Starting phenix.real_space_refine on Wed May 21 09:49:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p3o_17387/05_2025/8p3o_17387.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p3o_17387/05_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_17387/05_2025/8p3o_17387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p3o_17387/05_2025/8p3o_17387.map" model { file = "/net/cci-nas-00/data/ceres_data/8p3o_17387/05_2025/8p3o_17387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p3o_17387/05_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 13.06, per 1000 atoms: 0.62 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: 4.47 Conformation dependent library (CDL) restraints added in 2.4 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: 1.63 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: 6.01 Time building geometry restraints manager: 5.30 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: 0.03 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: 8.350 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: 0.840 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 43.100 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.250 ------------------------------------------------------------------------------- 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 : 2.607 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: 1.6872 time to fit residues: 327.0981 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 : 2.491 ------------------------------------------------------------------------------- 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 = 59)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.044521 restraints weight = 92344.129| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 5.05 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 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 : 2.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 68 MET cc_start: 0.9195 (pmm) cc_final: 0.8907 (pmt) REVERT: D 256 MET cc_start: 0.9255 (mpp) cc_final: 0.8745 (mpp) REVERT: B 97 MET cc_start: 0.8823 (mpp) cc_final: 0.8604 (mpt) REVERT: B 140 ASP cc_start: 0.9383 (t0) cc_final: 0.9100 (t0) REVERT: B 256 MET cc_start: 0.9073 (mpp) cc_final: 0.8748 (mpp) REVERT: G 36 MET cc_start: 0.8543 (pp-130) cc_final: 0.8180 (ppp) REVERT: A 42 LEU cc_start: 0.9214 (tm) cc_final: 0.8837 (pp) REVERT: F 97 MET cc_start: 0.8673 (mtm) cc_final: 0.8469 (mpt) REVERT: F 140 ASP cc_start: 0.9372 (t0) cc_final: 0.9118 (t0) REVERT: F 256 MET cc_start: 0.9132 (mpp) cc_final: 0.8811 (mpp) REVERT: H 36 MET cc_start: 0.8475 (ppp) cc_final: 0.8229 (ppp) REVERT: H 40 PHE cc_start: 0.9649 (m-80) cc_final: 0.9256 (m-10) REVERT: H 97 MET cc_start: 0.8785 (mpp) cc_final: 0.8533 (mpp) REVERT: H 256 MET cc_start: 0.9224 (mpp) cc_final: 0.8617 (mpp) REVERT: E 317 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8934 (ttp80) outliers start: 54 outliers final: 8 residues processed: 203 average time/residue: 1.5568 time to fit residues: 354.1687 Evaluate side-chains 155 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 2.439 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain E residue 317 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 73 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 180 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 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: 1.6186 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.075069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.045875 restraints weight = 91838.291| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 5.06 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2272 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= 0.174 Angle : 0.593 15.376 29256 Z= 0.299 Chirality : 0.037 0.151 3184 Planarity : 0.003 0.041 3832 Dihedral : 3.823 17.555 2952 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.82 % Allowed : 23.14 % Favored : 75.05 % 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: 2.46 (0.17), residues: 2640 helix: 2.94 (0.12), residues: 1676 sheet: 0.98 (0.43), residues: 216 loop : -1.41 (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 A 237 PHE 0.019 0.001 PHE G 23 TYR 0.011 0.001 TYR G 47 ARG 0.008 0.000 ARG H 63 Details of bonding type rmsd hydrogen bonds : bond 0.08865 ( 1378) hydrogen bonds : angle 3.80178 ( 4020) covalent geometry : bond 0.00346 (21616) covalent geometry : angle 0.59271 (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 187 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 2.482 Fit side-chains REVERT: D 68 MET cc_start: 0.9242 (pmm) cc_final: 0.8989 (pmt) REVERT: D 256 MET cc_start: 0.9217 (mpp) cc_final: 0.8611 (mpp) REVERT: B 140 ASP cc_start: 0.9373 (t0) cc_final: 0.9070 (t0) REVERT: B 256 MET cc_start: 0.9041 (mpp) cc_final: 0.8540 (mpp) REVERT: G 36 MET cc_start: 0.8490 (pp-130) cc_final: 0.8119 (ppp) REVERT: A 42 LEU cc_start: 0.9275 (tm) cc_final: 0.8853 (pp) REVERT: F 140 ASP cc_start: 0.9376 (t0) cc_final: 0.9107 (t0) REVERT: F 256 MET cc_start: 0.9091 (mpp) cc_final: 0.8657 (mpp) REVERT: H 36 MET cc_start: 0.8443 (ppp) cc_final: 0.8114 (ppp) REVERT: H 40 PHE cc_start: 0.9648 (m-80) cc_final: 0.9244 (m-10) REVERT: H 256 MET cc_start: 0.9191 (mpp) cc_final: 0.8540 (mpp) outliers start: 40 outliers final: 6 residues processed: 186 average time/residue: 1.5359 time to fit residues: 320.4779 Evaluate side-chains 150 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 144 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain G residue 324 PHE 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: 0.7980 chunk 137 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 145 optimal weight: 0.8980 chunk 205 optimal weight: 10.0000 chunk 262 optimal weight: 10.0000 chunk 133 optimal weight: 30.0000 chunk 108 optimal weight: 4.9990 chunk 256 optimal weight: 6.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.073635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.044420 restraints weight = 93759.868| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 4.98 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 21616 Z= 0.243 Angle : 0.633 11.519 29256 Z= 0.321 Chirality : 0.039 0.154 3184 Planarity : 0.003 0.029 3832 Dihedral : 3.894 16.128 2952 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.91 % Allowed : 23.64 % 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: 2.53 (0.17), residues: 2640 helix: 2.98 (0.12), residues: 1680 sheet: 1.11 (0.43), residues: 200 loop : -1.35 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 111 HIS 0.003 0.001 HIS C 237 PHE 0.021 0.002 PHE G 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 0.09252 ( 1378) hydrogen bonds : angle 3.93337 ( 4020) covalent geometry : bond 0.00543 (21616) covalent geometry : angle 0.63350 (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 189 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 2.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 40 PHE cc_start: 0.9613 (m-80) cc_final: 0.9246 (m-10) REVERT: D 68 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8913 (pmt) REVERT: D 256 MET cc_start: 0.9283 (mpp) cc_final: 0.8673 (mpp) REVERT: B 140 ASP cc_start: 0.9403 (t0) cc_final: 0.9132 (t0) REVERT: B 256 MET cc_start: 0.9084 (mpp) cc_final: 0.8576 (mpp) REVERT: G 36 MET cc_start: 0.8459 (pp-130) cc_final: 0.8058 (ppp) REVERT: A 42 LEU cc_start: 0.9297 (tm) cc_final: 0.8869 (pp) REVERT: F 140 ASP cc_start: 0.9396 (t0) cc_final: 0.9156 (t0) REVERT: F 256 MET cc_start: 0.9135 (mpp) cc_final: 0.8578 (mpp) REVERT: H 36 MET cc_start: 0.8398 (ppp) cc_final: 0.8108 (ppp) REVERT: H 40 PHE cc_start: 0.9633 (m-80) cc_final: 0.9220 (m-10) REVERT: H 256 MET cc_start: 0.9272 (mpp) cc_final: 0.8676 (mpp) outliers start: 42 outliers final: 15 residues processed: 188 average time/residue: 1.4879 time to fit residues: 316.2042 Evaluate side-chains 161 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 2.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain G residue 324 PHE 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 227 ILE 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: 0.0770 chunk 255 optimal weight: 10.0000 chunk 198 optimal weight: 50.0000 chunk 26 optimal weight: 2.9990 chunk 233 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 184 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.074464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.045364 restraints weight = 92539.756| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 4.97 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 21616 Z= 0.180 Angle : 0.603 10.030 29256 Z= 0.301 Chirality : 0.037 0.152 3184 Planarity : 0.003 0.029 3832 Dihedral : 3.804 16.173 2952 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.77 % Allowed : 23.73 % Favored : 74.50 % 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: 2.58 (0.17), residues: 2640 helix: 3.05 (0.12), residues: 1676 sheet: 1.01 (0.43), residues: 216 loop : -1.40 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 111 HIS 0.003 0.000 HIS B 237 PHE 0.035 0.001 PHE E 23 TYR 0.018 0.001 TYR E 47 ARG 0.005 0.000 ARG E 24 Details of bonding type rmsd hydrogen bonds : bond 0.08525 ( 1378) hydrogen bonds : angle 3.70288 ( 4020) covalent geometry : bond 0.00377 (21616) covalent geometry : angle 0.60289 (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 185 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 2.449 Fit side-chains revert: symmetry clash REVERT: D 40 PHE cc_start: 0.9595 (m-80) cc_final: 0.9215 (m-10) REVERT: D 68 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8908 (pmt) REVERT: D 256 MET cc_start: 0.9328 (mpp) cc_final: 0.8639 (mpp) REVERT: B 140 ASP cc_start: 0.9399 (t0) cc_final: 0.9122 (t0) REVERT: B 256 MET cc_start: 0.9137 (mpp) cc_final: 0.8588 (mpp) REVERT: B 318 ASP cc_start: 0.9301 (OUTLIER) cc_final: 0.8944 (t0) REVERT: C 328 MET cc_start: 0.8008 (ppp) cc_final: 0.7707 (ppp) REVERT: C 342 LEU cc_start: 0.4871 (OUTLIER) cc_final: 0.4471 (mm) REVERT: G 36 MET cc_start: 0.8368 (pp-130) cc_final: 0.7941 (ppp) REVERT: G 42 LEU cc_start: 0.9367 (tm) cc_final: 0.8943 (pp) REVERT: G 68 MET cc_start: 0.9205 (pmm) cc_final: 0.9002 (pmm) REVERT: A 42 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8837 (pp) REVERT: A 68 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.8946 (pmm) REVERT: F 140 ASP cc_start: 0.9390 (t0) cc_final: 0.9120 (t0) REVERT: F 256 MET cc_start: 0.9195 (mpp) cc_final: 0.8625 (mpp) REVERT: H 36 MET cc_start: 0.8344 (ppp) cc_final: 0.8032 (ppp) REVERT: H 40 PHE cc_start: 0.9626 (m-80) cc_final: 0.9199 (m-10) REVERT: H 256 MET cc_start: 0.9290 (mpp) cc_final: 0.8617 (mpp) REVERT: E 23 PHE cc_start: 0.5194 (OUTLIER) cc_final: 0.4967 (OUTLIER) REVERT: E 344 ARG cc_start: 0.2936 (OUTLIER) cc_final: 0.2553 (tpm170) outliers start: 39 outliers final: 7 residues processed: 182 average time/residue: 1.4711 time to fit residues: 301.5861 Evaluate side-chains 158 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 2.456 ------------------------------------------------------------------------------- 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 291 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 324 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain E residue 23 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 92 optimal weight: 0.2980 chunk 152 optimal weight: 0.9990 chunk 206 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 254 optimal weight: 0.0050 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 GLN D 237 HIS B 75 GLN F 75 GLN H 75 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.076123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.047387 restraints weight = 92179.659| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 5.05 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21616 Z= 0.141 Angle : 0.596 9.932 29256 Z= 0.289 Chirality : 0.036 0.149 3184 Planarity : 0.003 0.027 3832 Dihedral : 3.640 16.306 2952 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.77 % Allowed : 23.64 % 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: 2.90 (0.17), residues: 2640 helix: 3.28 (0.12), residues: 1660 sheet: 1.28 (0.43), residues: 216 loop : -1.16 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 111 HIS 0.005 0.001 HIS F 237 PHE 0.032 0.001 PHE F 40 TYR 0.018 0.001 TYR E 47 ARG 0.005 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.07436 ( 1378) hydrogen bonds : angle 3.41579 ( 4020) covalent geometry : bond 0.00251 (21616) covalent geometry : angle 0.59644 (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 186 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 2.378 Fit side-chains revert: symmetry clash REVERT: D 68 MET cc_start: 0.9212 (OUTLIER) cc_final: 0.8921 (pmt) REVERT: D 256 MET cc_start: 0.9248 (tpp) cc_final: 0.8268 (mpt) REVERT: B 140 ASP cc_start: 0.9365 (t0) cc_final: 0.9049 (t0) REVERT: B 256 MET cc_start: 0.9134 (mpp) cc_final: 0.8614 (mpp) REVERT: B 318 ASP cc_start: 0.9253 (OUTLIER) cc_final: 0.8901 (t0) REVERT: G 36 MET cc_start: 0.8302 (pp-130) cc_final: 0.7851 (ppp) REVERT: G 42 LEU cc_start: 0.9369 (tm) cc_final: 0.8953 (pp) REVERT: G 68 MET cc_start: 0.9213 (OUTLIER) cc_final: 0.8910 (pmm) REVERT: A 42 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8845 (pp) REVERT: A 68 MET cc_start: 0.9196 (pmm) cc_final: 0.8937 (pmm) REVERT: F 140 ASP cc_start: 0.9367 (t0) cc_final: 0.9062 (t0) REVERT: F 256 MET cc_start: 0.9208 (mpp) cc_final: 0.8641 (mpp) REVERT: H 36 MET cc_start: 0.8296 (ppp) cc_final: 0.7998 (ppp) REVERT: H 40 PHE cc_start: 0.9617 (m-80) cc_final: 0.9189 (m-10) REVERT: H 237 HIS cc_start: 0.7755 (OUTLIER) cc_final: 0.7495 (m90) REVERT: H 256 MET cc_start: 0.9179 (tpp) cc_final: 0.8229 (mpt) REVERT: E 23 PHE cc_start: 0.4973 (OUTLIER) cc_final: 0.4723 (OUTLIER) REVERT: E 344 ARG cc_start: 0.2911 (OUTLIER) cc_final: 0.2538 (tpm170) outliers start: 39 outliers final: 11 residues processed: 182 average time/residue: 1.4892 time to fit residues: 305.2359 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 : 2.472 ------------------------------------------------------------------------------- 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 203 ILE Chi-restraints excluded: chain C residue 291 THR 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 47 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 291 THR 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: 3.9990 chunk 143 optimal weight: 0.5980 chunk 112 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 259 optimal weight: 0.0970 chunk 47 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 201 optimal weight: 8.9990 overall best weight: 1.0980 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.075779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.046911 restraints weight = 92476.017| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 5.12 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21616 Z= 0.148 Angle : 0.628 11.010 29256 Z= 0.300 Chirality : 0.036 0.151 3184 Planarity : 0.003 0.028 3832 Dihedral : 3.609 15.858 2952 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.32 % Allowed : 24.50 % Favored : 74.18 % 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: 2.95 (0.17), residues: 2640 helix: 3.30 (0.12), residues: 1668 sheet: 1.29 (0.43), residues: 216 loop : -1.16 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 111 HIS 0.002 0.000 HIS C 237 PHE 0.035 0.001 PHE F 40 TYR 0.017 0.001 TYR E 47 ARG 0.005 0.000 ARG A 241 Details of bonding type rmsd hydrogen bonds : bond 0.07497 ( 1378) hydrogen bonds : angle 3.43012 ( 4020) covalent geometry : bond 0.00291 (21616) covalent geometry : angle 0.62792 (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 174 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 2.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 40 PHE cc_start: 0.9586 (m-80) cc_final: 0.9201 (m-80) REVERT: D 68 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8886 (pmt) REVERT: D 256 MET cc_start: 0.9198 (tpp) cc_final: 0.8247 (mpt) REVERT: B 140 ASP cc_start: 0.9379 (t0) cc_final: 0.9081 (t0) REVERT: B 256 MET cc_start: 0.9078 (mpp) cc_final: 0.8577 (mpp) REVERT: G 23 PHE cc_start: 0.6512 (OUTLIER) cc_final: 0.6113 (p90) REVERT: G 36 MET cc_start: 0.8280 (pp-130) cc_final: 0.7830 (ppp) REVERT: G 68 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8938 (pmm) REVERT: A 42 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8846 (pp) REVERT: A 68 MET cc_start: 0.9203 (pmm) cc_final: 0.8938 (pmm) REVERT: F 140 ASP cc_start: 0.9365 (t0) cc_final: 0.9085 (t0) REVERT: F 256 MET cc_start: 0.9162 (mpp) cc_final: 0.8640 (mpp) REVERT: H 36 MET cc_start: 0.8263 (ppp) cc_final: 0.7969 (ppp) REVERT: H 40 PHE cc_start: 0.9615 (m-80) cc_final: 0.9186 (m-10) REVERT: H 86 SER cc_start: 0.7866 (OUTLIER) cc_final: 0.7226 (p) REVERT: H 237 HIS cc_start: 0.7601 (OUTLIER) cc_final: 0.7310 (m90) REVERT: H 256 MET cc_start: 0.9172 (tpp) cc_final: 0.8254 (mpt) REVERT: E 23 PHE cc_start: 0.5000 (OUTLIER) cc_final: 0.4751 (OUTLIER) REVERT: E 68 MET cc_start: 0.9152 (pmm) cc_final: 0.8899 (pmm) REVERT: E 344 ARG cc_start: 0.2923 (OUTLIER) cc_final: 0.2558 (tpm170) outliers start: 29 outliers final: 13 residues processed: 169 average time/residue: 1.5633 time to fit residues: 296.5779 Evaluate side-chains 164 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 237 HIS Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain C residue 203 ILE 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 203 ILE Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain A residue 42 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 56 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 chunk 236 optimal weight: 3.9990 chunk 238 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 227 optimal weight: 0.0050 chunk 130 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.075794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.047036 restraints weight = 93005.898| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 5.12 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21616 Z= 0.147 Angle : 0.643 11.811 29256 Z= 0.304 Chirality : 0.036 0.152 3184 Planarity : 0.003 0.026 3832 Dihedral : 3.587 15.497 2952 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.18 % Allowed : 24.68 % Favored : 74.14 % 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: 2.93 (0.17), residues: 2640 helix: 3.29 (0.12), residues: 1664 sheet: 1.29 (0.43), residues: 216 loop : -1.14 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 329 HIS 0.002 0.000 HIS F 237 PHE 0.018 0.001 PHE F 40 TYR 0.014 0.001 TYR E 47 ARG 0.005 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.07389 ( 1378) hydrogen bonds : angle 3.41316 ( 4020) covalent geometry : bond 0.00291 (21616) covalent geometry : angle 0.64307 (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 170 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 2.361 Fit side-chains revert: symmetry clash REVERT: D 40 PHE cc_start: 0.9570 (m-80) cc_final: 0.9198 (m-80) REVERT: D 68 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.8898 (pmt) REVERT: D 256 MET cc_start: 0.9142 (tpp) cc_final: 0.8251 (mpt) REVERT: B 140 ASP cc_start: 0.9364 (t0) cc_final: 0.9058 (t0) REVERT: B 256 MET cc_start: 0.9073 (mpp) cc_final: 0.8603 (mpp) REVERT: B 318 ASP cc_start: 0.9310 (OUTLIER) cc_final: 0.8922 (t0) REVERT: C 68 MET cc_start: 0.9149 (pmm) cc_final: 0.8912 (pmm) REVERT: C 256 MET cc_start: 0.9305 (ppp) cc_final: 0.8500 (mtt) REVERT: G 23 PHE cc_start: 0.6511 (OUTLIER) cc_final: 0.6110 (p90) REVERT: G 36 MET cc_start: 0.8164 (pp-130) cc_final: 0.7670 (ppp) REVERT: G 42 LEU cc_start: 0.9327 (tm) cc_final: 0.8918 (pp) REVERT: G 68 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8950 (pmm) REVERT: A 42 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8828 (pp) REVERT: A 68 MET cc_start: 0.9212 (pmm) cc_final: 0.8945 (pmm) REVERT: F 140 ASP cc_start: 0.9372 (t0) cc_final: 0.9076 (t0) REVERT: F 256 MET cc_start: 0.9124 (mpp) cc_final: 0.8617 (mpp) REVERT: H 36 MET cc_start: 0.8212 (ppp) cc_final: 0.7943 (ppp) REVERT: H 40 PHE cc_start: 0.9581 (m-80) cc_final: 0.9143 (m-10) REVERT: H 256 MET cc_start: 0.9126 (tpp) cc_final: 0.8231 (mpt) REVERT: E 23 PHE cc_start: 0.4883 (OUTLIER) cc_final: 0.4638 (OUTLIER) REVERT: E 68 MET cc_start: 0.9131 (pmm) cc_final: 0.8865 (pmm) REVERT: E 344 ARG cc_start: 0.2735 (OUTLIER) cc_final: 0.2330 (tpm170) outliers start: 26 outliers final: 14 residues processed: 166 average time/residue: 1.5313 time to fit residues: 284.3349 Evaluate side-chains 165 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 MET 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 203 ILE 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 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 203 ILE Chi-restraints excluded: chain E residue 291 THR 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: 0.9990 chunk 228 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 227 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 154 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 chunk 139 optimal weight: 0.3980 chunk 94 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.075951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.047189 restraints weight = 92110.965| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 5.08 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3235 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= 0.145 Angle : 0.658 12.355 29256 Z= 0.309 Chirality : 0.036 0.151 3184 Planarity : 0.003 0.028 3832 Dihedral : 3.584 16.423 2952 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.36 % Allowed : 24.73 % Favored : 73.91 % 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: 2.94 (0.17), residues: 2640 helix: 3.29 (0.12), residues: 1668 sheet: 1.29 (0.43), residues: 216 loop : -1.15 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 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 0.006 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.07293 ( 1378) hydrogen bonds : angle 3.41434 ( 4020) covalent geometry : bond 0.00287 (21616) covalent geometry : angle 0.65798 (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 175 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 2.411 Fit side-chains revert: symmetry clash REVERT: D 40 PHE cc_start: 0.9545 (m-80) cc_final: 0.9146 (m-80) REVERT: D 68 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8908 (pmt) REVERT: D 256 MET cc_start: 0.9147 (tpp) cc_final: 0.8193 (mpt) REVERT: B 140 ASP cc_start: 0.9369 (t0) cc_final: 0.9093 (t0) REVERT: B 256 MET cc_start: 0.9097 (mpp) cc_final: 0.8600 (mpp) REVERT: C 68 MET cc_start: 0.9120 (pmm) cc_final: 0.8872 (pmm) REVERT: G 23 PHE cc_start: 0.6496 (OUTLIER) cc_final: 0.6095 (p90) REVERT: G 36 MET cc_start: 0.8246 (pp-130) cc_final: 0.7798 (ppp) REVERT: G 42 LEU cc_start: 0.9355 (tm) cc_final: 0.8961 (pp) REVERT: G 68 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8968 (pmm) REVERT: A 42 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8821 (pp) REVERT: A 68 MET cc_start: 0.9211 (pmm) cc_final: 0.8942 (pmm) REVERT: F 140 ASP cc_start: 0.9350 (t0) cc_final: 0.9060 (t0) REVERT: F 256 MET cc_start: 0.9119 (mpp) cc_final: 0.8615 (mpp) REVERT: H 36 MET cc_start: 0.8225 (ppp) cc_final: 0.7948 (ppp) REVERT: H 40 PHE cc_start: 0.9579 (m-80) cc_final: 0.9134 (m-10) REVERT: H 256 MET cc_start: 0.9113 (tpp) cc_final: 0.8223 (mpt) REVERT: E 23 PHE cc_start: 0.4979 (OUTLIER) cc_final: 0.4739 (OUTLIER) REVERT: E 68 MET cc_start: 0.9128 (pmm) cc_final: 0.8860 (pmm) REVERT: E 344 ARG cc_start: 0.2782 (OUTLIER) cc_final: 0.2396 (tpm170) outliers start: 30 outliers final: 17 residues processed: 170 average time/residue: 1.5423 time to fit residues: 297.1778 Evaluate side-chains 166 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 2.484 ------------------------------------------------------------------------------- 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 203 ILE 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 47 TYR 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 H residue 237 HIS Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 97 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: 6.9990 chunk 46 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 159 optimal weight: 0.9990 chunk 228 optimal weight: 0.7980 chunk 115 optimal weight: 0.0770 chunk 103 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 236 optimal weight: 0.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.075880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.047056 restraints weight = 92578.531| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 5.09 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21616 Z= 0.149 Angle : 0.677 12.777 29256 Z= 0.318 Chirality : 0.037 0.148 3184 Planarity : 0.003 0.030 3832 Dihedral : 3.612 17.497 2952 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.27 % Allowed : 24.77 % Favored : 73.95 % 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: 2.93 (0.17), residues: 2640 helix: 3.28 (0.12), residues: 1668 sheet: 1.27 (0.43), residues: 216 loop : -1.14 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 329 HIS 0.002 0.000 HIS F 237 PHE 0.018 0.001 PHE A 153 TYR 0.013 0.001 TYR E 47 ARG 0.011 0.000 ARG G 85 Details of bonding type rmsd hydrogen bonds : bond 0.07333 ( 1378) hydrogen bonds : angle 3.47146 ( 4020) covalent geometry : bond 0.00300 (21616) covalent geometry : angle 0.67693 (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: 28 poor density : 144 time to evaluate : 2.379 Fit side-chains revert: symmetry clash REVERT: D 40 PHE cc_start: 0.9536 (m-80) cc_final: 0.9142 (m-80) REVERT: D 68 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8899 (pmt) REVERT: D 256 MET cc_start: 0.9127 (tpp) cc_final: 0.8141 (mpt) REVERT: B 140 ASP cc_start: 0.9384 (t0) cc_final: 0.9095 (t0) REVERT: B 256 MET cc_start: 0.9102 (mpp) cc_final: 0.8659 (mpp) REVERT: C 68 MET cc_start: 0.9129 (pmm) cc_final: 0.8886 (pmm) REVERT: C 256 MET cc_start: 0.9260 (ppp) cc_final: 0.8409 (mtt) REVERT: G 23 PHE cc_start: 0.6505 (OUTLIER) cc_final: 0.6107 (p90) REVERT: G 36 MET cc_start: 0.8196 (pp-130) cc_final: 0.7740 (ppp) REVERT: G 42 LEU cc_start: 0.9348 (tm) cc_final: 0.8960 (pp) REVERT: G 68 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8952 (pmm) REVERT: A 42 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8816 (pp) REVERT: A 68 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8969 (pmm) REVERT: F 140 ASP cc_start: 0.9378 (t0) cc_final: 0.9096 (t0) REVERT: F 256 MET cc_start: 0.9150 (mpp) cc_final: 0.8645 (mpp) REVERT: H 36 MET cc_start: 0.8205 (ppp) cc_final: 0.7907 (ppp) REVERT: H 40 PHE cc_start: 0.9560 (m-80) cc_final: 0.9115 (m-10) REVERT: H 256 MET cc_start: 0.9084 (tpp) cc_final: 0.8233 (mpt) REVERT: E 23 PHE cc_start: 0.4959 (OUTLIER) cc_final: 0.4722 (OUTLIER) REVERT: E 68 MET cc_start: 0.9120 (pmm) cc_final: 0.8896 (pmm) REVERT: E 344 ARG cc_start: 0.2789 (OUTLIER) cc_final: 0.2387 (tpm170) outliers start: 28 outliers final: 14 residues processed: 166 average time/residue: 1.5812 time to fit residues: 294.0915 Evaluate side-chains 163 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain C residue 203 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 97 MET 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 68 MET 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 H residue 237 HIS Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 97 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 227 optimal weight: 0.9980 chunk 233 optimal weight: 0.0770 chunk 162 optimal weight: 9.9990 chunk 29 optimal weight: 0.0670 chunk 220 optimal weight: 0.0050 chunk 147 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 144 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 chunk 203 optimal weight: 1.9990 overall best weight: 0.3090 ------------------------------------------------------------------------------- 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 C 172 ASN G 172 ASN A 172 ASN F 75 GLN H 75 GLN E 172 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.077786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.049560 restraints weight = 93454.493| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 4.95 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21616 Z= 0.135 Angle : 0.686 12.676 29256 Z= 0.319 Chirality : 0.037 0.152 3184 Planarity : 0.003 0.093 3832 Dihedral : 3.533 17.287 2952 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.27 % Allowed : 24.82 % Favored : 73.91 % 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: 2.95 (0.17), residues: 2640 helix: 3.29 (0.12), residues: 1672 sheet: 1.37 (0.44), residues: 216 loop : -1.16 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 329 HIS 0.003 0.000 HIS F 237 PHE 0.033 0.001 PHE F 40 TYR 0.013 0.001 TYR E 47 ARG 0.009 0.000 ARG E 85 Details of bonding type rmsd hydrogen bonds : bond 0.06402 ( 1378) hydrogen bonds : angle 3.28053 ( 4020) covalent geometry : bond 0.00249 (21616) covalent geometry : angle 0.68590 (29256) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13276.58 seconds wall clock time: 229 minutes 17.26 seconds (13757.26 seconds total)