Starting phenix.real_space_refine on Wed Jun 18 13:32:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p3o_17387/06_2025/8p3o_17387.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p3o_17387/06_2025/8p3o_17387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p3o_17387/06_2025/8p3o_17387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p3o_17387/06_2025/8p3o_17387.map" model { file = "/net/cci-nas-00/data/ceres_data/8p3o_17387/06_2025/8p3o_17387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p3o_17387/06_2025/8p3o_17387.cif" } resolution = 2.9 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= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 13392 2.51 5 N 3776 2.21 5 O 3904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21192 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2649 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "B" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2649 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "C" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2649 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "G" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2649 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "A" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2649 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "F" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2649 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "H" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2649 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "E" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2649 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Time building chain proxies: 13.33, per 1000 atoms: 0.63 Number of scatterers: 21192 At special positions: 0 Unit cell: (131.008, 131.008, 172.652, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 3904 8.00 N 3776 7.00 C 13392 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.52 Conformation dependent library (CDL) restraints added in 2.6 seconds 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5040 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 8 sheets defined 67.7% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'D' and resid 18 through 29 removed outlier: 3.660A pdb=" N ARG D 24 " --> pdb=" O ARG D 20 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY D 29 " --> pdb=" O THR D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 49 removed outlier: 3.644A pdb=" N ILE D 33 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 86 removed outlier: 3.574A pdb=" N GLN D 75 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU D 82 " --> pdb=" O PHE D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 110 Processing helix chain 'D' and resid 110 through 120 removed outlier: 3.545A pdb=" N TRP D 118 " --> pdb=" O ARG D 114 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU D 119 " --> pdb=" O ARG D 115 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'D' and resid 131 through 144 removed outlier: 3.749A pdb=" N ASN D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 238 removed outlier: 3.556A pdb=" N LEU D 175 " --> pdb=" O ALA D 171 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG D 176 " --> pdb=" O ASN D 172 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN D 208 " --> pdb=" O GLN D 204 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 209 " --> pdb=" O MET D 205 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS D 210 " --> pdb=" O LYS D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 251 removed outlier: 3.520A pdb=" N LEU D 251 " --> pdb=" O ALA D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 275 Processing helix chain 'D' and resid 279 through 295 removed outlier: 3.854A pdb=" N ASP D 283 " --> pdb=" O ASP D 279 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR D 291 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL D 294 " --> pdb=" O ASN D 290 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY D 295 " --> pdb=" O THR D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 348 Processing helix chain 'B' and resid 18 through 29 Processing helix chain 'B' and resid 29 through 49 removed outlier: 3.716A pdb=" N ILE B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 86 removed outlier: 3.576A pdb=" N GLN B 75 " --> pdb=" O GLY B 71 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 82 " --> pdb=" O PHE B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 110 Processing helix chain 'B' and resid 110 through 120 removed outlier: 3.546A pdb=" N TRP B 118 " --> pdb=" O ARG B 114 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN B 120 " --> pdb=" O GLU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 131 through 144 removed outlier: 3.522A pdb=" N ALA B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 238 removed outlier: 3.554A pdb=" N LEU B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG B 176 " --> pdb=" O ASN B 172 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN B 208 " --> pdb=" O GLN B 204 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 209 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS B 210 " --> pdb=" O LYS B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 251 removed outlier: 3.513A pdb=" N LEU B 251 " --> pdb=" O ALA B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 279 through 295 removed outlier: 3.839A pdb=" N ASP B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY B 295 " --> pdb=" O THR B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 348 Processing helix chain 'C' and resid 18 through 29 removed outlier: 3.799A pdb=" N ARG C 24 " --> pdb=" O ARG C 20 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TRP C 27 " --> pdb=" O PHE C 23 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA C 28 " --> pdb=" O ARG C 24 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY C 29 " --> pdb=" O THR C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 48 removed outlier: 4.215A pdb=" N ILE C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA C 39 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 86 removed outlier: 3.751A pdb=" N GLN C 75 " --> pdb=" O GLY C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 109 Processing helix chain 'C' and resid 110 through 119 removed outlier: 3.512A pdb=" N ARG C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 119 " --> pdb=" O ARG C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 144 removed outlier: 3.521A pdb=" N ASN C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 235 removed outlier: 3.888A pdb=" N ASN C 172 " --> pdb=" O ALA C 168 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 175 " --> pdb=" O ALA C 171 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 249 Processing helix chain 'C' and resid 260 through 273 removed outlier: 3.743A pdb=" N LEU C 264 " --> pdb=" O GLY C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 295 removed outlier: 3.794A pdb=" N ASP C 283 " --> pdb=" O ASP C 279 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY C 295 " --> pdb=" O THR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 348 removed outlier: 4.157A pdb=" N LEU C 325 " --> pdb=" O ARG C 321 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE C 327 " --> pdb=" O ALA C 323 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N CYS C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 29 removed outlier: 3.705A pdb=" N ARG G 24 " --> pdb=" O ARG G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 43 removed outlier: 3.860A pdb=" N ILE G 33 " --> pdb=" O GLY G 29 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU G 38 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA G 39 " --> pdb=" O GLY G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 86 removed outlier: 3.752A pdb=" N GLN G 75 " --> pdb=" O GLY G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 109 Processing helix chain 'G' and resid 110 through 119 removed outlier: 3.545A pdb=" N ARG G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU G 119 " --> pdb=" O ARG G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 144 removed outlier: 3.544A pdb=" N ASN G 144 " --> pdb=" O ASP G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 235 removed outlier: 3.885A pdb=" N ASN G 172 " --> pdb=" O ALA G 168 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU G 175 " --> pdb=" O ALA G 171 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS G 210 " --> pdb=" O LYS G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 249 Processing helix chain 'G' and resid 260 through 273 removed outlier: 3.743A pdb=" N LEU G 264 " --> pdb=" O GLY G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 295 removed outlier: 3.795A pdb=" N ASP G 283 " --> pdb=" O ASP G 279 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR G 291 " --> pdb=" O ALA G 287 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL G 294 " --> pdb=" O ASN G 290 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY G 295 " --> pdb=" O THR G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 348 removed outlier: 4.238A pdb=" N LEU G 325 " --> pdb=" O ARG G 321 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N MET G 326 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE G 327 " --> pdb=" O ALA G 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 29 removed outlier: 3.745A pdb=" N GLY A 29 " --> pdb=" O THR A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 43 removed outlier: 3.773A pdb=" N ILE A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 71 through 86 removed outlier: 3.749A pdb=" N GLN A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 109 Processing helix chain 'A' and resid 110 through 119 removed outlier: 3.512A pdb=" N ARG A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 144 removed outlier: 3.541A pdb=" N ASN A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 235 removed outlier: 3.890A pdb=" N ASN A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A 210 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.742A pdb=" N LEU A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 295 removed outlier: 3.795A pdb=" N ASP A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 327 through 348 Processing helix chain 'F' and resid 18 through 29 removed outlier: 3.595A pdb=" N ARG F 24 " --> pdb=" O ARG F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 49 removed outlier: 4.172A pdb=" N ILE F 33 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU F 38 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA F 39 " --> pdb=" O GLY F 35 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE F 49 " --> pdb=" O LEU F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 84 removed outlier: 3.572A pdb=" N GLN F 75 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU F 82 " --> pdb=" O PHE F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 110 Processing helix chain 'F' and resid 110 through 120 removed outlier: 3.546A pdb=" N TRP F 118 " --> pdb=" O ARG F 114 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU F 119 " --> pdb=" O ARG F 115 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN F 120 " --> pdb=" O GLU F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 126 Processing helix chain 'F' and resid 131 through 144 removed outlier: 3.747A pdb=" N ASN F 144 " --> pdb=" O ASP F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 238 removed outlier: 3.555A pdb=" N LEU F 175 " --> pdb=" O ALA F 171 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG F 176 " --> pdb=" O ASN F 172 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN F 208 " --> pdb=" O GLN F 204 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL F 209 " --> pdb=" O MET F 205 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS F 210 " --> pdb=" O LYS F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 251 removed outlier: 3.501A pdb=" N LEU F 251 " --> pdb=" O ALA F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 275 Processing helix chain 'F' and resid 279 through 295 removed outlier: 3.840A pdb=" N ASP F 283 " --> pdb=" O ASP F 279 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR F 291 " --> pdb=" O ALA F 287 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL F 294 " --> pdb=" O ASN F 290 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY F 295 " --> pdb=" O THR F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 348 removed outlier: 3.504A pdb=" N LEU F 325 " --> pdb=" O ARG F 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 29 removed outlier: 3.558A pdb=" N ARG H 24 " --> pdb=" O ARG H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 49 removed outlier: 3.749A pdb=" N ILE H 33 " --> pdb=" O GLY H 29 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE H 49 " --> pdb=" O LEU H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 86 removed outlier: 3.574A pdb=" N GLN H 75 " --> pdb=" O GLY H 71 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU H 82 " --> pdb=" O PHE H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 110 Processing helix chain 'H' and resid 110 through 120 removed outlier: 3.546A pdb=" N TRP H 118 " --> pdb=" O ARG H 114 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU H 119 " --> pdb=" O ARG H 115 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN H 120 " --> pdb=" O GLU H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 126 Processing helix chain 'H' and resid 131 through 144 removed outlier: 3.749A pdb=" N ASN H 144 " --> pdb=" O ASP H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 238 removed outlier: 3.555A pdb=" N LEU H 175 " --> pdb=" O ALA H 171 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG H 176 " --> pdb=" O ASN H 172 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN H 208 " --> pdb=" O GLN H 204 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL H 209 " --> pdb=" O MET H 205 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS H 210 " --> pdb=" O LYS H 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 251 removed outlier: 3.512A pdb=" N LEU H 251 " --> pdb=" O ALA H 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 260 through 275 Processing helix chain 'H' and resid 279 through 295 removed outlier: 3.875A pdb=" N ASP H 283 " --> pdb=" O ASP H 279 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR H 291 " --> pdb=" O ALA H 287 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL H 294 " --> pdb=" O ASN H 290 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY H 295 " --> pdb=" O THR H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 322 through 348 Processing helix chain 'E' and resid 18 through 29 removed outlier: 3.551A pdb=" N ARG E 24 " --> pdb=" O ARG E 20 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA E 28 " --> pdb=" O ARG E 24 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY E 29 " --> pdb=" O THR E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 removed outlier: 3.629A pdb=" N MET E 36 " --> pdb=" O TRP E 32 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU E 38 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA E 39 " --> pdb=" O GLY E 35 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA E 44 " --> pdb=" O PHE E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 86 removed outlier: 3.751A pdb=" N GLN E 75 " --> pdb=" O GLY E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 109 Processing helix chain 'E' and resid 110 through 119 removed outlier: 3.545A pdb=" N ARG E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU E 119 " --> pdb=" O ARG E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 144 removed outlier: 3.536A pdb=" N ASN E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 235 removed outlier: 3.889A pdb=" N ASN E 172 " --> pdb=" O ALA E 168 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU E 175 " --> pdb=" O ALA E 171 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS E 210 " --> pdb=" O LYS E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 249 Processing helix chain 'E' and resid 261 through 273 Processing helix chain 'E' and resid 279 through 295 removed outlier: 3.794A pdb=" N ASP E 283 " --> pdb=" O ASP E 279 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR E 291 " --> pdb=" O ALA E 287 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL E 294 " --> pdb=" O ASN E 290 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY E 295 " --> pdb=" O THR E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 348 removed outlier: 4.023A pdb=" N LEU E 325 " --> pdb=" O ARG E 321 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 146 through 149 removed outlier: 6.109A pdb=" N ILE D 60 " --> pdb=" O LEU D 308 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 146 through 149 removed outlier: 6.108A pdb=" N ILE B 60 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 146 through 149 removed outlier: 6.100A pdb=" N ILE C 60 " --> pdb=" O LEU C 308 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 146 through 149 removed outlier: 6.081A pdb=" N ILE G 60 " --> pdb=" O LEU G 308 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 149 removed outlier: 6.098A pdb=" N ILE A 60 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 146 through 149 removed outlier: 6.107A pdb=" N ILE F 60 " --> pdb=" O LEU F 308 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 146 through 149 removed outlier: 6.107A pdb=" N ILE H 60 " --> pdb=" O LEU H 308 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 146 through 149 removed outlier: 6.100A pdb=" N ILE E 60 " --> pdb=" O LEU E 308 " (cutoff:3.500A) 1378 hydrogen bonds defined for protein. 4020 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: 5.93 Time building geometry restraints manager: 5.49 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: 7094 1.34 - 1.46: 3667 1.46 - 1.58: 10623 1.58 - 1.70: 0 1.70 - 1.82: 232 Bond restraints: 21616 Sorted by residual: bond pdb=" N VAL H 84 " pdb=" CA VAL H 84 " ideal model delta sigma weight residual 1.458 1.497 -0.038 1.32e-02 5.74e+03 8.47e+00 bond pdb=" N VAL B 84 " pdb=" CA VAL B 84 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.32e-02 5.74e+03 7.94e+00 bond pdb=" CA ARG F 85 " pdb=" C ARG F 85 " ideal model delta sigma weight residual 1.520 1.559 -0.038 1.39e-02 5.18e+03 7.64e+00 bond pdb=" N VAL F 84 " pdb=" CA VAL F 84 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.29e-02 6.01e+03 7.25e+00 bond pdb=" N VAL D 84 " pdb=" CA VAL D 84 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.23e-02 6.61e+03 6.89e+00 ... (remaining 21611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 28721 2.21 - 4.41: 383 4.41 - 6.62: 96 6.62 - 8.83: 34 8.83 - 11.03: 22 Bond angle restraints: 29256 Sorted by residual: angle pdb=" N ASP H 83 " pdb=" CA ASP H 83 " pdb=" C ASP H 83 " ideal model delta sigma weight residual 113.18 108.33 4.85 1.21e+00 6.83e-01 1.61e+01 angle pdb=" N ASP B 83 " pdb=" CA ASP B 83 " pdb=" C ASP B 83 " ideal model delta sigma weight residual 113.18 108.39 4.79 1.21e+00 6.83e-01 1.57e+01 angle pdb=" CA SER F 86 " pdb=" C SER F 86 " pdb=" O SER F 86 " ideal model delta sigma weight residual 121.68 117.06 4.62 1.18e+00 7.18e-01 1.53e+01 angle pdb=" N PRO F 262 " pdb=" CA PRO F 262 " pdb=" C PRO F 262 " ideal model delta sigma weight residual 113.40 108.28 5.12 1.34e+00 5.57e-01 1.46e+01 angle pdb=" N PRO D 262 " pdb=" CA PRO D 262 " pdb=" C PRO D 262 " ideal model delta sigma weight residual 113.40 108.32 5.08 1.34e+00 5.57e-01 1.44e+01 ... (remaining 29251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 11203 17.58 - 35.15: 1427 35.15 - 52.73: 372 52.73 - 70.31: 101 70.31 - 87.88: 25 Dihedral angle restraints: 13128 sinusoidal: 5352 harmonic: 7776 Sorted by residual: dihedral pdb=" CA GLU D 255 " pdb=" C GLU D 255 " pdb=" N MET D 256 " pdb=" CA MET D 256 " ideal model delta harmonic sigma weight residual 180.00 160.74 19.26 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA SER H 254 " pdb=" C SER H 254 " pdb=" N GLU H 255 " pdb=" CA GLU H 255 " ideal model delta harmonic sigma weight residual -180.00 -161.83 -18.17 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA SER B 254 " pdb=" C SER B 254 " pdb=" N GLU B 255 " pdb=" CA GLU B 255 " ideal model delta harmonic sigma weight residual 180.00 -161.87 -18.13 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 13125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2695 0.051 - 0.101: 392 0.101 - 0.152: 77 0.152 - 0.202: 9 0.202 - 0.253: 11 Chirality restraints: 3184 Sorted by residual: chirality pdb=" CG LEU G 26 " pdb=" CB LEU G 26 " pdb=" CD1 LEU G 26 " pdb=" CD2 LEU G 26 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA SER H 160 " pdb=" N SER H 160 " pdb=" C SER H 160 " pdb=" CB SER H 160 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA SER B 160 " pdb=" N SER B 160 " pdb=" C SER B 160 " pdb=" CB SER B 160 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 3181 not shown) Planarity restraints: 3832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 85 " 0.229 9.50e-02 1.11e+02 1.03e-01 6.46e+00 pdb=" NE ARG B 85 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 85 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 85 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 85 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE G 324 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C PHE G 324 " -0.044 2.00e-02 2.50e+03 pdb=" O PHE G 324 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU G 325 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 153 " -0.010 2.00e-02 2.50e+03 1.23e-02 2.66e+00 pdb=" CG PHE C 153 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE C 153 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 153 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 153 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 153 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 153 " -0.000 2.00e-02 2.50e+03 ... (remaining 3829 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1915 2.74 - 3.28: 20837 3.28 - 3.82: 33214 3.82 - 4.36: 37184 4.36 - 4.90: 65071 Nonbonded interactions: 158221 Sorted by model distance: nonbonded pdb=" ND2 ASN A 270 " pdb=" O SER H 254 " model vdw 2.204 3.120 nonbonded pdb=" O LEU G 22 " pdb=" OG1 THR G 25 " model vdw 2.217 3.040 nonbonded pdb=" O LEU H 45 " pdb=" OG1 THR H 48 " model vdw 2.225 3.040 nonbonded pdb=" O LEU D 45 " pdb=" OG1 THR D 48 " model vdw 2.229 3.040 nonbonded pdb=" O LEU C 45 " pdb=" OG1 THR C 48 " model vdw 2.231 3.040 ... (remaining 158216 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 10.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.880 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 45.070 Find NCS groups from input model: 0.950 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: 0.000 Load rotamer database and sin/cos tables:13.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 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 0.043 21616 Z= 0.164 Angle : 0.721 11.032 29256 Z= 0.379 Chirality : 0.041 0.253 3184 Planarity : 0.004 0.103 3832 Dihedral : 17.208 87.883 8088 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.41 % Allowed : 26.77 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.16), residues: 2640 helix: 1.51 (0.12), residues: 1660 sheet: 0.91 (0.44), residues: 200 loop : -1.21 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 329 HIS 0.002 0.000 HIS C 237 PHE 0.028 0.001 PHE C 153 TYR 0.011 0.001 TYR G 124 ARG 0.009 0.000 ARG E 241 Details of bonding type rmsd hydrogen bonds : bond 0.28613 ( 1378) hydrogen bonds : angle 5.51194 ( 4020) covalent geometry : bond 0.00290 (21616) covalent geometry : angle 0.72072 (29256) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 169 time to evaluate : 2.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 68 MET cc_start: 0.9218 (pmm) cc_final: 0.9018 (pmt) REVERT: D 256 MET cc_start: 0.9370 (mpp) cc_final: 0.9164 (mpp) REVERT: B 140 ASP cc_start: 0.9444 (t0) cc_final: 0.9197 (t0) REVERT: C 97 MET cc_start: 0.9423 (mpp) cc_final: 0.9134 (mpp) REVERT: C 155 ARG cc_start: 0.9380 (ttm-80) cc_final: 0.9153 (mtm110) REVERT: G 36 MET cc_start: 0.8103 (pp-130) cc_final: 0.7609 (ppp) REVERT: G 42 LEU cc_start: 0.9312 (tm) cc_final: 0.8844 (pp) REVERT: A 42 LEU cc_start: 0.9228 (tm) cc_final: 0.8742 (pp) REVERT: F 140 ASP cc_start: 0.9446 (t0) cc_final: 0.9243 (t0) REVERT: H 36 MET cc_start: 0.7978 (ppp) cc_final: 0.7721 (pp-130) REVERT: H 40 PHE cc_start: 0.9354 (m-80) cc_final: 0.8838 (m-10) REVERT: H 155 ARG cc_start: 0.9375 (mtm-85) cc_final: 0.9150 (mtm110) REVERT: H 256 MET cc_start: 0.9359 (mpp) cc_final: 0.9119 (mpp) outliers start: 9 outliers final: 0 residues processed: 175 average time/residue: 1.8014 time to fit residues: 349.6079 Evaluate side-chains 147 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 6.9990 chunk 200 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 206 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 239 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN G 75 GLN A 75 GLN E 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.073945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.044515 restraints weight = 92344.054| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 5.06 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 21616 Z= 0.255 Angle : 0.652 10.616 29256 Z= 0.344 Chirality : 0.040 0.198 3184 Planarity : 0.004 0.035 3832 Dihedral : 3.988 18.867 2952 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.45 % Allowed : 22.91 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.24 (0.17), residues: 2640 helix: 2.71 (0.12), residues: 1680 sheet: 0.95 (0.44), residues: 200 loop : -1.33 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 32 HIS 0.003 0.001 HIS A 237 PHE 0.019 0.002 PHE A 153 TYR 0.014 0.002 TYR G 47 ARG 0.009 0.000 ARG F 85 Details of bonding type rmsd hydrogen bonds : bond 0.10399 ( 1378) hydrogen bonds : angle 4.19994 ( 4020) covalent geometry : bond 0.00563 (21616) covalent geometry : angle 0.65236 (29256) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 154 time to evaluate : 2.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 68 MET cc_start: 0.9198 (pmm) cc_final: 0.8910 (pmt) REVERT: D 256 MET cc_start: 0.9252 (mpp) cc_final: 0.8746 (mpp) REVERT: B 97 MET cc_start: 0.8828 (mpp) cc_final: 0.8608 (mpt) REVERT: B 140 ASP cc_start: 0.9378 (t0) cc_final: 0.9097 (t0) REVERT: B 256 MET cc_start: 0.9070 (mpp) cc_final: 0.8746 (mpp) REVERT: G 36 MET cc_start: 0.8549 (pp-130) cc_final: 0.8190 (ppp) REVERT: A 42 LEU cc_start: 0.9214 (tm) cc_final: 0.8837 (pp) REVERT: F 97 MET cc_start: 0.8678 (mtm) cc_final: 0.8471 (mpt) REVERT: F 140 ASP cc_start: 0.9367 (t0) cc_final: 0.9114 (t0) REVERT: F 256 MET cc_start: 0.9131 (mpp) cc_final: 0.8812 (mpp) REVERT: H 36 MET cc_start: 0.8479 (ppp) cc_final: 0.8232 (ppp) REVERT: H 40 PHE cc_start: 0.9650 (m-80) cc_final: 0.9258 (m-10) REVERT: H 97 MET cc_start: 0.8787 (mpp) cc_final: 0.8537 (mpp) REVERT: H 256 MET cc_start: 0.9221 (mpp) cc_final: 0.8616 (mpp) outliers start: 54 outliers final: 8 residues processed: 203 average time/residue: 1.9381 time to fit residues: 437.8860 Evaluate side-chains 154 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 2.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain G residue 226 SER Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 324 PHE Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain H residue 226 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 73 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 214 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 209 optimal weight: 0.4980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN H 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.075262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.046137 restraints weight = 91636.588| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 5.04 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21616 Z= 0.165 Angle : 0.590 15.906 29256 Z= 0.296 Chirality : 0.037 0.151 3184 Planarity : 0.003 0.041 3832 Dihedral : 3.812 17.701 2952 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.68 % Allowed : 23.18 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.48 (0.17), residues: 2640 helix: 2.95 (0.12), residues: 1676 sheet: 1.02 (0.43), residues: 216 loop : -1.42 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 111 HIS 0.002 0.000 HIS G 237 PHE 0.019 0.001 PHE G 23 TYR 0.011 0.001 TYR G 47 ARG 0.008 0.000 ARG B 63 Details of bonding type rmsd hydrogen bonds : bond 0.08759 ( 1378) hydrogen bonds : angle 3.76616 ( 4020) covalent geometry : bond 0.00322 (21616) covalent geometry : angle 0.59009 (29256) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 2.747 Fit side-chains REVERT: D 68 MET cc_start: 0.9245 (pmm) cc_final: 0.8986 (pmt) REVERT: D 256 MET cc_start: 0.9226 (mpp) cc_final: 0.8525 (mpp) REVERT: B 140 ASP cc_start: 0.9371 (t0) cc_final: 0.9061 (t0) REVERT: B 256 MET cc_start: 0.9047 (mpp) cc_final: 0.8546 (mpp) REVERT: G 36 MET cc_start: 0.8446 (pp-130) cc_final: 0.8054 (ppp) REVERT: A 42 LEU cc_start: 0.9275 (tm) cc_final: 0.8840 (pp) REVERT: F 140 ASP cc_start: 0.9368 (t0) cc_final: 0.9104 (t0) REVERT: F 256 MET cc_start: 0.9100 (mpp) cc_final: 0.8659 (mpp) REVERT: H 36 MET cc_start: 0.8430 (ppp) cc_final: 0.8094 (ppp) REVERT: H 40 PHE cc_start: 0.9639 (m-80) cc_final: 0.9215 (m-10) REVERT: H 97 MET cc_start: 0.8701 (mpp) cc_final: 0.8495 (mpp) REVERT: H 256 MET cc_start: 0.9200 (mpp) cc_final: 0.8537 (mpp) outliers start: 37 outliers final: 5 residues processed: 184 average time/residue: 1.7021 time to fit residues: 350.2725 Evaluate side-chains 150 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 145 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 342 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 213 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 205 optimal weight: 8.9990 chunk 262 optimal weight: 8.9990 chunk 133 optimal weight: 30.0000 chunk 108 optimal weight: 1.9990 chunk 256 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 GLN B 75 GLN F 75 GLN H 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.074009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.044805 restraints weight = 93576.405| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 4.99 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 21616 Z= 0.220 Angle : 0.625 11.832 29256 Z= 0.315 Chirality : 0.038 0.152 3184 Planarity : 0.003 0.029 3832 Dihedral : 3.846 16.346 2952 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.82 % Allowed : 23.59 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.56 (0.17), residues: 2640 helix: 3.02 (0.12), residues: 1680 sheet: 0.94 (0.43), residues: 216 loop : -1.39 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 111 HIS 0.002 0.000 HIS E 237 PHE 0.021 0.001 PHE C 153 TYR 0.015 0.001 TYR E 47 ARG 0.008 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.09021 ( 1378) hydrogen bonds : angle 3.85912 ( 4020) covalent geometry : bond 0.00486 (21616) covalent geometry : angle 0.62512 (29256) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 2.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 40 PHE cc_start: 0.9609 (m-80) cc_final: 0.9241 (m-10) REVERT: D 68 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8898 (pmt) REVERT: D 256 MET cc_start: 0.9282 (mpp) cc_final: 0.8675 (mpp) REVERT: B 140 ASP cc_start: 0.9411 (t0) cc_final: 0.9139 (t0) REVERT: B 256 MET cc_start: 0.9047 (mpp) cc_final: 0.8544 (mpp) REVERT: G 36 MET cc_start: 0.8439 (pp-130) cc_final: 0.8033 (ppp) REVERT: A 42 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8863 (pp) REVERT: F 140 ASP cc_start: 0.9398 (t0) cc_final: 0.9125 (t0) REVERT: F 256 MET cc_start: 0.9128 (mpp) cc_final: 0.8584 (mpp) REVERT: H 36 MET cc_start: 0.8387 (ppp) cc_final: 0.8089 (ppp) REVERT: H 40 PHE cc_start: 0.9632 (m-80) cc_final: 0.9207 (m-10) REVERT: H 256 MET cc_start: 0.9257 (mpp) cc_final: 0.8668 (mpp) outliers start: 40 outliers final: 15 residues processed: 185 average time/residue: 1.4961 time to fit residues: 311.4966 Evaluate side-chains 162 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 2.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain H residue 226 SER Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 342 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 209 optimal weight: 0.1980 chunk 255 optimal weight: 10.0000 chunk 198 optimal weight: 50.0000 chunk 26 optimal weight: 0.9980 chunk 233 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 184 optimal weight: 0.9990 chunk 201 optimal weight: 6.9990 chunk 1 optimal weight: 30.0000 chunk 60 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 GLN D 236 GLN B 75 GLN F 75 GLN H 75 GLN H 236 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.074779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.045762 restraints weight = 92524.385| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 4.93 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 21616 Z= 0.171 Angle : 0.599 9.937 29256 Z= 0.298 Chirality : 0.037 0.152 3184 Planarity : 0.003 0.029 3832 Dihedral : 3.770 16.636 2952 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.73 % Allowed : 23.55 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.69 (0.17), residues: 2640 helix: 3.15 (0.12), residues: 1652 sheet: 1.09 (0.43), residues: 216 loop : -1.26 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 111 HIS 0.002 0.000 HIS G 237 PHE 0.040 0.001 PHE E 23 TYR 0.018 0.001 TYR E 47 ARG 0.007 0.000 ARG E 24 Details of bonding type rmsd hydrogen bonds : bond 0.08373 ( 1378) hydrogen bonds : angle 3.65276 ( 4020) covalent geometry : bond 0.00351 (21616) covalent geometry : angle 0.59864 (29256) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 2.235 Fit side-chains revert: symmetry clash REVERT: D 40 PHE cc_start: 0.9589 (m-80) cc_final: 0.9215 (m-10) REVERT: D 68 MET cc_start: 0.9200 (OUTLIER) cc_final: 0.8904 (pmt) REVERT: D 256 MET cc_start: 0.9302 (mpp) cc_final: 0.8650 (mpp) REVERT: B 140 ASP cc_start: 0.9394 (t0) cc_final: 0.9114 (t0) REVERT: B 256 MET cc_start: 0.9080 (mpp) cc_final: 0.8496 (mpp) REVERT: B 318 ASP cc_start: 0.9295 (OUTLIER) cc_final: 0.8934 (t0) REVERT: C 342 LEU cc_start: 0.4828 (OUTLIER) cc_final: 0.4428 (mm) REVERT: G 36 MET cc_start: 0.8319 (pp-130) cc_final: 0.7887 (ppp) REVERT: G 68 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8977 (pmm) REVERT: A 42 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8829 (pp) REVERT: F 140 ASP cc_start: 0.9383 (t0) cc_final: 0.9109 (t0) REVERT: F 256 MET cc_start: 0.9145 (mpp) cc_final: 0.8592 (mpp) REVERT: H 36 MET cc_start: 0.8301 (ppp) cc_final: 0.8012 (ppp) REVERT: H 40 PHE cc_start: 0.9614 (m-80) cc_final: 0.9182 (m-10) REVERT: H 86 SER cc_start: 0.7768 (OUTLIER) cc_final: 0.7124 (p) REVERT: H 256 MET cc_start: 0.9267 (mpp) cc_final: 0.8224 (mpt) REVERT: E 23 PHE cc_start: 0.5115 (OUTLIER) cc_final: 0.4843 (OUTLIER) REVERT: E 68 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8983 (pmm) outliers start: 38 outliers final: 9 residues processed: 180 average time/residue: 1.4674 time to fit residues: 297.0095 Evaluate side-chains 160 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 342 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 92 optimal weight: 0.6980 chunk 152 optimal weight: 0.7980 chunk 206 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 186 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 14 optimal weight: 0.0030 chunk 254 optimal weight: 5.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 GLN B 75 GLN F 75 GLN H 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.076329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.047648 restraints weight = 92316.465| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 5.06 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21616 Z= 0.138 Angle : 0.595 9.393 29256 Z= 0.288 Chirality : 0.036 0.170 3184 Planarity : 0.003 0.027 3832 Dihedral : 3.610 16.593 2952 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.64 % Allowed : 23.77 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.91 (0.17), residues: 2640 helix: 3.28 (0.12), residues: 1664 sheet: 1.33 (0.43), residues: 216 loop : -1.20 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 111 HIS 0.002 0.001 HIS A 237 PHE 0.018 0.001 PHE A 153 TYR 0.017 0.001 TYR E 47 ARG 0.004 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.07303 ( 1378) hydrogen bonds : angle 3.39408 ( 4020) covalent geometry : bond 0.00251 (21616) covalent geometry : angle 0.59484 (29256) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 2.269 Fit side-chains revert: symmetry clash REVERT: D 68 MET cc_start: 0.9204 (pmm) cc_final: 0.8905 (pmt) REVERT: D 237 HIS cc_start: 0.7568 (OUTLIER) cc_final: 0.7308 (m90) REVERT: D 256 MET cc_start: 0.9201 (tpp) cc_final: 0.8319 (mpt) REVERT: B 140 ASP cc_start: 0.9351 (t0) cc_final: 0.9066 (t0) REVERT: B 256 MET cc_start: 0.9078 (mpp) cc_final: 0.8581 (mpp) REVERT: B 318 ASP cc_start: 0.9263 (OUTLIER) cc_final: 0.8899 (t0) REVERT: C 68 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8994 (pmm) REVERT: C 342 LEU cc_start: 0.4902 (OUTLIER) cc_final: 0.4502 (mm) REVERT: G 36 MET cc_start: 0.8214 (pp-130) cc_final: 0.7730 (ppp) REVERT: G 42 LEU cc_start: 0.9343 (tm) cc_final: 0.8935 (pp) REVERT: G 68 MET cc_start: 0.9182 (pmm) cc_final: 0.8946 (pmm) REVERT: A 42 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8846 (pp) REVERT: A 68 MET cc_start: 0.9174 (pmm) cc_final: 0.8969 (pmm) REVERT: F 140 ASP cc_start: 0.9347 (t0) cc_final: 0.9063 (t0) REVERT: F 256 MET cc_start: 0.9144 (mpp) cc_final: 0.8548 (mpp) REVERT: H 36 MET cc_start: 0.8231 (ppp) cc_final: 0.7962 (ppp) REVERT: H 40 PHE cc_start: 0.9604 (m-80) cc_final: 0.9178 (m-10) REVERT: H 86 SER cc_start: 0.7693 (OUTLIER) cc_final: 0.7077 (p) REVERT: H 237 HIS cc_start: 0.7704 (OUTLIER) cc_final: 0.7371 (m90) REVERT: H 256 MET cc_start: 0.9117 (tpp) cc_final: 0.8224 (mpt) REVERT: E 23 PHE cc_start: 0.4958 (OUTLIER) cc_final: 0.4707 (OUTLIER) REVERT: E 68 MET cc_start: 0.9171 (pmm) cc_final: 0.8938 (pmm) REVERT: E 344 ARG cc_start: 0.2846 (OUTLIER) cc_final: 0.2450 (tpm170) outliers start: 36 outliers final: 13 residues processed: 180 average time/residue: 1.5430 time to fit residues: 313.7078 Evaluate side-chains 164 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 237 HIS Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain G residue 47 TYR Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 237 HIS Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 344 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 12 optimal weight: 0.6980 chunk 143 optimal weight: 0.2980 chunk 112 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 259 optimal weight: 0.1980 chunk 47 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 201 optimal weight: 8.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 GLN B 75 GLN F 75 GLN H 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.076733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.048206 restraints weight = 92657.368| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 5.02 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21616 Z= 0.136 Angle : 0.617 11.201 29256 Z= 0.292 Chirality : 0.036 0.152 3184 Planarity : 0.003 0.025 3832 Dihedral : 3.503 16.131 2952 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.41 % Allowed : 24.14 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.99 (0.17), residues: 2640 helix: 3.36 (0.12), residues: 1664 sheet: 1.37 (0.43), residues: 216 loop : -1.22 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 329 HIS 0.002 0.000 HIS F 237 PHE 0.034 0.001 PHE F 40 TYR 0.014 0.001 TYR E 47 ARG 0.009 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.06960 ( 1378) hydrogen bonds : angle 3.30337 ( 4020) covalent geometry : bond 0.00251 (21616) covalent geometry : angle 0.61697 (29256) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 2.310 Fit side-chains revert: symmetry clash REVERT: D 68 MET cc_start: 0.9199 (OUTLIER) cc_final: 0.8899 (pmt) REVERT: D 256 MET cc_start: 0.9121 (tpp) cc_final: 0.8293 (mpt) REVERT: B 140 ASP cc_start: 0.9373 (t0) cc_final: 0.9080 (t0) REVERT: B 256 MET cc_start: 0.9021 (mpp) cc_final: 0.8554 (mpp) REVERT: B 318 ASP cc_start: 0.9292 (OUTLIER) cc_final: 0.8927 (t0) REVERT: C 68 MET cc_start: 0.9106 (pmm) cc_final: 0.8886 (pmm) REVERT: C 256 MET cc_start: 0.9280 (ppp) cc_final: 0.8450 (mtt) REVERT: G 23 PHE cc_start: 0.6497 (OUTLIER) cc_final: 0.6100 (p90) REVERT: G 36 MET cc_start: 0.8223 (pp-130) cc_final: 0.7753 (ppp) REVERT: G 42 LEU cc_start: 0.9337 (tm) cc_final: 0.8921 (pp) REVERT: G 68 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8936 (pmm) REVERT: A 42 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8824 (pp) REVERT: A 68 MET cc_start: 0.9126 (pmm) cc_final: 0.8910 (pmm) REVERT: A 256 MET cc_start: 0.9279 (ppp) cc_final: 0.8410 (mtt) REVERT: F 140 ASP cc_start: 0.9368 (t0) cc_final: 0.9082 (t0) REVERT: F 256 MET cc_start: 0.9088 (mpp) cc_final: 0.8599 (mpp) REVERT: H 36 MET cc_start: 0.8229 (ppp) cc_final: 0.7912 (ppp) REVERT: H 40 PHE cc_start: 0.9584 (m-80) cc_final: 0.9139 (m-10) REVERT: H 86 SER cc_start: 0.7763 (OUTLIER) cc_final: 0.7156 (p) REVERT: H 256 MET cc_start: 0.9069 (tpp) cc_final: 0.8283 (mpt) REVERT: E 23 PHE cc_start: 0.4993 (OUTLIER) cc_final: 0.4748 (OUTLIER) REVERT: E 68 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8932 (pmm) REVERT: E 344 ARG cc_start: 0.2799 (OUTLIER) cc_final: 0.2445 (tpm170) outliers start: 31 outliers final: 9 residues processed: 172 average time/residue: 1.4998 time to fit residues: 289.4455 Evaluate side-chains 159 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain G residue 23 PHE Chi-restraints excluded: chain G residue 47 TYR Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 344 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 56 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 194 optimal weight: 0.9980 chunk 236 optimal weight: 3.9990 chunk 238 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 227 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 GLN B 75 GLN F 75 GLN H 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.074701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.045622 restraints weight = 93302.087| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 5.05 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21616 Z= 0.198 Angle : 0.667 12.553 29256 Z= 0.321 Chirality : 0.038 0.161 3184 Planarity : 0.003 0.026 3832 Dihedral : 3.656 15.354 2952 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.36 % Allowed : 24.41 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.85 (0.17), residues: 2640 helix: 3.30 (0.12), residues: 1668 sheet: 1.14 (0.43), residues: 216 loop : -1.36 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 111 HIS 0.002 0.000 HIS C 237 PHE 0.017 0.001 PHE A 153 TYR 0.014 0.001 TYR E 47 ARG 0.010 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.08077 ( 1378) hydrogen bonds : angle 3.60939 ( 4020) covalent geometry : bond 0.00437 (21616) covalent geometry : angle 0.66688 (29256) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 2.434 Fit side-chains revert: symmetry clash REVERT: D 40 PHE cc_start: 0.9540 (m-80) cc_final: 0.9157 (m-80) REVERT: D 68 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8953 (pmm) REVERT: D 256 MET cc_start: 0.9205 (tpp) cc_final: 0.8270 (mpt) REVERT: D 264 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.9004 (mm) REVERT: B 140 ASP cc_start: 0.9393 (t0) cc_final: 0.9122 (t0) REVERT: B 256 MET cc_start: 0.9087 (mpp) cc_final: 0.8619 (mpp) REVERT: G 23 PHE cc_start: 0.6486 (OUTLIER) cc_final: 0.6081 (p90) REVERT: G 36 MET cc_start: 0.8229 (pp-130) cc_final: 0.7754 (ppp) REVERT: G 42 LEU cc_start: 0.9368 (tm) cc_final: 0.8968 (pp) REVERT: G 68 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8961 (pmm) REVERT: A 42 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8830 (pp) REVERT: A 68 MET cc_start: 0.9147 (pmm) cc_final: 0.8811 (pmt) REVERT: F 140 ASP cc_start: 0.9388 (t0) cc_final: 0.9114 (t0) REVERT: F 256 MET cc_start: 0.9127 (mpp) cc_final: 0.8657 (mpp) REVERT: H 36 MET cc_start: 0.8229 (ppp) cc_final: 0.7908 (ppp) REVERT: H 40 PHE cc_start: 0.9574 (m-80) cc_final: 0.9120 (m-10) REVERT: H 86 SER cc_start: 0.7990 (OUTLIER) cc_final: 0.7382 (p) REVERT: H 256 MET cc_start: 0.9161 (tpp) cc_final: 0.8227 (mpt) REVERT: E 23 PHE cc_start: 0.4916 (OUTLIER) cc_final: 0.4672 (OUTLIER) REVERT: E 68 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8961 (pmm) REVERT: E 344 ARG cc_start: 0.2723 (OUTLIER) cc_final: 0.2326 (tpm170) outliers start: 30 outliers final: 8 residues processed: 170 average time/residue: 1.7124 time to fit residues: 325.6386 Evaluate side-chains 160 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain G residue 23 PHE Chi-restraints excluded: chain G residue 47 TYR Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 344 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 60 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 90 optimal weight: 0.0870 chunk 227 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 GLN B 75 GLN F 75 GLN H 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.075662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.046872 restraints weight = 92311.685| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 4.97 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21616 Z= 0.149 Angle : 0.665 12.446 29256 Z= 0.314 Chirality : 0.037 0.150 3184 Planarity : 0.003 0.051 3832 Dihedral : 3.629 16.397 2952 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.32 % Allowed : 24.36 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.90 (0.17), residues: 2640 helix: 3.25 (0.12), residues: 1664 sheet: 1.22 (0.43), residues: 216 loop : -1.11 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 329 HIS 0.002 0.000 HIS F 237 PHE 0.034 0.001 PHE F 40 TYR 0.013 0.001 TYR E 47 ARG 0.011 0.000 ARG D 261 Details of bonding type rmsd hydrogen bonds : bond 0.07537 ( 1378) hydrogen bonds : angle 3.46642 ( 4020) covalent geometry : bond 0.00295 (21616) covalent geometry : angle 0.66467 (29256) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 2.245 Fit side-chains revert: symmetry clash REVERT: D 40 PHE cc_start: 0.9494 (m-80) cc_final: 0.9099 (m-80) REVERT: D 68 MET cc_start: 0.9213 (OUTLIER) cc_final: 0.8915 (pmt) REVERT: D 256 MET cc_start: 0.9144 (tpp) cc_final: 0.8205 (mpt) REVERT: B 140 ASP cc_start: 0.9382 (t0) cc_final: 0.9092 (t0) REVERT: B 256 MET cc_start: 0.9086 (mpp) cc_final: 0.8636 (mpp) REVERT: C 256 MET cc_start: 0.9253 (ppp) cc_final: 0.8434 (mtt) REVERT: G 23 PHE cc_start: 0.6466 (OUTLIER) cc_final: 0.6053 (p90) REVERT: G 36 MET cc_start: 0.8134 (pp-130) cc_final: 0.7649 (ppp) REVERT: G 42 LEU cc_start: 0.9352 (tm) cc_final: 0.8949 (pp) REVERT: G 68 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8981 (pmm) REVERT: A 42 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8794 (pp) REVERT: A 68 MET cc_start: 0.9175 (pmm) cc_final: 0.8827 (pmt) REVERT: A 256 MET cc_start: 0.9283 (ppp) cc_final: 0.8444 (mtt) REVERT: F 140 ASP cc_start: 0.9380 (t0) cc_final: 0.9093 (t0) REVERT: F 256 MET cc_start: 0.9130 (mpp) cc_final: 0.8647 (mpp) REVERT: H 36 MET cc_start: 0.8194 (ppp) cc_final: 0.7910 (ppp) REVERT: H 40 PHE cc_start: 0.9555 (m-80) cc_final: 0.9091 (m-10) REVERT: H 256 MET cc_start: 0.9090 (tpp) cc_final: 0.8205 (mpt) REVERT: E 23 PHE cc_start: 0.4930 (OUTLIER) cc_final: 0.4686 (OUTLIER) REVERT: E 68 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8977 (pmm) REVERT: E 344 ARG cc_start: 0.2923 (OUTLIER) cc_final: 0.2459 (tpm170) outliers start: 29 outliers final: 13 residues processed: 165 average time/residue: 1.5564 time to fit residues: 287.3189 Evaluate side-chains 164 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain G residue 23 PHE Chi-restraints excluded: chain G residue 47 TYR Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 344 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 199 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 244 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 159 optimal weight: 0.9990 chunk 228 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 236 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 GLN B 75 GLN F 75 GLN H 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.074701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.045666 restraints weight = 92495.251| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 5.01 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 21616 Z= 0.188 Angle : 0.694 12.888 29256 Z= 0.331 Chirality : 0.038 0.153 3184 Planarity : 0.003 0.050 3832 Dihedral : 3.700 16.854 2952 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.32 % Allowed : 24.36 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.76 (0.17), residues: 2640 helix: 3.19 (0.12), residues: 1672 sheet: 1.11 (0.43), residues: 216 loop : -1.34 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 111 HIS 0.002 0.000 HIS G 237 PHE 0.018 0.001 PHE C 153 TYR 0.013 0.001 TYR E 47 ARG 0.009 0.000 ARG D 261 Details of bonding type rmsd hydrogen bonds : bond 0.08074 ( 1378) hydrogen bonds : angle 3.66015 ( 4020) covalent geometry : bond 0.00408 (21616) covalent geometry : angle 0.69364 (29256) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 4.456 Fit side-chains revert: symmetry clash REVERT: D 40 PHE cc_start: 0.9505 (m-80) cc_final: 0.9108 (m-80) REVERT: D 68 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8954 (pmm) REVERT: D 256 MET cc_start: 0.9190 (tpp) cc_final: 0.8563 (mpp) REVERT: B 140 ASP cc_start: 0.9387 (t0) cc_final: 0.9117 (t0) REVERT: B 256 MET cc_start: 0.9117 (mpp) cc_final: 0.8674 (mpp) REVERT: C 256 MET cc_start: 0.9247 (ppp) cc_final: 0.8432 (mtt) REVERT: G 23 PHE cc_start: 0.6538 (OUTLIER) cc_final: 0.6133 (p90) REVERT: G 36 MET cc_start: 0.8233 (pp-130) cc_final: 0.7792 (ppp) REVERT: G 68 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8978 (pmm) REVERT: A 42 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8815 (pp) REVERT: A 68 MET cc_start: 0.9146 (pmm) cc_final: 0.8796 (pmt) REVERT: F 140 ASP cc_start: 0.9386 (t0) cc_final: 0.9116 (t0) REVERT: F 256 MET cc_start: 0.9120 (mpp) cc_final: 0.8655 (mpp) REVERT: H 36 MET cc_start: 0.8210 (ppp) cc_final: 0.7906 (ppp) REVERT: H 40 PHE cc_start: 0.9566 (m-80) cc_final: 0.9112 (m-10) REVERT: H 256 MET cc_start: 0.9114 (tpp) cc_final: 0.8202 (mpt) REVERT: E 23 PHE cc_start: 0.4990 (OUTLIER) cc_final: 0.4748 (OUTLIER) REVERT: E 68 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8978 (pmm) REVERT: E 344 ARG cc_start: 0.2903 (OUTLIER) cc_final: 0.2474 (tpm170) outliers start: 29 outliers final: 9 residues processed: 166 average time/residue: 1.9316 time to fit residues: 359.7326 Evaluate side-chains 159 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 2.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain G residue 23 PHE Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 344 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 227 optimal weight: 0.0770 chunk 233 optimal weight: 1.9990 chunk 162 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 220 optimal weight: 0.5980 chunk 147 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 193 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 203 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 GLN B 75 GLN F 75 GLN H 75 GLN E 270 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.076444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.047844 restraints weight = 92883.811| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 5.04 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21616 Z= 0.141 Angle : 0.688 12.745 29256 Z= 0.322 Chirality : 0.037 0.159 3184 Planarity : 0.003 0.051 3832 Dihedral : 3.602 18.059 2952 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.82 % Allowed : 24.95 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.92 (0.17), residues: 2640 helix: 3.26 (0.12), residues: 1668 sheet: 1.25 (0.43), residues: 216 loop : -1.12 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 329 HIS 0.006 0.001 HIS G 237 PHE 0.032 0.001 PHE F 40 TYR 0.011 0.001 TYR E 47 ARG 0.009 0.000 ARG D 261 Details of bonding type rmsd hydrogen bonds : bond 0.07046 ( 1378) hydrogen bonds : angle 3.41034 ( 4020) covalent geometry : bond 0.00267 (21616) covalent geometry : angle 0.68836 (29256) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13755.45 seconds wall clock time: 239 minutes 29.66 seconds (14369.66 seconds total)