Starting phenix.real_space_refine on Sun Aug 24 16:25:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p3o_17387/08_2025/8p3o_17387.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p3o_17387/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8p3o_17387/08_2025/8p3o_17387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p3o_17387/08_2025/8p3o_17387.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p3o_17387/08_2025/8p3o_17387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p3o_17387/08_2025/8p3o_17387.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.84, per 1000 atoms: 0.18 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: 1.36 Conformation dependent library (CDL) restraints added in 619.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.41 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: 2.61 Time building geometry restraints manager: 1.74 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: 0.01 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: 6.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.510 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.930 ------------------------------------------------------------------------------- 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 : 7.05 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.009 0.000 ARG E 241 TYR 0.011 0.001 TYR G 124 PHE 0.028 0.001 PHE C 153 TRP 0.021 0.001 TRP A 329 HIS 0.002 0.000 HIS C 237 Details of bonding type rmsd covalent geometry : bond 0.00290 (21616) covalent geometry : angle 0.72072 (29256) hydrogen bonds : bond 0.28613 ( 1378) hydrogen bonds : angle 5.51194 ( 4020) *********************** 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 : 0.745 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: 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: 0.6870 time to fit residues: 132.9964 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 : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 50.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.074652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.045375 restraints weight = 92470.282| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 4.98 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 21616 Z= 0.210 Angle : 0.626 9.945 29256 Z= 0.330 Chirality : 0.039 0.189 3184 Planarity : 0.004 0.031 3832 Dihedral : 3.903 18.859 2952 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.27 % Allowed : 23.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.29 (0.17), residues: 2640 helix: 2.75 (0.12), residues: 1676 sheet: 1.08 (0.44), residues: 200 loop : -1.34 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 85 TYR 0.013 0.002 TYR G 47 PHE 0.020 0.002 PHE A 153 TRP 0.022 0.002 TRP H 32 HIS 0.002 0.001 HIS G 237 Details of bonding type rmsd covalent geometry : bond 0.00441 (21616) covalent geometry : angle 0.62646 (29256) hydrogen bonds : bond 0.10117 ( 1378) hydrogen bonds : angle 4.09591 ( 4020) *********************** 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 204 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 154 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: D 68 MET cc_start: 0.9172 (pmm) cc_final: 0.8893 (pmt) REVERT: D 256 MET cc_start: 0.9220 (mpp) cc_final: 0.8716 (mpp) REVERT: B 97 MET cc_start: 0.8802 (mpp) cc_final: 0.8595 (mpt) REVERT: B 140 ASP cc_start: 0.9412 (t0) cc_final: 0.9073 (t0) REVERT: B 256 MET cc_start: 0.8993 (mpp) cc_final: 0.8625 (mpp) REVERT: G 36 MET cc_start: 0.8496 (pp-130) cc_final: 0.8104 (ppp) REVERT: A 42 LEU cc_start: 0.9193 (tm) cc_final: 0.8823 (pp) REVERT: F 140 ASP cc_start: 0.9387 (t0) cc_final: 0.9096 (t0) REVERT: F 256 MET cc_start: 0.9090 (mpp) cc_final: 0.8773 (mpp) REVERT: H 36 MET cc_start: 0.8438 (ppp) cc_final: 0.8204 (ppp) REVERT: H 40 PHE cc_start: 0.9639 (m-80) cc_final: 0.9246 (m-10) REVERT: H 97 MET cc_start: 0.8784 (mpp) cc_final: 0.8502 (mpp) REVERT: H 256 MET cc_start: 0.9187 (mpp) cc_final: 0.8582 (mpp) REVERT: E 317 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8913 (ttp80) outliers start: 50 outliers final: 3 residues processed: 199 average time/residue: 0.7316 time to fit residues: 161.5691 Evaluate side-chains 150 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 146 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D 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 45 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 chunk 172 optimal weight: 20.0000 chunk 161 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.074607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.045287 restraints weight = 92794.295| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 5.10 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 21616 Z= 0.198 Angle : 0.605 14.838 29256 Z= 0.308 Chirality : 0.038 0.152 3184 Planarity : 0.003 0.038 3832 Dihedral : 3.851 18.488 2952 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.95 % Allowed : 23.32 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.17), residues: 2640 helix: 2.92 (0.12), residues: 1676 sheet: 0.92 (0.43), residues: 216 loop : -1.39 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 63 TYR 0.011 0.001 TYR G 47 PHE 0.020 0.001 PHE G 23 TRP 0.014 0.001 TRP E 111 HIS 0.003 0.000 HIS G 237 Details of bonding type rmsd covalent geometry : bond 0.00422 (21616) covalent geometry : angle 0.60516 (29256) hydrogen bonds : bond 0.09151 ( 1378) hydrogen bonds : angle 3.88316 ( 4020) *********************** 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 189 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 146 time to evaluate : 0.841 Fit side-chains REVERT: D 68 MET cc_start: 0.9204 (pmm) cc_final: 0.8989 (pmt) REVERT: D 256 MET cc_start: 0.9146 (mpp) cc_final: 0.8624 (mpp) REVERT: B 140 ASP cc_start: 0.9381 (t0) cc_final: 0.9094 (t0) REVERT: B 256 MET cc_start: 0.9012 (mpp) cc_final: 0.8548 (mpp) REVERT: G 36 MET cc_start: 0.8525 (pp-130) cc_final: 0.8156 (ppp) REVERT: G 291 THR cc_start: 0.9739 (OUTLIER) cc_final: 0.9526 (p) REVERT: A 42 LEU cc_start: 0.9284 (tm) cc_final: 0.8858 (pp) REVERT: F 140 ASP cc_start: 0.9377 (t0) cc_final: 0.9115 (t0) REVERT: F 256 MET cc_start: 0.9038 (mpp) cc_final: 0.8551 (mpp) REVERT: H 36 MET cc_start: 0.8479 (ppp) cc_final: 0.8154 (ppp) REVERT: H 40 PHE cc_start: 0.9652 (m-80) cc_final: 0.9254 (m-10) REVERT: H 256 MET cc_start: 0.9179 (mpp) cc_final: 0.8554 (mpp) outliers start: 43 outliers final: 9 residues processed: 187 average time/residue: 0.7441 time to fit residues: 155.1617 Evaluate side-chains 154 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D 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 291 THR 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 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 223 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 168 optimal weight: 8.9990 chunk 89 optimal weight: 0.0470 chunk 142 optimal weight: 3.9990 chunk 176 optimal weight: 0.0010 chunk 15 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 overall best weight: 0.7486 ------------------------------------------------------------------------------- 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 B 236 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 = 0.3780 r_free = 0.3780 target = 0.076183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.047299 restraints weight = 92656.945| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 5.11 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21616 Z= 0.144 Angle : 0.586 12.093 29256 Z= 0.288 Chirality : 0.036 0.148 3184 Planarity : 0.003 0.027 3832 Dihedral : 3.703 17.621 2952 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.41 % Allowed : 23.82 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.72 (0.17), residues: 2640 helix: 3.17 (0.12), residues: 1652 sheet: 1.23 (0.43), residues: 216 loop : -1.28 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 85 TYR 0.017 0.001 TYR E 47 PHE 0.013 0.001 PHE G 23 TRP 0.012 0.001 TRP E 111 HIS 0.001 0.000 HIS E 237 Details of bonding type rmsd covalent geometry : bond 0.00257 (21616) covalent geometry : angle 0.58553 (29256) hydrogen bonds : bond 0.07802 ( 1378) hydrogen bonds : angle 3.51194 ( 4020) *********************** 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 178 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.709 Fit side-chains REVERT: D 68 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8885 (pmt) REVERT: D 256 MET cc_start: 0.9138 (mpp) cc_final: 0.8580 (mpp) REVERT: B 140 ASP cc_start: 0.9376 (t0) cc_final: 0.9051 (t0) REVERT: B 256 MET cc_start: 0.9024 (mpp) cc_final: 0.8536 (mpp) REVERT: C 342 LEU cc_start: 0.4866 (OUTLIER) cc_final: 0.4503 (mm) REVERT: G 36 MET cc_start: 0.8351 (pp-130) cc_final: 0.7930 (ppp) REVERT: A 42 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8854 (pp) REVERT: F 140 ASP cc_start: 0.9361 (t0) cc_final: 0.9062 (t0) REVERT: F 256 MET cc_start: 0.9061 (mpp) cc_final: 0.8522 (mpp) REVERT: H 36 MET cc_start: 0.8347 (ppp) cc_final: 0.8043 (ppp) REVERT: H 40 PHE cc_start: 0.9633 (m-80) cc_final: 0.9202 (m-10) REVERT: H 256 MET cc_start: 0.9199 (mpp) cc_final: 0.8632 (mpp) REVERT: E 23 PHE cc_start: 0.4849 (OUTLIER) cc_final: 0.4643 (OUTLIER) outliers start: 31 outliers final: 6 residues processed: 176 average time/residue: 0.7012 time to fit residues: 138.0283 Evaluate side-chains 153 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 MET 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 A residue 42 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 207 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 245 optimal weight: 0.0030 chunk 124 optimal weight: 0.9980 chunk 231 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 overall best weight: 1.7994 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.075071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.046085 restraints weight = 92858.901| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 4.93 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2734 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= 0.176 Angle : 0.603 9.939 29256 Z= 0.297 Chirality : 0.037 0.149 3184 Planarity : 0.003 0.026 3832 Dihedral : 3.676 16.815 2952 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.05 % Allowed : 24.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.84 (0.17), residues: 2640 helix: 3.33 (0.12), residues: 1628 sheet: 1.16 (0.43), residues: 216 loop : -1.23 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 85 TYR 0.015 0.001 TYR E 47 PHE 0.019 0.001 PHE A 153 TRP 0.012 0.001 TRP B 111 HIS 0.002 0.000 HIS E 237 Details of bonding type rmsd covalent geometry : bond 0.00370 (21616) covalent geometry : angle 0.60278 (29256) hydrogen bonds : bond 0.08202 ( 1378) hydrogen bonds : angle 3.60787 ( 4020) *********************** 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 169 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.833 Fit side-chains REVERT: D 40 PHE cc_start: 0.9592 (m-80) cc_final: 0.9226 (m-80) REVERT: D 68 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8879 (pmt) REVERT: D 256 MET cc_start: 0.9153 (mpp) cc_final: 0.8576 (mpp) REVERT: B 140 ASP cc_start: 0.9390 (t0) cc_final: 0.9101 (t0) REVERT: B 256 MET cc_start: 0.8990 (mpp) cc_final: 0.8454 (mpp) REVERT: C 342 LEU cc_start: 0.4776 (OUTLIER) cc_final: 0.4405 (mm) REVERT: G 36 MET cc_start: 0.8234 (pp-130) cc_final: 0.7774 (ppp) REVERT: G 68 MET cc_start: 0.9134 (pmm) cc_final: 0.8770 (pmt) REVERT: A 42 LEU cc_start: 0.9273 (tm) cc_final: 0.8840 (pp) REVERT: F 140 ASP cc_start: 0.9389 (t0) cc_final: 0.9112 (t0) REVERT: F 256 MET cc_start: 0.9084 (mpp) cc_final: 0.8550 (mpp) REVERT: H 36 MET cc_start: 0.8261 (ppp) cc_final: 0.7994 (ppp) REVERT: H 40 PHE cc_start: 0.9603 (m-80) cc_final: 0.9159 (m-10) REVERT: H 256 MET cc_start: 0.9215 (mpp) cc_final: 0.8597 (mpp) REVERT: E 23 PHE cc_start: 0.4803 (OUTLIER) cc_final: 0.4586 (OUTLIER) REVERT: E 68 MET cc_start: 0.9139 (pmm) cc_final: 0.8773 (pmt) outliers start: 23 outliers final: 6 residues processed: 167 average time/residue: 0.6989 time to fit residues: 130.0208 Evaluate side-chains 153 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 MET 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 167 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 50.0000 chunk 119 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 238 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 chunk 159 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.075948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.047076 restraints weight = 93020.170| |-----------------------------------------------------------------------------| 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: 0.8662 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21616 Z= 0.144 Angle : 0.593 9.264 29256 Z= 0.288 Chirality : 0.036 0.148 3184 Planarity : 0.003 0.027 3832 Dihedral : 3.609 16.696 2952 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.55 % Allowed : 23.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.91 (0.17), residues: 2640 helix: 3.38 (0.12), residues: 1640 sheet: 1.25 (0.43), residues: 216 loop : -1.28 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 85 TYR 0.016 0.001 TYR E 47 PHE 0.012 0.001 PHE F 40 TRP 0.011 0.001 TRP G 111 HIS 0.002 0.000 HIS C 237 Details of bonding type rmsd covalent geometry : bond 0.00276 (21616) covalent geometry : angle 0.59251 (29256) hydrogen bonds : bond 0.07550 ( 1378) hydrogen bonds : angle 3.42667 ( 4020) *********************** 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 181 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.837 Fit side-chains REVERT: D 40 PHE cc_start: 0.9587 (m-80) cc_final: 0.9212 (m-80) REVERT: D 68 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8900 (pmt) REVERT: D 237 HIS cc_start: 0.7781 (OUTLIER) cc_final: 0.7508 (m90) REVERT: D 256 MET cc_start: 0.9156 (mpp) cc_final: 0.8546 (mpp) REVERT: B 140 ASP cc_start: 0.9364 (t0) cc_final: 0.9054 (t0) REVERT: B 237 HIS cc_start: 0.7744 (OUTLIER) cc_final: 0.7448 (m90) REVERT: B 256 MET cc_start: 0.9052 (mpp) cc_final: 0.8575 (mpp) REVERT: C 342 LEU cc_start: 0.4858 (OUTLIER) cc_final: 0.4491 (mm) REVERT: G 36 MET cc_start: 0.8265 (pp-130) cc_final: 0.7805 (ppp) REVERT: G 42 LEU cc_start: 0.9347 (tm) cc_final: 0.8933 (pp) REVERT: G 68 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8903 (pmm) REVERT: A 42 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8846 (pp) REVERT: F 140 ASP cc_start: 0.9363 (t0) cc_final: 0.9064 (t0) REVERT: F 256 MET cc_start: 0.9098 (mpp) cc_final: 0.8549 (mpp) REVERT: H 36 MET cc_start: 0.8264 (ppp) cc_final: 0.7941 (ppp) REVERT: H 40 PHE cc_start: 0.9612 (m-80) cc_final: 0.9174 (m-10) REVERT: H 237 HIS cc_start: 0.7743 (OUTLIER) cc_final: 0.7443 (m90) REVERT: H 256 MET cc_start: 0.9181 (mpp) cc_final: 0.8573 (mpp) REVERT: E 23 PHE cc_start: 0.4855 (OUTLIER) cc_final: 0.4630 (OUTLIER) REVERT: E 68 MET cc_start: 0.9147 (pmm) cc_final: 0.8887 (pmm) outliers start: 34 outliers final: 11 residues processed: 176 average time/residue: 0.6229 time to fit residues: 122.7882 Evaluate side-chains 162 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 227 ILE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 227 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 291 THR Chi-restraints excluded: chain E residue 342 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 119 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 207 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 195 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 GLN B 75 GLN F 75 GLN H 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.074684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.045684 restraints weight = 92978.307| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 4.89 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 21616 Z= 0.195 Angle : 0.640 11.192 29256 Z= 0.311 Chirality : 0.038 0.149 3184 Planarity : 0.003 0.026 3832 Dihedral : 3.689 15.544 2952 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.50 % Allowed : 24.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.81 (0.17), residues: 2640 helix: 3.29 (0.12), residues: 1664 sheet: 1.08 (0.43), residues: 216 loop : -1.38 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 85 TYR 0.015 0.001 TYR E 47 PHE 0.016 0.001 PHE G 153 TRP 0.023 0.001 TRP C 329 HIS 0.003 0.001 HIS C 237 Details of bonding type rmsd covalent geometry : bond 0.00426 (21616) covalent geometry : angle 0.63956 (29256) hydrogen bonds : bond 0.08251 ( 1378) hydrogen bonds : angle 3.63779 ( 4020) *********************** 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 180 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.893 Fit side-chains REVERT: D 40 PHE cc_start: 0.9562 (m-80) cc_final: 0.9177 (m-80) REVERT: D 68 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8943 (pmm) REVERT: D 237 HIS cc_start: 0.7908 (OUTLIER) cc_final: 0.7650 (m90) REVERT: D 256 MET cc_start: 0.9149 (tpp) cc_final: 0.8224 (mpt) REVERT: B 140 ASP cc_start: 0.9387 (t0) cc_final: 0.9123 (t0) REVERT: B 237 HIS cc_start: 0.7714 (OUTLIER) cc_final: 0.7445 (m90) REVERT: B 256 MET cc_start: 0.9034 (mpp) cc_final: 0.8569 (mpp) REVERT: C 68 MET cc_start: 0.9139 (pmm) cc_final: 0.8771 (pmt) REVERT: C 342 LEU cc_start: 0.4749 (OUTLIER) cc_final: 0.4378 (mm) REVERT: G 23 PHE cc_start: 0.6483 (OUTLIER) cc_final: 0.6095 (p90) REVERT: G 36 MET cc_start: 0.8147 (pp-130) cc_final: 0.7653 (ppp) REVERT: A 42 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8824 (pp) REVERT: F 140 ASP cc_start: 0.9386 (t0) cc_final: 0.9121 (t0) REVERT: F 256 MET cc_start: 0.9121 (mpp) cc_final: 0.8666 (mpp) REVERT: H 36 MET cc_start: 0.8201 (ppp) cc_final: 0.7926 (ppp) REVERT: H 40 PHE cc_start: 0.9577 (m-80) cc_final: 0.9123 (m-10) REVERT: H 237 HIS cc_start: 0.7828 (OUTLIER) cc_final: 0.7532 (m90) REVERT: H 256 MET cc_start: 0.9205 (tpp) cc_final: 0.8255 (mpt) REVERT: E 23 PHE cc_start: 0.4892 (OUTLIER) cc_final: 0.4657 (OUTLIER) REVERT: E 40 PHE cc_start: 0.9477 (t80) cc_final: 0.9277 (t80) REVERT: E 68 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.8943 (pmm) REVERT: E 344 ARG cc_start: 0.2999 (OUTLIER) cc_final: 0.2555 (tpm170) outliers start: 33 outliers final: 13 residues processed: 176 average time/residue: 0.7034 time to fit residues: 138.4453 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 : 0.853 ------------------------------------------------------------------------------- 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 263 MET Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain G residue 23 PHE Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain H residue 237 HIS Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 227 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 103 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 chunk 232 optimal weight: 0.9980 chunk 250 optimal weight: 0.0000 chunk 239 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 241 optimal weight: 0.9980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.076159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.047352 restraints weight = 92877.016| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 5.10 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21616 Z= 0.141 Angle : 0.643 11.618 29256 Z= 0.304 Chirality : 0.037 0.161 3184 Planarity : 0.003 0.030 3832 Dihedral : 3.624 15.908 2952 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.32 % Allowed : 24.41 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.95 (0.17), residues: 2640 helix: 3.43 (0.12), residues: 1640 sheet: 1.22 (0.43), residues: 216 loop : -1.27 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 85 TYR 0.015 0.001 TYR E 47 PHE 0.035 0.001 PHE F 40 TRP 0.016 0.001 TRP C 329 HIS 0.001 0.000 HIS F 237 Details of bonding type rmsd covalent geometry : bond 0.00263 (21616) covalent geometry : angle 0.64269 (29256) hydrogen bonds : bond 0.07334 ( 1378) hydrogen bonds : angle 3.37896 ( 4020) *********************** 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 173 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: D 40 PHE cc_start: 0.9535 (m-80) cc_final: 0.9157 (m-80) REVERT: D 68 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8908 (pmt) REVERT: D 256 MET cc_start: 0.9130 (tpp) cc_final: 0.8244 (mpt) REVERT: B 140 ASP cc_start: 0.9355 (t0) cc_final: 0.9069 (t0) REVERT: B 256 MET cc_start: 0.9081 (mpp) cc_final: 0.8626 (mpp) REVERT: C 68 MET cc_start: 0.9149 (pmm) cc_final: 0.8944 (pmm) REVERT: C 342 LEU cc_start: 0.4865 (OUTLIER) cc_final: 0.4509 (mm) REVERT: G 23 PHE cc_start: 0.6470 (OUTLIER) cc_final: 0.6067 (p90) REVERT: G 36 MET cc_start: 0.8233 (pp-130) cc_final: 0.7768 (ppp) REVERT: G 42 LEU cc_start: 0.9335 (tm) cc_final: 0.8916 (pp) REVERT: G 68 MET cc_start: 0.9135 (pmm) cc_final: 0.8768 (pmt) REVERT: A 42 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8817 (pp) REVERT: A 256 MET cc_start: 0.9298 (ppp) cc_final: 0.8458 (mtt) REVERT: F 140 ASP cc_start: 0.9358 (t0) cc_final: 0.9061 (t0) REVERT: F 256 MET cc_start: 0.9107 (mpp) cc_final: 0.8631 (mpp) REVERT: H 36 MET cc_start: 0.8267 (ppp) cc_final: 0.7975 (ppp) REVERT: H 40 PHE cc_start: 0.9582 (m-80) cc_final: 0.9140 (m-10) REVERT: H 256 MET cc_start: 0.9139 (tpp) cc_final: 0.8263 (mpt) REVERT: E 23 PHE cc_start: 0.4948 (OUTLIER) cc_final: 0.4709 (OUTLIER) REVERT: E 68 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8890 (pmm) REVERT: E 344 ARG cc_start: 0.2817 (OUTLIER) cc_final: 0.2442 (tpm170) outliers start: 29 outliers final: 17 residues processed: 169 average time/residue: 0.6496 time to fit residues: 122.8677 Evaluate side-chains 165 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain G residue 23 PHE Chi-restraints excluded: chain G residue 47 TYR Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain H residue 237 HIS Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 97 MET 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 15 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 154 optimal weight: 8.9990 chunk 130 optimal weight: 8.9990 chunk 115 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 184 optimal weight: 0.9990 chunk 231 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.074882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.045899 restraints weight = 92358.382| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 4.94 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 21616 Z= 0.186 Angle : 0.682 12.540 29256 Z= 0.324 Chirality : 0.038 0.152 3184 Planarity : 0.003 0.029 3832 Dihedral : 3.680 15.248 2952 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.27 % Allowed : 24.41 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.82 (0.17), residues: 2640 helix: 3.30 (0.12), residues: 1664 sheet: 1.07 (0.43), residues: 216 loop : -1.39 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 85 TYR 0.013 0.001 TYR E 47 PHE 0.017 0.001 PHE A 153 TRP 0.013 0.001 TRP F 111 HIS 0.002 0.000 HIS C 237 Details of bonding type rmsd covalent geometry : bond 0.00404 (21616) covalent geometry : angle 0.68154 (29256) hydrogen bonds : bond 0.08043 ( 1378) hydrogen bonds : angle 3.60517 ( 4020) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.875 Fit side-chains REVERT: D 40 PHE cc_start: 0.9517 (m-80) cc_final: 0.9114 (m-80) REVERT: D 68 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8938 (pmm) REVERT: D 256 MET cc_start: 0.9089 (tpp) cc_final: 0.8109 (mpt) REVERT: B 140 ASP cc_start: 0.9394 (t0) cc_final: 0.9123 (t0) REVERT: B 256 MET cc_start: 0.9079 (mpp) cc_final: 0.8627 (mpp) REVERT: C 68 MET cc_start: 0.9131 (pmm) cc_final: 0.8794 (pmt) REVERT: C 256 MET cc_start: 0.9260 (ppp) cc_final: 0.8432 (mtt) REVERT: G 23 PHE cc_start: 0.6474 (OUTLIER) cc_final: 0.6084 (p90) REVERT: G 36 MET cc_start: 0.8148 (pp-130) cc_final: 0.7656 (ppp) REVERT: G 42 LEU cc_start: 0.9358 (tm) cc_final: 0.8956 (pp) REVERT: A 42 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8823 (pp) REVERT: F 140 ASP cc_start: 0.9389 (t0) cc_final: 0.9129 (t0) REVERT: F 256 MET cc_start: 0.9110 (mpp) cc_final: 0.8655 (mpp) REVERT: H 36 MET cc_start: 0.8187 (ppp) cc_final: 0.7899 (ppp) REVERT: H 40 PHE cc_start: 0.9553 (m-80) cc_final: 0.9093 (m-10) REVERT: H 256 MET cc_start: 0.9129 (tpp) cc_final: 0.8187 (mpt) REVERT: E 23 PHE cc_start: 0.4896 (OUTLIER) cc_final: 0.4661 (OUTLIER) REVERT: E 40 PHE cc_start: 0.9493 (t80) cc_final: 0.9291 (t80) REVERT: E 68 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8930 (pmm) REVERT: E 344 ARG cc_start: 0.2944 (OUTLIER) cc_final: 0.2474 (tpm170) outliers start: 28 outliers final: 14 residues processed: 168 average time/residue: 0.6726 time to fit residues: 126.3179 Evaluate side-chains 163 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 237 HIS Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain G residue 23 PHE Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain F residue 226 SER 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 68 MET Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 344 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 70 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 212 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 141 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 200 optimal weight: 8.9990 chunk 150 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.075219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.046299 restraints weight = 92681.246| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 4.95 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21616 Z= 0.165 Angle : 0.683 12.781 29256 Z= 0.324 Chirality : 0.037 0.157 3184 Planarity : 0.003 0.058 3832 Dihedral : 3.693 18.602 2952 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.36 % Allowed : 24.36 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.87 (0.17), residues: 2640 helix: 3.31 (0.12), residues: 1648 sheet: 1.10 (0.43), residues: 216 loop : -1.20 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 261 TYR 0.013 0.001 TYR E 47 PHE 0.034 0.001 PHE F 40 TRP 0.013 0.001 TRP C 329 HIS 0.001 0.000 HIS G 237 Details of bonding type rmsd covalent geometry : bond 0.00343 (21616) covalent geometry : angle 0.68274 (29256) hydrogen bonds : bond 0.07809 ( 1378) hydrogen bonds : angle 3.56577 ( 4020) ********************** 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 173 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: D 40 PHE cc_start: 0.9493 (m-80) cc_final: 0.9073 (m-80) REVERT: D 68 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8895 (pmt) REVERT: D 256 MET cc_start: 0.9084 (tpp) cc_final: 0.8119 (mpt) REVERT: B 140 ASP cc_start: 0.9388 (t0) cc_final: 0.9106 (t0) REVERT: B 256 MET cc_start: 0.9117 (mpp) cc_final: 0.8630 (mpp) REVERT: C 68 MET cc_start: 0.9127 (pmm) cc_final: 0.8781 (pmt) REVERT: G 23 PHE cc_start: 0.6497 (OUTLIER) cc_final: 0.6112 (p90) REVERT: G 36 MET cc_start: 0.8187 (pp-130) cc_final: 0.7728 (ppp) REVERT: A 42 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8801 (pp) REVERT: A 256 MET cc_start: 0.9267 (ppp) cc_final: 0.8415 (mtt) REVERT: F 140 ASP cc_start: 0.9381 (t0) cc_final: 0.9094 (t0) REVERT: F 256 MET cc_start: 0.9137 (mpp) cc_final: 0.8662 (mpp) REVERT: H 36 MET cc_start: 0.8232 (ppp) cc_final: 0.7924 (ppp) REVERT: H 40 PHE cc_start: 0.9566 (m-80) cc_final: 0.9093 (m-10) REVERT: H 256 MET cc_start: 0.9132 (tpp) cc_final: 0.8173 (mpt) REVERT: E 23 PHE cc_start: 0.4988 (OUTLIER) cc_final: 0.4752 (OUTLIER) REVERT: E 68 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8938 (pmm) REVERT: E 344 ARG cc_start: 0.2914 (OUTLIER) cc_final: 0.2461 (tpm170) outliers start: 30 outliers final: 15 residues processed: 169 average time/residue: 0.6388 time to fit residues: 120.8318 Evaluate side-chains 161 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 237 HIS Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain G residue 23 PHE Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain F residue 226 SER 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 68 MET Chi-restraints excluded: chain E residue 227 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.6245 > 50: distance: 8 - 13: 11.756 distance: 13 - 14: 26.175 distance: 14 - 15: 14.950 distance: 14 - 17: 48.608 distance: 15 - 16: 40.181 distance: 15 - 20: 20.696 distance: 17 - 18: 33.685 distance: 17 - 19: 36.303 distance: 20 - 21: 15.360 distance: 21 - 22: 19.290 distance: 21 - 24: 51.271 distance: 22 - 23: 35.775 distance: 22 - 28: 21.256 distance: 24 - 25: 17.951 distance: 25 - 26: 28.723 distance: 25 - 27: 22.096 distance: 28 - 29: 19.939 distance: 29 - 30: 42.733 distance: 29 - 32: 9.408 distance: 30 - 31: 49.011 distance: 30 - 36: 51.083 distance: 32 - 33: 40.003 distance: 33 - 34: 47.781 distance: 34 - 35: 28.506 distance: 36 - 37: 44.178 distance: 37 - 38: 19.655 distance: 37 - 40: 14.173 distance: 38 - 39: 50.123 distance: 38 - 44: 29.643 distance: 40 - 41: 48.512 distance: 41 - 42: 36.855 distance: 41 - 43: 46.583 distance: 45 - 46: 68.624 distance: 46 - 48: 31.411 distance: 48 - 49: 41.437 distance: 49 - 50: 19.650 distance: 50 - 51: 41.011 distance: 50 - 52: 13.038 distance: 52 - 53: 13.297 distance: 53 - 54: 33.716 distance: 53 - 56: 15.569 distance: 54 - 55: 17.206 distance: 54 - 64: 36.978 distance: 55 - 91: 23.918 distance: 56 - 57: 21.070 distance: 57 - 58: 16.586 distance: 57 - 59: 25.958 distance: 58 - 60: 37.317 distance: 59 - 61: 16.384 distance: 60 - 62: 19.791 distance: 61 - 62: 15.177 distance: 62 - 63: 25.718 distance: 65 - 66: 45.237 distance: 66 - 67: 32.358 distance: 66 - 76: 32.759 distance: 67 - 99: 27.239 distance: 68 - 69: 35.675 distance: 69 - 70: 40.817 distance: 69 - 71: 41.027 distance: 70 - 72: 31.164 distance: 71 - 73: 11.778 distance: 72 - 74: 21.541 distance: 73 - 74: 26.046 distance: 74 - 75: 25.884 distance: 76 - 77: 20.124 distance: 77 - 78: 4.080 distance: 77 - 80: 50.213 distance: 78 - 79: 15.217 distance: 78 - 82: 51.591 distance: 79 - 107: 22.815 distance: 80 - 81: 40.058 distance: 82 - 83: 34.048 distance: 83 - 84: 33.789 distance: 83 - 86: 56.247 distance: 84 - 85: 48.524 distance: 84 - 91: 23.924 distance: 85 - 114: 31.544 distance: 86 - 87: 39.715 distance: 87 - 88: 48.117 distance: 88 - 89: 19.619 distance: 88 - 90: 13.602 distance: 179 - 190: 3.053