 (mppt) cc_final: 0.8427 (mmmm) REVERT: C 417 LYS cc_start: 0.9231 (ttpp) cc_final: 0.8991 (ttmm) REVERT: D 374 GLN cc_start: 0.7976 (tp40) cc_final: 0.7642 (tm-30) REVERT: E 72 TYR cc_start: 0.9083 (m-10) cc_final: 0.8855 (m-10) REVERT: E 326 LYS cc_start: 0.9097 (mppt) cc_final: 0.8872 (mppt) REVERT: E 329 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8315 (mp0) REVERT: E 334 GLU cc_start: 0.8403 (mp0) cc_final: 0.8197 (mp0) REVERT: E 341 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8200 (pp-130) REVERT: F 1 MET cc_start: 0.2382 (pmm) cc_final: 0.0815 (ptp) REVERT: F 21 MET cc_start: 0.4493 (tpt) cc_final: 0.3421 (tmm) REVERT: F 36 PHE cc_start: 0.4225 (t80) cc_final: 0.3843 (t80) REVERT: F 73 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.5687 (pp) REVERT: F 390 MET cc_start: 0.3106 (pp-130) cc_final: 0.1093 (mtp) outliers start: 54 outliers final: 21 residues processed: 289 average time/residue: 1.4953 time to fit residues: 480.8255 Evaluate side-chains 257 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 230 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 292 ASN 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 341 MET Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 241 GLN 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 147 MET Chi-restraints excluded: chain F residue 254 VAL 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 221 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 chunk 224 optimal weight: 8.9990 chunk 237 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 chunk 212 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 378 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 GLN E 388 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20214 Z= 0.289 Angle : 0.596 8.270 27252 Z= 0.285 Chirality : 0.042 0.184 3096 Planarity : 0.004 0.047 3528 Dihedral : 9.313 171.746 2809 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.17 % Allowed : 16.57 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.17), residues: 2496 helix: 1.45 (0.16), residues: 1162 sheet: 0.46 (0.26), residues: 372 loop : 0.09 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 381 HIS 0.004 0.001 HIS F 256 PHE 0.015 0.001 PHE F 64 TYR 0.017 0.001 TYR F 72 ARG 0.009 0.000 ARG E 362 *********************** 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 309 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 241 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8251 (mp0) REVERT: A 405 MET cc_start: 0.9002 (mtt) cc_final: 0.8543 (mpp) REVERT: B 59 GLN cc_start: 0.8786 (pm20) cc_final: 0.8369 (pm20) REVERT: B 109 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7894 (ptt90) REVERT: B 162 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9117 (mm) REVERT: B 244 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8428 (mm-30) REVERT: C 32 GLN cc_start: 0.9097 (mm-40) cc_final: 0.8845 (mp10) REVERT: C 322 ASP cc_start: 0.8088 (t0) cc_final: 0.7548 (t0) REVERT: C 326 LYS cc_start: 0.8673 (mppt) cc_final: 0.8439 (mmmm) REVERT: C 417 LYS cc_start: 0.9260 (ttpp) cc_final: 0.9011 (ttmm) REVERT: D 374 GLN cc_start: 0.8180 (tp40) cc_final: 0.7737 (tm-30) REVERT: E 326 LYS cc_start: 0.9169 (mppt) cc_final: 0.8939 (mppt) REVERT: E 329 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8287 (mp0) REVERT: E 334 GLU cc_start: 0.8472 (mp0) cc_final: 0.8265 (mp0) REVERT: E 341 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8375 (pp-130) REVERT: F 1 MET cc_start: 0.2344 (pmm) cc_final: 0.0734 (ptp) REVERT: F 21 MET cc_start: 0.4429 (tpt) cc_final: 0.3419 (tmm) REVERT: F 73 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.5780 (pp) REVERT: F 390 MET cc_start: 0.3305 (OUTLIER) cc_final: 0.1101 (mtp) outliers start: 68 outliers final: 31 residues processed: 285 average time/residue: 1.3954 time to fit residues: 444.8978 Evaluate side-chains 278 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 240 time to evaluate : 2.398 ------------------------------------------------------------------------------- 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 185 THR Chi-restraints excluded: chain A residue 244 GLU 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 162 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 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 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 390 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 198 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 202 optimal weight: 0.8980 chunk 164 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 121 optimal weight: 0.8980 chunk 213 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 378 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 GLN E 388 HIS F 374 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20214 Z= 0.258 Angle : 0.598 8.699 27252 Z= 0.284 Chirality : 0.042 0.182 3096 Planarity : 0.004 0.044 3528 Dihedral : 9.185 169.473 2806 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.12 % Allowed : 17.13 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.17), residues: 2496 helix: 1.43 (0.16), residues: 1157 sheet: 0.37 (0.26), residues: 378 loop : 0.08 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 381 HIS 0.003 0.001 HIS E 388 PHE 0.022 0.001 PHE F 300 TYR 0.019 0.001 TYR A 80 ARG 0.010 0.000 ARG E 362 *********************** 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 318 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 251 time to evaluate : 2.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 THR cc_start: 0.9324 (OUTLIER) cc_final: 0.9022 (p) REVERT: A 193 GLN cc_start: 0.9082 (pt0) cc_final: 0.8650 (pm20) REVERT: A 220 GLN cc_start: 0.8801 (mt0) cc_final: 0.8307 (mp10) REVERT: A 244 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8259 (mp0) REVERT: A 405 MET cc_start: 0.8973 (mtt) cc_final: 0.8491 (mpp) REVERT: B 59 GLN cc_start: 0.8785 (pm20) cc_final: 0.8364 (pm20) REVERT: B 109 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7832 (ptt90) REVERT: B 162 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9120 (mm) REVERT: B 244 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8442 (mm-30) REVERT: C 32 GLN cc_start: 0.9088 (mm-40) cc_final: 0.8844 (mp10) REVERT: C 322 ASP cc_start: 0.8204 (t0) cc_final: 0.7641 (t0) REVERT: C 326 LYS cc_start: 0.8657 (mppt) cc_final: 0.8410 (mmmm) REVERT: C 417 LYS cc_start: 0.9263 (ttpp) cc_final: 0.9015 (ttmm) REVERT: D 374 GLN cc_start: 0.8226 (tp40) cc_final: 0.7707 (tp40) REVERT: D 378 GLN cc_start: 0.8711 (mt0) cc_final: 0.8464 (mt0) REVERT: E 326 LYS cc_start: 0.9186 (mppt) cc_final: 0.8950 (mppt) REVERT: E 329 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8296 (mp0) REVERT: E 334 GLU cc_start: 0.8545 (mp0) cc_final: 0.8310 (mp0) REVERT: F 1 MET cc_start: 0.2553 (pmm) cc_final: 0.0963 (ptp) REVERT: F 21 MET cc_start: 0.4412 (tpt) cc_final: 0.3421 (tmm) REVERT: F 36 PHE cc_start: 0.3927 (t80) cc_final: 0.3545 (t80) REVERT: F 73 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.5818 (pp) REVERT: F 111 PHE cc_start: 0.7617 (m-10) cc_final: 0.7404 (m-10) REVERT: F 275 ASN cc_start: 0.9063 (t0) cc_final: 0.8810 (t0) REVERT: F 390 MET cc_start: 0.3070 (OUTLIER) cc_final: 0.1042 (mtp) outliers start: 67 outliers final: 39 residues processed: 294 average time/residue: 1.4590 time to fit residues: 478.8156 Evaluate side-chains 283 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 237 time to evaluate : 2.393 ------------------------------------------------------------------------------- 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 158 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 244 GLU 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 162 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 116 VAL 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 381 TRP 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 222 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 390 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 0.9980 chunk 214 optimal weight: 4.9990 chunk 47 optimal weight: 0.3980 chunk 139 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 238 optimal weight: 8.9990 chunk 197 optimal weight: 2.9990 chunk 110 optimal weight: 0.0980 chunk 19 optimal weight: 0.9980 chunk 78 optimal weight: 0.0170 chunk 124 optimal weight: 0.7980 overall best weight: 0.3818 ------------------------------------------------------------------------------- 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 378 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN D 193 GLN D 374 GLN D 378 GLN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 GLN E 388 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20214 Z= 0.153 Angle : 0.595 8.744 27252 Z= 0.280 Chirality : 0.041 0.190 3096 Planarity : 0.003 0.047 3528 Dihedral : 8.995 176.913 2806 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.56 % Allowed : 18.39 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.17), residues: 2496 helix: 1.53 (0.16), residues: 1157 sheet: 0.46 (0.26), residues: 372 loop : 0.07 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 381 HIS 0.003 0.001 HIS E 388 PHE 0.020 0.001 PHE F 300 TYR 0.019 0.001 TYR E 197 ARG 0.011 0.000 ARG E 362 *********************** 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 301 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 246 time to evaluate : 2.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8167 (mp0) REVERT: A 333 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8146 (tm-30) REVERT: B 59 GLN cc_start: 0.8787 (pm20) cc_final: 0.8357 (pm20) REVERT: B 162 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9104 (mm) REVERT: B 244 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8429 (mm-30) REVERT: B 272 ARG cc_start: 0.8487 (mtp85) cc_final: 0.8068 (mtt-85) REVERT: B 362 ARG cc_start: 0.9003 (mtm-85) cc_final: 0.8779 (mtp85) REVERT: C 32 GLN cc_start: 0.9082 (mm-40) cc_final: 0.8857 (mp10) REVERT: C 322 ASP cc_start: 0.8180 (t0) cc_final: 0.7651 (t0) REVERT: C 326 LYS cc_start: 0.8608 (mppt) cc_final: 0.8354 (mmmm) REVERT: C 417 LYS cc_start: 0.9260 (ttpp) cc_final: 0.9017 (ttmm) REVERT: D 374 GLN cc_start: 0.8130 (tp-100) cc_final: 0.7682 (tp40) REVERT: D 378 GLN cc_start: 0.8707 (mt0) cc_final: 0.8476 (mt0) REVERT: E 72 TYR cc_start: 0.9115 (m-10) cc_final: 0.8891 (m-10) REVERT: E 326 LYS cc_start: 0.9233 (mppt) cc_final: 0.9002 (mppt) REVERT: E 329 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8296 (mp0) REVERT: E 334 GLU cc_start: 0.8542 (mp0) cc_final: 0.8288 (mp0) REVERT: F 1 MET cc_start: 0.2633 (pmm) cc_final: 0.1089 (ptp) REVERT: F 21 MET cc_start: 0.4390 (tpt) cc_final: 0.3432 (tmm) REVERT: F 36 PHE cc_start: 0.3935 (t80) cc_final: 0.3712 (t80) REVERT: F 50 PHE cc_start: 0.7244 (t80) cc_final: 0.6908 (m-80) REVERT: F 73 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.5828 (pp) REVERT: F 390 MET cc_start: 0.2888 (OUTLIER) cc_final: 0.0992 (mtp) outliers start: 55 outliers final: 28 residues processed: 283 average time/residue: 1.4029 time to fit residues: 444.2364 Evaluate side-chains 276 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 243 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 381 TRP Chi-restraints excluded: chain 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 222 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 390 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 229 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 135 optimal weight: 0.0270 chunk 173 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 chunk 200 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 237 optimal weight: 0.4980 chunk 148 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN C 41 GLN C 378 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 HIS D 193 GLN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 GLN E 388 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20214 Z= 0.197 Angle : 0.604 9.803 27252 Z= 0.285 Chirality : 0.042 0.218 3096 Planarity : 0.003 0.051 3528 Dihedral : 8.708 174.251 2805 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.75 % Allowed : 18.85 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.17), residues: 2496 helix: 1.51 (0.16), residues: 1158 sheet: 0.47 (0.26), residues: 372 loop : 0.10 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 381 HIS 0.003 0.001 HIS E 388 PHE 0.015 0.001 PHE F 300 TYR 0.022 0.001 TYR A 80 ARG 0.012 0.000 ARG E 362 *********************** 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 309 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 250 time to evaluate : 2.565 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 220 GLN cc_start: 0.8789 (mt0) cc_final: 0.8287 (mp10) REVERT: A 244 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8187 (mp0) REVERT: A 333 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8284 (tm-30) REVERT: B 41 GLN cc_start: 0.9046 (tp-100) cc_final: 0.8655 (tp40) REVERT: B 59 GLN cc_start: 0.8780 (pm20) cc_final: 0.8340 (pm20) REVERT: B 162 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9107 (mm) REVERT: B 244 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8386 (mm-30) REVERT: B 362 ARG cc_start: 0.9002 (mtm-85) cc_final: 0.8771 (mtp85) REVERT: C 32 GLN cc_start: 0.9085 (mm-40) cc_final: 0.8847 (mp10) REVERT: C 322 ASP cc_start: 0.8244 (t0) cc_final: 0.7718 (t0) REVERT: C 326 LYS cc_start: 0.8627 (mppt) cc_final: 0.8368 (mmmm) REVERT: C 374 GLN cc_start: 0.8362 (mm-40) cc_final: 0.8058 (tm-30) REVERT: C 417 LYS cc_start: 0.9269 (ttpp) cc_final: 0.9025 (ttmm) REVERT: D 374 GLN cc_start: 0.8301 (tp-100) cc_final: 0.7938 (tp40) REVERT: E 326 LYS cc_start: 0.9243 (mppt) cc_final: 0.9004 (mppt) REVERT: E 329 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8294 (mp0) REVERT: E 334 GLU cc_start: 0.8540 (mp0) cc_final: 0.8263 (mp0) REVERT: F 1 MET cc_start: 0.2762 (pmm) cc_final: 0.1219 (ptp) REVERT: F 21 MET cc_start: 0.4366 (tpt) cc_final: 0.3425 (tmm) REVERT: F 36 PHE cc_start: 0.4079 (t80) cc_final: 0.3742 (t80) REVERT: F 50 PHE cc_start: 0.7299 (t80) cc_final: 0.6824 (t80) REVERT: F 73 LEU cc_start: 0.6851 (OUTLIER) cc_final: 0.5881 (pp) REVERT: F 245 MET cc_start: 0.3642 (ptp) cc_final: 0.3348 (ttm) REVERT: F 261 ILE cc_start: 0.6752 (mp) cc_final: 0.6465 (tp) REVERT: F 390 MET cc_start: 0.2887 (OUTLIER) cc_final: 0.0999 (mtp) outliers start: 59 outliers final: 34 residues processed: 292 average time/residue: 1.4412 time to fit residues: 469.6809 Evaluate side-chains 281 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 242 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 378 GLN 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 259 ASP Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 381 TRP Chi-restraints excluded: chain 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 126 ASN Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 390 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 146 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 150 optimal weight: 0.7980 chunk 161 optimal weight: 0.0050 chunk 117 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 186 optimal weight: 2.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN D 374 GLN D 378 GLN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 GLN E 292 ASN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20214 Z= 0.171 Angle : 0.608 10.426 27252 Z= 0.286 Chirality : 0.041 0.217 3096 Planarity : 0.003 0.055 3528 Dihedral : 8.310 175.089 2803 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.37 % Allowed : 19.65 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.17), residues: 2496 helix: 1.54 (0.16), residues: 1161 sheet: 0.41 (0.25), residues: 378 loop : 0.14 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 381 HIS 0.002 0.000 HIS E 388 PHE 0.021 0.001 PHE F 300 TYR 0.020 0.001 TYR E 197 ARG 0.014 0.000 ARG F 299 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 249 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8787 (mt0) cc_final: 0.8279 (mp10) REVERT: A 244 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8186 (mp0) REVERT: A 333 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8199 (tm-30) REVERT: B 41 GLN cc_start: 0.9059 (tp-100) cc_final: 0.8659 (tp40) REVERT: B 59 GLN cc_start: 0.8784 (pm20) cc_final: 0.8354 (pm20) REVERT: B 162 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9106 (mm) REVERT: B 244 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8402 (mm-30) REVERT: B 272 ARG cc_start: 0.8400 (mtp85) cc_final: 0.8135 (mtt-85) REVERT: B 362 ARG cc_start: 0.8993 (mtm-85) cc_final: 0.8762 (mtp85) REVERT: C 32 GLN cc_start: 0.9084 (mm-40) cc_final: 0.8839 (mp10) REVERT: C 186 MET cc_start: 0.9237 (mtp) cc_final: 0.8939 (mtm) REVERT: C 322 ASP cc_start: 0.8290 (t0) cc_final: 0.7757 (t0) REVERT: C 326 LYS cc_start: 0.8639 (mppt) cc_final: 0.8369 (mmmm) REVERT: C 417 LYS cc_start: 0.9265 (ttpp) cc_final: 0.9026 (ttmm) REVERT: D 374 GLN cc_start: 0.8332 (tp40) cc_final: 0.8069 (tp40) REVERT: E 41 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8330 (tm-30) REVERT: E 72 TYR cc_start: 0.9081 (m-10) cc_final: 0.8866 (m-10) REVERT: E 326 LYS cc_start: 0.9243 (mppt) cc_final: 0.9026 (mppt) REVERT: E 329 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8297 (mp0) REVERT: E 334 GLU cc_start: 0.8558 (mp0) cc_final: 0.8275 (mp0) REVERT: E 390 MET cc_start: 0.8651 (ptt) cc_final: 0.8404 (ptt) REVERT: F 1 MET cc_start: 0.2967 (pmm) cc_final: 0.1400 (ptp) REVERT: F 21 MET cc_start: 0.4380 (tpt) cc_final: 0.3421 (tmm) REVERT: F 36 PHE cc_start: 0.4089 (t80) cc_final: 0.3774 (t80) REVERT: F 50 PHE cc_start: 0.7343 (t80) cc_final: 0.6853 (t80) REVERT: F 73 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.5877 (pp) REVERT: F 111 PHE cc_start: 0.7586 (m-10) cc_final: 0.7299 (m-10) REVERT: F 261 ILE cc_start: 0.6656 (mp) cc_final: 0.6413 (tp) REVERT: F 390 MET cc_start: 0.2861 (OUTLIER) cc_final: 0.1008 (mtp) outliers start: 51 outliers final: 33 residues processed: 287 average time/residue: 1.4028 time to fit residues: 450.1306 Evaluate side-chains 275 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 236 time to evaluate : 2.174 ------------------------------------------------------------------------------- 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 158 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 381 TRP 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 126 ASN Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 390 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 215 optimal weight: 50.0000 chunk 227 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 220 optimal weight: 20.0000 chunk 132 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 173 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 chunk 208 optimal weight: 5.9990 chunk 145 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN C 41 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN E 42 HIS ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 20214 Z= 0.473 Angle : 0.690 11.648 27252 Z= 0.332 Chirality : 0.045 0.243 3096 Planarity : 0.004 0.061 3528 Dihedral : 8.214 153.613 2803 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.70 % Allowed : 19.32 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.17), residues: 2496 helix: 1.26 (0.15), residues: 1160 sheet: 0.34 (0.26), residues: 367 loop : 0.05 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 381 HIS 0.007 0.001 HIS E 239 PHE 0.015 0.002 PHE F 300 TYR 0.023 0.002 TYR A 80 ARG 0.013 0.001 ARG E 362 *********************** 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 290 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 232 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8252 (mp0) REVERT: A 405 MET cc_start: 0.8978 (mtt) cc_final: 0.8472 (mpp) REVERT: B 41 GLN cc_start: 0.9083 (tp-100) cc_final: 0.8758 (tp40) REVERT: B 59 GLN cc_start: 0.8793 (pm20) cc_final: 0.8380 (pm20) REVERT: B 109 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7696 (ptt90) REVERT: B 244 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8424 (mm-30) REVERT: B 272 ARG cc_start: 0.8487 (mtp85) cc_final: 0.8143 (mtt-85) REVERT: B 362 ARG cc_start: 0.9016 (mtm-85) cc_final: 0.8362 (mtm-85) REVERT: C 32 GLN cc_start: 0.9095 (mm-40) cc_final: 0.8841 (mp10) REVERT: C 322 ASP cc_start: 0.8496 (t0) cc_final: 0.8000 (t0) REVERT: C 326 LYS cc_start: 0.8740 (mppt) cc_final: 0.8465 (mmmm) REVERT: C 374 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8450 (mm-40) REVERT: C 417 LYS cc_start: 0.9264 (ttpp) cc_final: 0.9026 (ttmm) REVERT: D 374 GLN cc_start: 0.8484 (tp40) cc_final: 0.8010 (tp40) REVERT: E 41 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8318 (tm-30) REVERT: E 334 GLU cc_start: 0.8638 (mp0) cc_final: 0.8421 (mp0) REVERT: F 1 MET cc_start: 0.3183 (pmm) cc_final: 0.1520 (ptp) REVERT: F 20 ASN cc_start: 0.6312 (m-40) cc_final: 0.6055 (m-40) REVERT: F 21 MET cc_start: 0.4403 (tpt) cc_final: 0.3452 (tmm) REVERT: F 36 PHE cc_start: 0.4418 (t80) cc_final: 0.4136 (t80) REVERT: F 50 PHE cc_start: 0.7406 (t80) cc_final: 0.6892 (t80) REVERT: F 73 LEU cc_start: 0.6819 (OUTLIER) cc_final: 0.5873 (pp) REVERT: F 111 PHE cc_start: 0.7665 (m-10) cc_final: 0.7457 (m-10) REVERT: F 261 ILE cc_start: 0.6587 (mp) cc_final: 0.6364 (tp) REVERT: F 299 ARG cc_start: 0.7037 (ttp80) cc_final: 0.6190 (tmm-80) REVERT: F 390 MET cc_start: 0.2871 (OUTLIER) cc_final: 0.1015 (mtp) REVERT: F 415 MET cc_start: -0.1486 (tmm) cc_final: -0.1813 (tmm) outliers start: 58 outliers final: 38 residues processed: 273 average time/residue: 1.3853 time to fit residues: 423.5786 Evaluate side-chains 281 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 238 time to evaluate : 2.177 ------------------------------------------------------------------------------- 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 158 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 260 VAL 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 233 ASP Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 228 VAL 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 381 TRP 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 126 ASN Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 390 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 233 optimal weight: 40.0000 chunk 142 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 162 optimal weight: 0.8980 chunk 245 optimal weight: 7.9990 chunk 225 optimal weight: 9.9990 chunk 195 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 150 optimal weight: 0.0970 chunk 119 optimal weight: 0.7980 chunk 155 optimal weight: 0.4980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 193 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 HIS F 275 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20214 Z= 0.183 Angle : 0.645 12.285 27252 Z= 0.303 Chirality : 0.042 0.257 3096 Planarity : 0.003 0.057 3528 Dihedral : 7.635 137.908 2803 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.96 % Allowed : 20.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.17), residues: 2496 helix: 1.38 (0.16), residues: 1161 sheet: 0.38 (0.26), residues: 365 loop : 0.06 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 381 HIS 0.002 0.000 HIS E 388 PHE 0.019 0.001 PHE F 300 TYR 0.022 0.001 TYR E 197 ARG 0.013 0.000 ARG E 362 ********************** 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 294 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 252 time to evaluate : 2.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 THR cc_start: 0.9270 (OUTLIER) cc_final: 0.9011 (p) REVERT: A 220 GLN cc_start: 0.8775 (mt0) cc_final: 0.8273 (mp10) REVERT: A 244 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8235 (mp0) REVERT: B 41 GLN cc_start: 0.9086 (tp-100) cc_final: 0.8699 (tp40) REVERT: B 59 GLN cc_start: 0.8801 (pm20) cc_final: 0.8363 (pm20) REVERT: B 244 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8422 (mm-30) REVERT: B 272 ARG cc_start: 0.8308 (mtp85) cc_final: 0.8067 (mtt-85) REVERT: B 362 ARG cc_start: 0.8978 (mtm-85) cc_final: 0.8742 (mtp85) REVERT: C 32 GLN cc_start: 0.9081 (mm-40) cc_final: 0.8850 (mp10) REVERT: C 322 ASP cc_start: 0.8426 (t0) cc_final: 0.7929 (t0) REVERT: C 326 LYS cc_start: 0.8622 (mppt) cc_final: 0.8329 (mmmm) REVERT: C 374 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8401 (mm-40) REVERT: C 417 LYS cc_start: 0.9262 (ttpp) cc_final: 0.9026 (ttmm) REVERT: D 326 LYS cc_start: 0.8917 (mtpp) cc_final: 0.8711 (mmmm) REVERT: D 374 GLN cc_start: 0.8359 (tp40) cc_final: 0.7915 (tp40) REVERT: D 378 GLN cc_start: 0.8664 (mt0) cc_final: 0.8327 (mt0) REVERT: E 41 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8317 (tm-30) REVERT: E 59 GLN cc_start: 0.8882 (pm20) cc_final: 0.8675 (pp30) REVERT: E 334 GLU cc_start: 0.8622 (mp0) cc_final: 0.8347 (mp0) REVERT: E 390 MET cc_start: 0.8700 (ptt) cc_final: 0.8420 (ptt) REVERT: F 1 MET cc_start: 0.3214 (pmm) cc_final: 0.2551 (pp-130) REVERT: F 21 MET cc_start: 0.4149 (tpt) cc_final: 0.3201 (tmm) REVERT: F 36 PHE cc_start: 0.4380 (t80) cc_final: 0.4090 (t80) REVERT: F 73 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.5977 (pp) REVERT: F 111 PHE cc_start: 0.7637 (m-10) cc_final: 0.7417 (m-10) REVERT: F 245 MET cc_start: 0.3904 (ptp) cc_final: 0.3555 (ttm) REVERT: F 261 ILE cc_start: 0.6569 (mp) cc_final: 0.6361 (tp) REVERT: F 390 MET cc_start: 0.2848 (OUTLIER) cc_final: 0.1003 (mtp) outliers start: 42 outliers final: 32 residues processed: 283 average time/residue: 1.4415 time to fit residues: 454.4623 Evaluate side-chains 282 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 245 time to evaluate : 2.296 ------------------------------------------------------------------------------- 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 158 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 228 VAL 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 381 TRP 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 126 ASN Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 390 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 10.0000 chunk 59 optimal weight: 0.2980 chunk 179 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 195 optimal weight: 5.9990 chunk 81 optimal weight: 0.1980 chunk 200 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 171 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN C 41 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 GLN E 220 GLN E 388 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.123738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.078883 restraints weight = 41463.119| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.48 r_work: 0.2844 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20214 Z= 0.183 Angle : 0.635 12.335 27252 Z= 0.299 Chirality : 0.042 0.254 3096 Planarity : 0.003 0.055 3528 Dihedral : 6.985 121.411 2803 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.86 % Allowed : 20.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.17), residues: 2496 helix: 1.49 (0.16), residues: 1157 sheet: 0.41 (0.26), residues: 369 loop : 0.08 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 381 HIS 0.003 0.000 HIS E 388 PHE 0.012 0.001 PHE F 300 TYR 0.021 0.001 TYR E 197 ARG 0.013 0.000 ARG E 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7852.46 seconds wall clock time: 137 minutes 40.91 seconds (8260.91 seconds total)