Starting phenix.real_space_refine on Thu Aug 6 11:37:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oa8_70275/08_2026/9oa8_70275.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oa8_70275/08_2026/9oa8_70275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oa8_70275/08_2026/9oa8_70275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oa8_70275/08_2026/9oa8_70275.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oa8_70275/08_2026/9oa8_70275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oa8_70275/08_2026/9oa8_70275.map" } resolution = 3.59 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= 0.000 sd= 1.000 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: 7 Type Number sf(0) Gaussians Ca 8 9.91 5 K 3 8.98 5 S 104 5.16 5 Cl 8 4.86 5 C 9753 2.51 5 N 2713 2.21 5 O 2666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15255 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2758 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 2, 'GLU:plan': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2754 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 3, 'GLU:plan': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2754 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 3, 'GLU:plan': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2754 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 3, 'GLU:plan': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 60 Chain: "E" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1042 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "F" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1042 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "G" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1042 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "H" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1042 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' CA': 2, '1KP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' CA': 2, '1KP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' CA': 2, '1KP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' CA': 2, '1KP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.56, per 1000 atoms: 0.23 Number of scatterers: 15255 At special positions: 0 Unit cell: (141.04, 141.9, 106.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 8 19.99 K 3 19.00 Cl 8 17.00 S 104 16.00 O 2666 8.00 N 2713 7.00 C 9753 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: 1.26 Conformation dependent library (CDL) restraints added in 673.7 milliseconds 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3760 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 0 sheets defined 75.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 10 through 49 removed outlier: 4.086A pdb=" N LYS A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU A 32 " --> pdb=" O TRP A 28 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA A 33 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N MET A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL A 41 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 42 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N HIS A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 71 removed outlier: 3.815A pdb=" N VAL A 61 " --> pdb=" O TYR A 57 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER A 66 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 67 " --> pdb=" O CYS A 63 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 71 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 92 removed outlier: 4.029A pdb=" N VAL A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 115 removed outlier: 4.007A pdb=" N ALA A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 155 Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.894A pdb=" N ARG A 159 " --> pdb=" O MET A 156 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU A 160 " --> pdb=" O LEU A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 156 through 160' Processing helix chain 'A' and resid 161 through 172 removed outlier: 4.581A pdb=" N ARG A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLY A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 186 removed outlier: 3.577A pdb=" N ASN A 186 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 203 removed outlier: 3.831A pdb=" N VAL A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 212 removed outlier: 3.959A pdb=" N LEU A 207 " --> pdb=" O HIS A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 226 removed outlier: 3.662A pdb=" N ALA A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 249 removed outlier: 3.821A pdb=" N LEU A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TRP A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) Proline residue: A 245 - end of helix Processing helix chain 'A' and resid 265 through 289 removed outlier: 3.747A pdb=" N CYS A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 330 removed outlier: 3.541A pdb=" N GLN A 306 " --> pdb=" O MET A 302 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS A 309 " --> pdb=" O ILE A 305 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 368 removed outlier: 3.552A pdb=" N ALA A 346 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 386 Processing helix chain 'B' and resid 10 through 50 removed outlier: 4.227A pdb=" N LYS B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG B 17 " --> pdb=" O ARG B 13 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU B 18 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU B 20 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU B 32 " --> pdb=" O TRP B 28 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA B 33 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET B 40 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL B 41 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 42 " --> pdb=" O GLY B 38 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N HIS B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 81 removed outlier: 3.833A pdb=" N VAL B 61 " --> pdb=" O TYR B 57 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS B 63 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE B 65 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER B 66 " --> pdb=" O LYS B 62 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE B 67 " --> pdb=" O CYS B 63 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR B 69 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 71 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU B 72 " --> pdb=" O SER B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.518A pdb=" N PHE B 87 " --> pdb=" O GLU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 100 removed outlier: 4.259A pdb=" N ALA B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU B 100 " --> pdb=" O TRP B 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 95 through 100' Processing helix chain 'B' and resid 101 through 115 removed outlier: 4.008A pdb=" N ALA B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 155 Processing helix chain 'B' and resid 156 through 160 removed outlier: 3.940A pdb=" N ARG B 159 " --> pdb=" O MET B 156 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU B 160 " --> pdb=" O LEU B 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 156 through 160' Processing helix chain 'B' and resid 161 through 169 removed outlier: 4.518A pdb=" N ARG B 165 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 191 through 203 removed outlier: 3.551A pdb=" N VAL B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS B 203 " --> pdb=" O TYR B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 219 removed outlier: 3.648A pdb=" N LEU B 207 " --> pdb=" O HIS B 203 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 227 removed outlier: 3.508A pdb=" N ALA B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 249 removed outlier: 3.537A pdb=" N THR B 240 " --> pdb=" O HIS B 236 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N TRP B 242 " --> pdb=" O SER B 238 " (cutoff:3.500A) Proline residue: B 245 - end of helix Processing helix chain 'B' and resid 265 through 289 removed outlier: 3.707A pdb=" N CYS B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B 279 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 331 removed outlier: 3.968A pdb=" N ILE B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA B 316 " --> pdb=" O LYS B 312 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 369 removed outlier: 3.566A pdb=" N ALA B 346 " --> pdb=" O ARG B 342 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASN B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 361 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL B 369 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 386 Processing helix chain 'C' and resid 10 through 28 removed outlier: 3.580A pdb=" N LYS C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C 24 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 49 Processing helix chain 'C' and resid 60 through 92 removed outlier: 3.967A pdb=" N ILE C 65 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N SER C 66 " --> pdb=" O LYS C 62 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE C 67 " --> pdb=" O CYS C 63 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR C 69 " --> pdb=" O ILE C 65 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS C 80 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA C 81 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU C 83 " --> pdb=" O PHE C 79 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL C 84 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 115 removed outlier: 3.940A pdb=" N ALA C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA C 106 " --> pdb=" O GLY C 102 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 155 Processing helix chain 'C' and resid 156 through 160 removed outlier: 3.907A pdb=" N ARG C 159 " --> pdb=" O MET C 156 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU C 160 " --> pdb=" O LEU C 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 156 through 160' Processing helix chain 'C' and resid 161 through 168 removed outlier: 4.574A pdb=" N ARG C 165 " --> pdb=" O TYR C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'C' and resid 184 through 186 No H-bonds generated for 'chain 'C' and resid 184 through 186' Processing helix chain 'C' and resid 191 through 203 removed outlier: 3.535A pdb=" N VAL C 195 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS C 203 " --> pdb=" O TYR C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.836A pdb=" N LEU C 207 " --> pdb=" O HIS C 203 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU C 208 " --> pdb=" O PRO C 204 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 209 " --> pdb=" O GLY C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 227 removed outlier: 3.574A pdb=" N GLU C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 249 removed outlier: 3.542A pdb=" N THR C 240 " --> pdb=" O HIS C 236 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N TRP C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) Proline residue: C 245 - end of helix Processing helix chain 'C' and resid 260 through 289 removed outlier: 3.691A pdb=" N LYS C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE C 265 " --> pdb=" O MET C 261 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N CYS C 276 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA C 279 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU C 289 " --> pdb=" O VAL C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 328 removed outlier: 3.653A pdb=" N GLN C 306 " --> pdb=" O MET C 302 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS C 309 " --> pdb=" O ILE C 305 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS C 312 " --> pdb=" O THR C 308 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA C 316 " --> pdb=" O LYS C 312 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG C 317 " --> pdb=" O GLU C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 367 removed outlier: 3.664A pdb=" N ARG C 352 " --> pdb=" O ILE C 348 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN C 353 " --> pdb=" O ASN C 349 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 386 Processing helix chain 'D' and resid 10 through 26 removed outlier: 3.538A pdb=" N SER D 24 " --> pdb=" O GLU D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 50 removed outlier: 4.116A pdb=" N VAL D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU D 32 " --> pdb=" O TRP D 28 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA D 33 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N MET D 40 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL D 41 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU D 42 " --> pdb=" O GLY D 38 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N HIS D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 68 removed outlier: 3.710A pdb=" N ILE D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER D 66 " --> pdb=" O LYS D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 92 Processing helix chain 'D' and resid 95 through 100 removed outlier: 4.170A pdb=" N ALA D 99 " --> pdb=" O ASP D 95 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU D 100 " --> pdb=" O TRP D 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 95 through 100' Processing helix chain 'D' and resid 103 through 115 Processing helix chain 'D' and resid 146 through 155 Processing helix chain 'D' and resid 156 through 160 removed outlier: 3.928A pdb=" N ARG D 159 " --> pdb=" O MET D 156 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU D 160 " --> pdb=" O LEU D 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 156 through 160' Processing helix chain 'D' and resid 161 through 169 removed outlier: 4.544A pdb=" N ARG D 165 " --> pdb=" O TYR D 161 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 185 removed outlier: 3.553A pdb=" N ALA D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU D 185 " --> pdb=" O SER D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 203 removed outlier: 3.550A pdb=" N VAL D 195 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS D 203 " --> pdb=" O TYR D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 227 removed outlier: 3.816A pdb=" N LEU D 207 " --> pdb=" O HIS D 203 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR D 219 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA D 220 " --> pdb=" O TRP D 216 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TRP D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL D 222 " --> pdb=" O THR D 218 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER D 224 " --> pdb=" O ALA D 220 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU D 227 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 249 removed outlier: 3.938A pdb=" N LEU D 241 " --> pdb=" O LEU D 237 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TRP D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) Proline residue: D 245 - end of helix Processing helix chain 'D' and resid 260 through 289 removed outlier: 3.864A pdb=" N LYS D 264 " --> pdb=" O THR D 260 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE D 265 " --> pdb=" O MET D 261 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL D 266 " --> pdb=" O TRP D 262 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ALA D 279 " --> pdb=" O VAL D 275 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU D 280 " --> pdb=" O CYS D 276 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU D 281 " --> pdb=" O CYS D 277 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU D 289 " --> pdb=" O VAL D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 330 removed outlier: 4.017A pdb=" N ILE D 305 " --> pdb=" O PHE D 301 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG D 317 " --> pdb=" O GLU D 313 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA D 322 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TRP D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 369 removed outlier: 3.604A pdb=" N LEU D 345 " --> pdb=" O GLN D 341 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA D 346 " --> pdb=" O ARG D 342 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER D 367 " --> pdb=" O GLU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 Processing helix chain 'E' and resid 5 through 20 removed outlier: 3.501A pdb=" N ILE E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU E 18 " --> pdb=" O GLU E 14 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 40 removed outlier: 3.524A pdb=" N LEU E 32 " --> pdb=" O THR E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 54 Processing helix chain 'E' and resid 64 through 76 removed outlier: 4.112A pdb=" N THR E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N MET E 71 " --> pdb=" O GLU E 67 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG E 74 " --> pdb=" O THR E 70 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS E 75 " --> pdb=" O MET E 71 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET E 76 " --> pdb=" O MET E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 91 removed outlier: 3.648A pdb=" N ALA E 88 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE E 89 " --> pdb=" O ILE E 85 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG E 90 " --> pdb=" O ARG E 86 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL E 91 " --> pdb=" O GLU E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 110 Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 137 through 147 Processing helix chain 'F' and resid 5 through 20 removed outlier: 3.761A pdb=" N PHE F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 39 removed outlier: 3.669A pdb=" N LEU F 32 " --> pdb=" O THR F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 56 removed outlier: 4.060A pdb=" N VAL F 55 " --> pdb=" O MET F 51 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP F 56 " --> pdb=" O ILE F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 76 removed outlier: 3.874A pdb=" N THR F 70 " --> pdb=" O PRO F 66 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG F 74 " --> pdb=" O THR F 70 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS F 75 " --> pdb=" O MET F 71 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET F 76 " --> pdb=" O MET F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 87 Processing helix chain 'F' and resid 101 through 109 removed outlier: 4.037A pdb=" N LEU F 105 " --> pdb=" O SER F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 129 Processing helix chain 'F' and resid 137 through 146 removed outlier: 3.738A pdb=" N MET F 145 " --> pdb=" O PHE F 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 20 removed outlier: 3.653A pdb=" N PHE G 19 " --> pdb=" O ALA G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 39 removed outlier: 3.603A pdb=" N LEU G 32 " --> pdb=" O THR G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 54 Processing helix chain 'G' and resid 64 through 73 removed outlier: 3.930A pdb=" N THR G 70 " --> pdb=" O PRO G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 91 removed outlier: 3.597A pdb=" N ALA G 88 " --> pdb=" O GLU G 84 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE G 89 " --> pdb=" O ILE G 85 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG G 90 " --> pdb=" O ARG G 86 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL G 91 " --> pdb=" O GLU G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 110 removed outlier: 3.854A pdb=" N LEU G 105 " --> pdb=" O SER G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 129 Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'H' and resid 5 through 20 removed outlier: 3.757A pdb=" N PHE H 19 " --> pdb=" O ALA H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 40 removed outlier: 3.928A pdb=" N LEU H 32 " --> pdb=" O THR H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 54 Processing helix chain 'H' and resid 64 through 76 removed outlier: 4.202A pdb=" N ARG H 74 " --> pdb=" O THR H 70 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS H 75 " --> pdb=" O MET H 71 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET H 76 " --> pdb=" O MET H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 87 Processing helix chain 'H' and resid 87 through 92 removed outlier: 3.896A pdb=" N VAL H 91 " --> pdb=" O GLU H 87 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 92' Processing helix chain 'H' and resid 101 through 109 removed outlier: 3.574A pdb=" N LEU H 105 " --> pdb=" O SER H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'H' and resid 137 through 147 removed outlier: 3.599A pdb=" N MET H 145 " --> pdb=" O PHE H 141 " (cutoff:3.500A) 892 hydrogen bonds defined for protein. 2676 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: 2.28 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2704 1.32 - 1.45: 3844 1.45 - 1.57: 8784 1.57 - 1.69: 0 1.69 - 1.81: 188 Bond restraints: 15520 Sorted by residual: bond pdb=" CG LEU B 319 " pdb=" CD1 LEU B 319 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.37e-01 bond pdb=" C MET B 302 " pdb=" O MET B 302 " ideal model delta sigma weight residual 1.236 1.246 -0.010 1.28e-02 6.10e+03 6.22e-01 bond pdb=" CB ASP H 24 " pdb=" CG ASP H 24 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.18e-01 bond pdb=" C MET D 302 " pdb=" O MET D 302 " ideal model delta sigma weight residual 1.237 1.247 -0.010 1.31e-02 5.83e+03 6.05e-01 bond pdb=" CB TYR A 179 " pdb=" CG TYR A 179 " ideal model delta sigma weight residual 1.512 1.496 0.016 2.20e-02 2.07e+03 5.15e-01 ... (remaining 15515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 20567 1.29 - 2.59: 371 2.59 - 3.88: 64 3.88 - 5.17: 22 5.17 - 6.47: 5 Bond angle restraints: 21029 Sorted by residual: angle pdb=" C THR G 26 " pdb=" N ILE G 27 " pdb=" CA ILE G 27 " ideal model delta sigma weight residual 121.95 126.97 -5.02 1.53e+00 4.27e-01 1.08e+01 angle pdb=" N VAL D 98 " pdb=" CA VAL D 98 " pdb=" C VAL D 98 " ideal model delta sigma weight residual 113.39 109.65 3.74 1.47e+00 4.63e-01 6.46e+00 angle pdb=" C ILE C 244 " pdb=" CA ILE C 244 " pdb=" CB ILE C 244 " ideal model delta sigma weight residual 114.00 110.95 3.05 1.31e+00 5.83e-01 5.42e+00 angle pdb=" C LEU C 243 " pdb=" N ILE C 244 " pdb=" CA ILE C 244 " ideal model delta sigma weight residual 120.33 122.17 -1.84 8.00e-01 1.56e+00 5.31e+00 angle pdb=" C ARG H 106 " pdb=" N HIS H 107 " pdb=" CA HIS H 107 " ideal model delta sigma weight residual 121.92 117.97 3.95 1.73e+00 3.34e-01 5.20e+00 ... (remaining 21024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 8250 17.92 - 35.84: 719 35.84 - 53.76: 141 53.76 - 71.67: 25 71.67 - 89.59: 20 Dihedral angle restraints: 9155 sinusoidal: 3351 harmonic: 5804 Sorted by residual: dihedral pdb=" CA ASP H 93 " pdb=" CB ASP H 93 " pdb=" CG ASP H 93 " pdb=" OD1 ASP H 93 " ideal model delta sinusoidal sigma weight residual -30.00 -86.62 56.62 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CB GLU C 111 " pdb=" CG GLU C 111 " pdb=" CD GLU C 111 " pdb=" OE1 GLU C 111 " ideal model delta sinusoidal sigma weight residual 0.00 89.59 -89.59 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU H 87 " pdb=" CG GLU H 87 " pdb=" CD GLU H 87 " pdb=" OE1 GLU H 87 " ideal model delta sinusoidal sigma weight residual 0.00 -88.79 88.79 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 9152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1539 0.032 - 0.063: 737 0.063 - 0.095: 149 0.095 - 0.127: 34 0.127 - 0.159: 1 Chirality restraints: 2460 Sorted by residual: chirality pdb=" CA ILE G 27 " pdb=" N ILE G 27 " pdb=" C ILE G 27 " pdb=" CB ILE G 27 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" CB VAL A 369 " pdb=" CA VAL A 369 " pdb=" CG1 VAL A 369 " pdb=" CG2 VAL A 369 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA PHE H 65 " pdb=" N PHE H 65 " pdb=" C PHE H 65 " pdb=" CB PHE H 65 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 2457 not shown) Planarity restraints: 2641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 92 " 0.009 2.00e-02 2.50e+03 1.01e-02 1.80e+00 pdb=" CG PHE H 92 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE H 92 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE H 92 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE H 92 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE H 92 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE H 92 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 141 " -0.012 2.00e-02 2.50e+03 9.00e-03 1.42e+00 pdb=" CG PHE E 141 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE E 141 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE E 141 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE E 141 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 141 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE E 141 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS D 118 " -0.018 5.00e-02 4.00e+02 2.72e-02 1.18e+00 pdb=" N PRO D 119 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO D 119 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 119 " -0.015 5.00e-02 4.00e+02 ... (remaining 2638 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.24: 12 2.24 - 2.97: 6983 2.97 - 3.69: 25119 3.69 - 4.42: 37370 4.42 - 5.14: 64069 Nonbonded interactions: 133553 Sorted by model distance: nonbonded pdb=" OD1 ASP H 22 " pdb=" OE2 GLU H 31 " model vdw 1.515 3.040 nonbonded pdb=" C THR G 26 " pdb="CA CA G 202 " model vdw 1.696 2.740 nonbonded pdb=" O THR G 26 " pdb="CA CA G 202 " model vdw 1.718 2.510 nonbonded pdb=" OD1 ASP F 56 " pdb=" OD1 ASP F 58 " model vdw 2.010 3.040 nonbonded pdb=" OD2 ASP F 56 " pdb=" O THR F 62 " model vdw 2.013 3.040 ... (remaining 133548 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 365 or (resid 366 and (name N or name CA or name \ C or name O or name CB )) or resid 367 through 385 or (resid 386 and (name N or \ name CA or name C or name O or name CB )))) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = 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 group one per residue 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: 11.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.250 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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 0.026 15520 Z= 0.132 Angle : 0.465 6.467 21029 Z= 0.250 Chirality : 0.036 0.159 2460 Planarity : 0.003 0.027 2641 Dihedral : 14.791 89.593 5395 Min Nonbonded Distance : 1.515 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.68 (0.20), residues: 2000 helix: 1.06 (0.15), residues: 1468 sheet: None (None), residues: 0 loop : -1.17 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 180 TYR 0.017 0.001 TYR A 179 PHE 0.022 0.001 PHE H 92 TRP 0.010 0.001 TRP C 54 HIS 0.004 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (15520) covalent geometry : angle 0.46484 / 0.25 (21029) hydrogen bonds : bond 0.07879 / 5.22 ( 892) hydrogen bonds : angle 3.36540 / 2.44 ( 2676) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 324 MET cc_start: 0.6929 (mmp) cc_final: 0.6621 (ttm) REVERT: B 326 TYR cc_start: 0.7638 (t80) cc_final: 0.7323 (t80) REVERT: C 40 MET cc_start: 0.8177 (tmm) cc_final: 0.7717 (ttp) REVERT: F 42 ASN cc_start: 0.8296 (p0) cc_final: 0.8093 (p0) REVERT: G 78 ASP cc_start: 0.8544 (t70) cc_final: 0.8216 (t0) REVERT: H 50 ASP cc_start: 0.7597 (t70) cc_final: 0.7157 (t0) REVERT: H 78 ASP cc_start: 0.8743 (t70) cc_final: 0.8515 (t0) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.1365 time to fit residues: 56.1825 Evaluate side-chains 215 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 68.4314 > 50:) chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.0970 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 HIS D 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.169241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.144068 restraints weight = 18460.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.136412 restraints weight = 25266.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.136891 restraints weight = 22058.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.136979 restraints weight = 19296.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.137205 restraints weight = 17811.349| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15520 Z= 0.135 Angle : 0.467 5.818 21029 Z= 0.247 Chirality : 0.037 0.132 2460 Planarity : 0.003 0.027 2641 Dihedral : 3.568 14.817 2160 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.44 % Allowed : 8.78 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.81 (0.20), residues: 2000 helix: 1.18 (0.15), residues: 1464 sheet: None (None), residues: 0 loop : -1.15 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 37 TYR 0.018 0.001 TYR D 326 PHE 0.022 0.001 PHE G 141 TRP 0.010 0.001 TRP C 242 HIS 0.010 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (15520) covalent geometry : angle 0.46697 / 0.25 (21029) hydrogen bonds : bond 0.04985 / 3.37 ( 892) hydrogen bonds : angle 3.10032 / 2.21 ( 2676) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 231 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.7492 (tpt) cc_final: 0.7037 (tpt) REVERT: B 324 MET cc_start: 0.6855 (mmt) cc_final: 0.6318 (ttm) REVERT: B 326 TYR cc_start: 0.7746 (t80) cc_final: 0.7319 (t80) REVERT: C 144 PHE cc_start: 0.5795 (OUTLIER) cc_final: 0.5381 (m-80) REVERT: C 261 MET cc_start: 0.8114 (tmm) cc_final: 0.7779 (ttt) REVERT: C 324 MET cc_start: 0.6053 (OUTLIER) cc_final: 0.5816 (ttm) REVERT: F 78 ASP cc_start: 0.8767 (t70) cc_final: 0.8518 (t0) REVERT: G 78 ASP cc_start: 0.8687 (t70) cc_final: 0.8332 (t0) REVERT: H 78 ASP cc_start: 0.8783 (t70) cc_final: 0.8551 (t0) outliers start: 21 outliers final: 10 residues processed: 241 average time/residue: 0.1075 time to fit residues: 39.9790 Evaluate side-chains 224 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 212 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 318 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 76 optimal weight: 0.0370 chunk 6 optimal weight: 0.6980 chunk 150 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 130 optimal weight: 0.3980 chunk 131 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 HIS H 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.169600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.147608 restraints weight = 18718.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.137810 restraints weight = 25189.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.137945 restraints weight = 21418.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.137948 restraints weight = 19560.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.137948 restraints weight = 19528.350| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15520 Z= 0.123 Angle : 0.452 5.995 21029 Z= 0.236 Chirality : 0.036 0.125 2460 Planarity : 0.003 0.027 2641 Dihedral : 3.481 14.411 2160 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.51 % Allowed : 10.49 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.88 (0.20), residues: 2000 helix: 1.23 (0.15), residues: 1464 sheet: None (None), residues: 0 loop : -1.13 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 86 TYR 0.019 0.001 TYR D 326 PHE 0.020 0.001 PHE G 141 TRP 0.009 0.001 TRP B 242 HIS 0.003 0.001 HIS C 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (15520) covalent geometry : angle 0.45173 / 0.24 (21029) hydrogen bonds : bond 0.04670 / 3.15 ( 892) hydrogen bonds : angle 3.04258 / 2.17 ( 2676) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 209 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.7394 (tpt) cc_final: 0.6994 (tpt) REVERT: B 324 MET cc_start: 0.6836 (mmt) cc_final: 0.6356 (ttm) REVERT: C 144 PHE cc_start: 0.5806 (OUTLIER) cc_final: 0.5458 (m-80) REVERT: C 324 MET cc_start: 0.6076 (ttm) cc_final: 0.5858 (ttm) REVERT: F 78 ASP cc_start: 0.8721 (t70) cc_final: 0.8482 (t0) REVERT: G 78 ASP cc_start: 0.8665 (t70) cc_final: 0.8349 (t0) REVERT: H 78 ASP cc_start: 0.8739 (t70) cc_final: 0.8507 (t0) outliers start: 22 outliers final: 12 residues processed: 219 average time/residue: 0.1076 time to fit residues: 36.2932 Evaluate side-chains 217 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 204 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain G residue 42 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 15 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 195 optimal weight: 0.1980 chunk 181 optimal weight: 0.0870 chunk 1 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 chunk 30 optimal weight: 9.9990 chunk 118 optimal weight: 0.5980 chunk 155 optimal weight: 9.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.170812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.148778 restraints weight = 18540.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.138619 restraints weight = 25413.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.139042 restraints weight = 23236.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.139206 restraints weight = 21291.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.139342 restraints weight = 19817.754| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15520 Z= 0.103 Angle : 0.423 6.187 21029 Z= 0.221 Chirality : 0.035 0.133 2460 Planarity : 0.002 0.030 2641 Dihedral : 3.338 13.855 2160 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.71 % Allowed : 12.00 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.05 (0.20), residues: 2000 helix: 1.35 (0.15), residues: 1456 sheet: None (None), residues: 0 loop : -1.02 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 338 TYR 0.018 0.001 TYR D 326 PHE 0.019 0.001 PHE G 141 TRP 0.007 0.001 TRP D 323 HIS 0.003 0.001 HIS G 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (15520) covalent geometry : angle 0.42283 / 0.22 (21029) hydrogen bonds : bond 0.04191 / 2.82 ( 892) hydrogen bonds : angle 2.91837 / 2.08 ( 2676) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 200 MET cc_start: 0.7428 (tpt) cc_final: 0.7033 (tpt) REVERT: B 324 MET cc_start: 0.6808 (mmt) cc_final: 0.6434 (ttm) REVERT: C 144 PHE cc_start: 0.5788 (OUTLIER) cc_final: 0.5501 (m-80) REVERT: F 78 ASP cc_start: 0.8664 (t70) cc_final: 0.8438 (t0) REVERT: G 78 ASP cc_start: 0.8628 (t70) cc_final: 0.8301 (t0) REVERT: H 78 ASP cc_start: 0.8722 (t70) cc_final: 0.8495 (t0) outliers start: 25 outliers final: 12 residues processed: 215 average time/residue: 0.1029 time to fit residues: 34.1668 Evaluate side-chains 211 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 198 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain F residue 107 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 25 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 80 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.163802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.138769 restraints weight = 18920.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.129735 restraints weight = 25686.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.130628 restraints weight = 23755.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.130845 restraints weight = 20307.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.130980 restraints weight = 19668.971| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15520 Z= 0.204 Angle : 0.540 6.624 21029 Z= 0.279 Chirality : 0.039 0.136 2460 Planarity : 0.003 0.031 2641 Dihedral : 3.699 17.345 2160 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.85 % Allowed : 13.92 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.79 (0.20), residues: 2000 helix: 1.21 (0.15), residues: 1432 sheet: None (None), residues: 0 loop : -1.18 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 339 TYR 0.021 0.002 TYR D 326 PHE 0.026 0.002 PHE G 141 TRP 0.013 0.002 TRP B 242 HIS 0.006 0.001 HIS C 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.20 (15520) covalent geometry : angle 0.53971 / 0.28 (21029) hydrogen bonds : bond 0.05784 / 3.90 ( 892) hydrogen bonds : angle 3.29360 / 2.34 ( 2676) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 209 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 200 MET cc_start: 0.7400 (tpt) cc_final: 0.7036 (tpt) REVERT: B 324 MET cc_start: 0.6834 (mmt) cc_final: 0.6106 (mtt) REVERT: C 144 PHE cc_start: 0.5929 (OUTLIER) cc_final: 0.5606 (m-80) REVERT: C 324 MET cc_start: 0.6024 (ttm) cc_final: 0.5818 (ttm) REVERT: F 78 ASP cc_start: 0.8791 (t70) cc_final: 0.8524 (t0) REVERT: G 78 ASP cc_start: 0.8738 (t70) cc_final: 0.8354 (t0) REVERT: H 78 ASP cc_start: 0.8823 (t70) cc_final: 0.8563 (t0) outliers start: 27 outliers final: 16 residues processed: 222 average time/residue: 0.1109 time to fit residues: 37.5677 Evaluate side-chains 218 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 201 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain G residue 42 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 181 optimal weight: 0.0060 chunk 143 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.167752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.145593 restraints weight = 18700.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.135121 restraints weight = 24758.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.135890 restraints weight = 21882.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.135804 restraints weight = 20802.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.135908 restraints weight = 19492.264| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15520 Z= 0.117 Angle : 0.448 6.421 21029 Z= 0.234 Chirality : 0.036 0.183 2460 Planarity : 0.003 0.031 2641 Dihedral : 3.480 14.611 2160 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.65 % Allowed : 15.02 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.02 (0.20), residues: 2000 helix: 1.38 (0.15), residues: 1432 sheet: None (None), residues: 0 loop : -1.10 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 14 TYR 0.019 0.001 TYR D 326 PHE 0.022 0.001 PHE G 141 TRP 0.009 0.001 TRP C 242 HIS 0.004 0.001 HIS C 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (15520) covalent geometry : angle 0.44821 / 0.23 (21029) hydrogen bonds : bond 0.04708 / 3.17 ( 892) hydrogen bonds : angle 3.04777 / 2.17 ( 2676) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 200 MET cc_start: 0.7395 (tpt) cc_final: 0.7013 (tpt) REVERT: A 201 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.8106 (t0) REVERT: B 324 MET cc_start: 0.6768 (mmt) cc_final: 0.6064 (mtm) REVERT: C 144 PHE cc_start: 0.5734 (OUTLIER) cc_final: 0.5469 (m-80) REVERT: F 78 ASP cc_start: 0.8720 (t70) cc_final: 0.8467 (t0) REVERT: G 78 ASP cc_start: 0.8653 (t70) cc_final: 0.8282 (t0) REVERT: H 78 ASP cc_start: 0.8745 (t70) cc_final: 0.8495 (t0) outliers start: 24 outliers final: 15 residues processed: 217 average time/residue: 0.1046 time to fit residues: 35.0052 Evaluate side-chains 217 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 200 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain G residue 42 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 177 optimal weight: 0.0770 chunk 163 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.168672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.149184 restraints weight = 18316.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 75)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.138776 restraints weight = 25683.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.138665 restraints weight = 23273.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.138567 restraints weight = 22694.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.138702 restraints weight = 20439.359| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15520 Z= 0.123 Angle : 0.459 6.796 21029 Z= 0.238 Chirality : 0.036 0.148 2460 Planarity : 0.003 0.031 2641 Dihedral : 3.424 14.605 2160 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.25 % Favored : 96.70 % Rotamer: Outliers : 1.99 % Allowed : 15.84 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.10 (0.20), residues: 2000 helix: 1.41 (0.15), residues: 1448 sheet: None (None), residues: 0 loop : -1.02 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 14 TYR 0.021 0.001 TYR D 326 PHE 0.015 0.001 PHE G 141 TRP 0.009 0.001 TRP C 242 HIS 0.007 0.001 HIS C 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (15520) covalent geometry : angle 0.45885 / 0.24 (21029) hydrogen bonds : bond 0.04637 / 3.12 ( 892) hydrogen bonds : angle 3.03043 / 2.16 ( 2676) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 200 MET cc_start: 0.7395 (tpt) cc_final: 0.7060 (tpt) REVERT: A 201 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.8113 (t0) REVERT: B 217 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8413 (tp) REVERT: B 324 MET cc_start: 0.6782 (mmt) cc_final: 0.6119 (mtm) REVERT: C 144 PHE cc_start: 0.5743 (OUTLIER) cc_final: 0.5491 (m-80) REVERT: F 78 ASP cc_start: 0.8708 (t70) cc_final: 0.8462 (t0) REVERT: G 78 ASP cc_start: 0.8641 (t70) cc_final: 0.8320 (t0) REVERT: H 78 ASP cc_start: 0.8726 (t70) cc_final: 0.8482 (t0) outliers start: 29 outliers final: 16 residues processed: 218 average time/residue: 0.1067 time to fit residues: 35.7029 Evaluate side-chains 217 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 198 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain G residue 42 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 195 optimal weight: 1.9990 chunk 149 optimal weight: 0.0010 chunk 147 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 158 optimal weight: 0.2980 chunk 17 optimal weight: 0.7980 chunk 131 optimal weight: 0.0980 chunk 144 optimal weight: 0.3980 chunk 183 optimal weight: 0.0070 chunk 47 optimal weight: 1.9990 overall best weight: 0.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.174241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.155036 restraints weight = 18373.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 85)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.144261 restraints weight = 27266.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.143870 restraints weight = 25852.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.144239 restraints weight = 24231.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.144422 restraints weight = 21911.591| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15520 Z= 0.090 Angle : 0.433 7.525 21029 Z= 0.222 Chirality : 0.034 0.166 2460 Planarity : 0.002 0.032 2641 Dihedral : 3.146 13.501 2160 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.35 % Favored : 97.60 % Rotamer: Outliers : 1.03 % Allowed : 17.22 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.34 (0.20), residues: 2000 helix: 1.54 (0.15), residues: 1472 sheet: None (None), residues: 0 loop : -0.90 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 14 TYR 0.019 0.001 TYR D 326 PHE 0.009 0.001 PHE A 87 TRP 0.009 0.001 TRP D 323 HIS 0.006 0.001 HIS C 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00178 / 0.09 (15520) covalent geometry : angle 0.43309 / 0.22 (21029) hydrogen bonds : bond 0.03419 / 2.29 ( 892) hydrogen bonds : angle 2.79021 / 2.00 ( 2676) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 213 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 200 MET cc_start: 0.7381 (tpt) cc_final: 0.7091 (tpt) REVERT: B 324 MET cc_start: 0.6787 (mmt) cc_final: 0.6084 (mtt) REVERT: C 144 PHE cc_start: 0.5705 (OUTLIER) cc_final: 0.5485 (m-80) REVERT: G 78 ASP cc_start: 0.8634 (t70) cc_final: 0.8321 (t0) outliers start: 15 outliers final: 10 residues processed: 220 average time/residue: 0.1069 time to fit residues: 36.4929 Evaluate side-chains 212 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 201 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain G residue 42 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 85 optimal weight: 0.2980 chunk 175 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.168129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.143364 restraints weight = 18736.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.135488 restraints weight = 26771.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.135533 restraints weight = 22085.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.135493 restraints weight = 19405.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.135648 restraints weight = 19154.366| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15520 Z= 0.136 Angle : 0.510 11.121 21029 Z= 0.254 Chirality : 0.037 0.153 2460 Planarity : 0.003 0.035 2641 Dihedral : 3.293 13.879 2160 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.50 % Favored : 96.45 % Rotamer: Outliers : 1.03 % Allowed : 17.76 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.27 (0.20), residues: 2000 helix: 1.55 (0.15), residues: 1444 sheet: None (None), residues: 0 loop : -1.01 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 14 TYR 0.022 0.001 TYR D 326 PHE 0.012 0.001 PHE C 291 TRP 0.010 0.001 TRP D 323 HIS 0.007 0.001 HIS C 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (15520) covalent geometry : angle 0.50951 / 0.25 (21029) hydrogen bonds : bond 0.04551 / 3.06 ( 892) hydrogen bonds : angle 2.97384 / 2.12 ( 2676) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 206 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 200 MET cc_start: 0.7349 (tpt) cc_final: 0.7078 (tpt) REVERT: B 324 MET cc_start: 0.6717 (mmt) cc_final: 0.6009 (mtm) REVERT: C 144 PHE cc_start: 0.5888 (OUTLIER) cc_final: 0.5585 (m-80) REVERT: G 78 ASP cc_start: 0.8752 (t70) cc_final: 0.8435 (t0) REVERT: G 145 MET cc_start: 0.6304 (ttm) cc_final: 0.5969 (ttp) outliers start: 15 outliers final: 11 residues processed: 212 average time/residue: 0.1081 time to fit residues: 35.3761 Evaluate side-chains 209 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 197 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain G residue 42 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 38 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 43 optimal weight: 0.3980 chunk 23 optimal weight: 0.9980 chunk 86 optimal weight: 0.0270 chunk 15 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.170346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.148350 restraints weight = 18469.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.137902 restraints weight = 25518.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.137965 restraints weight = 23808.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.138581 restraints weight = 21512.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.138650 restraints weight = 19636.840| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15520 Z= 0.111 Angle : 0.489 10.678 21029 Z= 0.244 Chirality : 0.036 0.144 2460 Planarity : 0.003 0.033 2641 Dihedral : 3.249 13.578 2160 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.00 % Favored : 96.95 % Rotamer: Outliers : 1.10 % Allowed : 17.90 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.37 (0.20), residues: 2000 helix: 1.60 (0.15), residues: 1456 sheet: None (None), residues: 0 loop : -0.95 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 14 TYR 0.020 0.001 TYR D 326 PHE 0.012 0.001 PHE G 141 TRP 0.011 0.001 TRP D 323 HIS 0.006 0.001 HIS C 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (15520) covalent geometry : angle 0.48885 / 0.24 (21029) hydrogen bonds : bond 0.04140 / 2.79 ( 892) hydrogen bonds : angle 2.90941 / 2.07 ( 2676) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 203 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 200 MET cc_start: 0.7408 (tpt) cc_final: 0.7085 (tpt) REVERT: B 324 MET cc_start: 0.6804 (mmt) cc_final: 0.6129 (mtt) REVERT: C 144 PHE cc_start: 0.5774 (OUTLIER) cc_final: 0.5532 (m-80) REVERT: G 78 ASP cc_start: 0.8686 (t70) cc_final: 0.8379 (t0) outliers start: 16 outliers final: 10 residues processed: 211 average time/residue: 0.0926 time to fit residues: 30.6700 Evaluate side-chains 213 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 202 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain G residue 42 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 52 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 142 optimal weight: 0.5980 chunk 163 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 198 optimal weight: 6.9990 chunk 86 optimal weight: 0.0570 chunk 103 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 181 optimal weight: 0.0270 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.171703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.152395 restraints weight = 18302.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 84)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.140756 restraints weight = 26078.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.139978 restraints weight = 27143.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.140044 restraints weight = 25837.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.140641 restraints weight = 22827.353| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15520 Z= 0.106 Angle : 0.485 10.519 21029 Z= 0.240 Chirality : 0.035 0.147 2460 Planarity : 0.002 0.034 2641 Dihedral : 3.175 14.604 2160 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.00 % Favored : 96.95 % Rotamer: Outliers : 1.03 % Allowed : 17.83 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.47 (0.20), residues: 2000 helix: 1.69 (0.15), residues: 1452 sheet: None (None), residues: 0 loop : -0.96 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 86 TYR 0.019 0.001 TYR D 326 PHE 0.011 0.001 PHE G 92 TRP 0.011 0.001 TRP D 323 HIS 0.006 0.001 HIS C 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (15520) covalent geometry : angle 0.48517 / 0.24 (21029) hydrogen bonds : bond 0.03891 / 2.62 ( 892) hydrogen bonds : angle 2.86500 / 2.04 ( 2676) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2366.59 seconds wall clock time: 41 minutes 26.21 seconds (2486.21 seconds total)