Starting phenix.real_space_refine on Sat Sep 12 13:19:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6cnn_7538/09_2026/6cnn_7538.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cnn_7538/09_2026/6cnn_7538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6cnn_7538/09_2026/6cnn_7538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cnn_7538/09_2026/6cnn_7538.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6cnn_7538/09_2026/6cnn_7538.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6cnn_7538/09_2026/6cnn_7538.cif" model { file = "/net/cci-nas-00/data/ceres_data/6cnn_7538/09_2026/6cnn_7538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cnn_7538/09_2026/6cnn_7538.cif" } resolution = 3.5 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= 0.004 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 12 9.91 5 K 4 8.98 5 P 4 5.49 5 S 108 5.16 5 C 10088 2.51 5 N 2744 2.21 5 O 2780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15740 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2781 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 3, 'TYR:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2781 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 3, 'TYR:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2781 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 3, 'TYR:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 50 Chain: "D" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2781 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 3, 'TYR:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1073 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 7, 'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 59 Chain: "F" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1073 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 7, 'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 59 Chain: "G" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1073 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 7, 'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 59 Chain: "H" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1073 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 7, 'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 59 Chain: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 81 Unusual residues: {' K': 4, 'LMT': 2, 'POV': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {'LMT': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {'LMT': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {'LMT': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.73, per 1000 atoms: 0.24 Number of scatterers: 15740 At special positions: 0 Unit cell: (139.05, 139.05, 109.18, 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 12 19.99 K 4 19.00 S 108 16.00 P 4 15.00 O 2780 8.00 N 2744 7.00 C 10088 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 728.6 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: 88 helices and 8 sheets defined 75.9% alpha, 1.2% 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 9 through 49 removed outlier: 3.560A pdb=" N ARG A 13 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG A 14 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 42 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TRP A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 91 removed outlier: 4.275A pdb=" N LEU A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 115 Processing helix chain 'A' and resid 147 through 155 removed outlier: 4.155A pdb=" N LEU A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 162 removed outlier: 3.818A pdb=" N LEU A 160 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR A 161 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU A 162 " --> pdb=" O ARG A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 170 Processing helix chain 'A' and resid 177 through 186 Processing helix chain 'A' and resid 192 through 202 removed outlier: 3.518A pdb=" N LYS A 197 " --> pdb=" O TRP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 227 removed outlier: 3.674A pdb=" N THR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA A 220 " --> pdb=" O TRP A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 249 removed outlier: 4.416A 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 261 through 289 removed outlier: 3.544A pdb=" N VAL A 266 " --> pdb=" O TRP A 262 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY A 271 " --> pdb=" O CYS A 267 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ALA A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 331 removed outlier: 4.037A pdb=" N HIS A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A 305 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS A 309 " --> pdb=" O ILE A 305 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET A 324 " --> pdb=" O GLN A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 367 removed outlier: 4.171A pdb=" N ARG A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS A 343 " --> pdb=" O ARG A 339 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN A 353 " --> pdb=" O ASN A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 386 removed outlier: 3.848A pdb=" N GLN A 383 " --> pdb=" O TYR A 379 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ASN A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N LEU A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N SER A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 49 removed outlier: 3.563A pdb=" N ARG B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG B 14 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ARG B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 42 " --> pdb=" O GLY B 38 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TRP B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 91 removed outlier: 4.277A pdb=" N LEU B 72 " --> pdb=" O SER B 68 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN B 91 " --> pdb=" O PHE B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 115 Processing helix chain 'B' and resid 147 through 155 removed outlier: 4.156A pdb=" N LEU B 151 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER B 153 " --> pdb=" O GLU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 162 removed outlier: 3.818A pdb=" N LEU B 160 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR B 161 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU B 162 " --> pdb=" O ARG B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 170 Processing helix chain 'B' and resid 177 through 186 Processing helix chain 'B' and resid 192 through 202 removed outlier: 3.524A pdb=" N LYS B 197 " --> pdb=" O TRP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 227 removed outlier: 3.677A pdb=" N THR B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA B 220 " --> pdb=" O TRP B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 249 removed outlier: 4.426A 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 261 through 289 removed outlier: 3.546A pdb=" N VAL B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 268 " --> pdb=" O LYS B 264 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY B 271 " --> pdb=" O CYS B 267 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS B 288 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 331 removed outlier: 4.040A pdb=" N HIS B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS B 309 " --> pdb=" O ILE B 305 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA B 316 " --> pdb=" O LYS B 312 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 319 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET B 324 " --> pdb=" O GLN B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 367 removed outlier: 4.149A pdb=" N ARG B 342 " --> pdb=" O ARG B 338 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS B 343 " --> pdb=" O ARG B 339 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN B 353 " --> pdb=" O ASN B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 386 removed outlier: 3.854A pdb=" N GLN B 383 " --> pdb=" O TYR B 379 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASN B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N LEU B 385 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N SER B 386 " --> pdb=" O GLN B 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 49 removed outlier: 3.560A pdb=" N ARG C 13 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG C 14 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ARG C 15 " --> pdb=" O ALA C 11 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY C 36 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 42 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 91 removed outlier: 4.274A pdb=" N LEU C 72 " --> pdb=" O SER C 68 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN C 91 " --> pdb=" O PHE C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 115 Processing helix chain 'C' and resid 147 through 155 removed outlier: 4.169A pdb=" N LEU C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER C 153 " --> pdb=" O GLU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 162 removed outlier: 3.819A pdb=" N LEU C 160 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR C 161 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU C 162 " --> pdb=" O ARG C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 170 Processing helix chain 'C' and resid 177 through 186 Processing helix chain 'C' and resid 192 through 202 removed outlier: 3.522A pdb=" N LYS C 197 " --> pdb=" O TRP C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 227 removed outlier: 3.676A pdb=" N THR C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY C 214 " --> pdb=" O GLY C 210 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR C 218 " --> pdb=" O GLY C 214 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA C 220 " --> pdb=" O TRP C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 249 removed outlier: 4.415A 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 261 through 289 removed outlier: 3.545A pdb=" N VAL C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 268 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY C 271 " --> pdb=" O CYS C 267 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA C 286 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS C 288 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU C 289 " --> pdb=" O VAL C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 331 removed outlier: 4.043A pdb=" N HIS C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL C 298 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS C 309 " --> pdb=" O ILE C 305 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA C 316 " --> pdb=" O LYS C 312 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU C 319 " --> pdb=" O ALA C 315 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET C 324 " --> pdb=" O GLN C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 367 removed outlier: 4.160A pdb=" N ARG C 342 " --> pdb=" O ARG C 338 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS C 343 " --> pdb=" O ARG C 339 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN C 353 " --> pdb=" O ASN C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 386 removed outlier: 3.850A pdb=" N GLN C 383 " --> pdb=" O TYR C 379 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ASN C 384 " --> pdb=" O ASP C 380 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LEU C 385 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N SER C 386 " --> pdb=" O GLN C 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 49 removed outlier: 3.557A pdb=" N ARG D 13 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG D 14 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ARG D 15 " --> pdb=" O ALA D 11 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA D 29 " --> pdb=" O LEU D 25 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY D 36 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU D 42 " --> pdb=" O GLY D 38 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TRP D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 91 removed outlier: 4.272A pdb=" N LEU D 72 " --> pdb=" O SER D 68 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN D 91 " --> pdb=" O PHE D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 115 Processing helix chain 'D' and resid 147 through 155 removed outlier: 4.165A pdb=" N LEU D 151 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER D 153 " --> pdb=" O GLU D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 162 removed outlier: 3.820A pdb=" N LEU D 160 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR D 161 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU D 162 " --> pdb=" O ARG D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 170 Processing helix chain 'D' and resid 177 through 186 Processing helix chain 'D' and resid 192 through 202 removed outlier: 3.519A pdb=" N LYS D 197 " --> pdb=" O TRP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 227 removed outlier: 3.676A pdb=" N THR D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY D 214 " --> pdb=" O GLY D 210 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR D 218 " --> pdb=" O GLY D 214 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA D 220 " --> pdb=" O TRP D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 249 removed outlier: 4.414A 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 261 through 289 removed outlier: 3.544A pdb=" N VAL D 266 " --> pdb=" O TRP D 262 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU D 268 " --> pdb=" O LYS D 264 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY D 271 " --> pdb=" O CYS D 267 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALA D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA D 286 " --> pdb=" O VAL D 282 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS D 288 " --> pdb=" O VAL D 284 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU D 289 " --> pdb=" O VAL D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 331 removed outlier: 4.041A pdb=" N HIS D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL D 298 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE D 305 " --> pdb=" O PHE D 301 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS D 309 " --> pdb=" O ILE D 305 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA D 316 " --> pdb=" O LYS D 312 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU D 319 " --> pdb=" O ALA D 315 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET D 324 " --> pdb=" O GLN D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 367 removed outlier: 4.173A pdb=" N ARG D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS D 343 " --> pdb=" O ARG D 339 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN D 353 " --> pdb=" O ASN D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 386 removed outlier: 3.845A pdb=" N GLN D 383 " --> pdb=" O TYR D 379 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASN D 384 " --> pdb=" O ASP D 380 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LEU D 385 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER D 386 " --> pdb=" O GLN D 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 20 removed outlier: 4.365A pdb=" N GLU E 14 " --> pdb=" O ALA E 10 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA E 15 " --> pdb=" O GLU E 11 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 39 removed outlier: 3.553A pdb=" N VAL E 35 " --> pdb=" O GLU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 4.548A pdb=" N VAL E 55 " --> pdb=" O MET E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 74 removed outlier: 3.764A pdb=" N THR E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG E 74 " --> pdb=" O THR E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 92 removed outlier: 3.820A pdb=" N ILE E 85 " --> pdb=" O SER E 81 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA E 88 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 110 removed outlier: 3.992A pdb=" N THR E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 129 removed outlier: 4.078A pdb=" N VAL E 121 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP E 122 " --> pdb=" O ASP E 118 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU E 123 " --> pdb=" O GLU E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 147 removed outlier: 3.690A pdb=" N ALA E 147 " --> pdb=" O GLN E 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 20 removed outlier: 4.364A pdb=" N GLU F 14 " --> pdb=" O ALA F 10 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA F 15 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 39 removed outlier: 3.552A pdb=" N VAL F 35 " --> pdb=" O GLU F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 55 removed outlier: 4.549A pdb=" N VAL F 55 " --> pdb=" O MET F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 74 removed outlier: 3.760A pdb=" N THR F 70 " --> pdb=" O PRO F 66 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG F 74 " --> pdb=" O THR F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 92 removed outlier: 3.820A pdb=" N ILE F 85 " --> pdb=" O SER F 81 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA F 88 " --> pdb=" O GLU F 84 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 110 removed outlier: 3.972A pdb=" N THR F 110 " --> pdb=" O ARG F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 129 removed outlier: 4.044A pdb=" N VAL F 121 " --> pdb=" O THR F 117 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP F 122 " --> pdb=" O ASP F 118 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU F 123 " --> pdb=" O GLU F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 147 removed outlier: 3.679A pdb=" N ALA F 147 " --> pdb=" O GLN F 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 20 removed outlier: 4.358A pdb=" N GLU G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA G 15 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE G 19 " --> pdb=" O ALA G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 39 removed outlier: 3.550A pdb=" N VAL G 35 " --> pdb=" O GLU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 55 removed outlier: 4.546A pdb=" N VAL G 55 " --> pdb=" O MET G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 74 removed outlier: 3.763A pdb=" N THR G 70 " --> pdb=" O PRO G 66 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG G 74 " --> pdb=" O THR G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 92 removed outlier: 3.819A pdb=" N ILE G 85 " --> pdb=" O SER G 81 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA G 88 " --> pdb=" O GLU G 84 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE G 92 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 110 removed outlier: 4.004A pdb=" N THR G 110 " --> pdb=" O ARG G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 129 removed outlier: 4.105A pdb=" N VAL G 121 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP G 122 " --> pdb=" O ASP G 118 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU G 123 " --> pdb=" O GLU G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 147 removed outlier: 3.684A pdb=" N ALA G 147 " --> pdb=" O GLN G 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 20 removed outlier: 4.361A pdb=" N GLU H 14 " --> pdb=" O ALA H 10 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA H 15 " --> pdb=" O GLU H 11 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE H 19 " --> pdb=" O ALA H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 39 removed outlier: 3.551A pdb=" N VAL H 35 " --> pdb=" O GLU H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 55 removed outlier: 4.550A pdb=" N VAL H 55 " --> pdb=" O MET H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 74 removed outlier: 3.766A pdb=" N THR H 70 " --> pdb=" O PRO H 66 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG H 74 " --> pdb=" O THR H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 92 removed outlier: 3.816A pdb=" N ILE H 85 " --> pdb=" O SER H 81 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA H 88 " --> pdb=" O GLU H 84 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 110 removed outlier: 3.980A pdb=" N THR H 110 " --> pdb=" O ARG H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 129 removed outlier: 4.065A pdb=" N VAL H 121 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP H 122 " --> pdb=" O ASP H 118 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU H 123 " --> pdb=" O GLU H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 147 removed outlier: 3.682A pdb=" N ALA H 147 " --> pdb=" O GLN H 143 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'E' and resid 26 through 27 Processing sheet with id=B, first strand: chain 'E' and resid 99 through 101 Processing sheet with id=C, first strand: chain 'F' and resid 26 through 27 Processing sheet with id=D, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=E, first strand: chain 'G' and resid 26 through 27 Processing sheet with id=F, first strand: chain 'G' and resid 99 through 101 Processing sheet with id=G, first strand: chain 'H' and resid 26 through 27 Processing sheet with id=H, first strand: chain 'H' and resid 99 through 101 940 hydrogen bonds defined for protein. 2796 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: 2.21 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4757 1.34 - 1.45: 2265 1.45 - 1.57: 8786 1.57 - 1.69: 8 1.69 - 1.80: 188 Bond restraints: 16004 Sorted by residual: bond pdb=" C31 POV B1101 " pdb=" O31 POV B1101 " ideal model delta sigma weight residual 1.327 1.455 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C31 POV A1101 " pdb=" O31 POV A1101 " ideal model delta sigma weight residual 1.327 1.455 -0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C31 POV C1101 " pdb=" O31 POV C1101 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" C31 POV D1101 " pdb=" O31 POV D1101 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" C21 POV C1101 " pdb=" O21 POV C1101 " ideal model delta sigma weight residual 1.330 1.454 -0.124 2.00e-02 2.50e+03 3.87e+01 ... (remaining 15999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 20346 1.96 - 3.92: 1025 3.92 - 5.88: 179 5.88 - 7.84: 38 7.84 - 9.80: 36 Bond angle restraints: 21624 Sorted by residual: angle pdb=" C2 LMT C1103 " pdb=" C3 LMT C1103 " pdb=" C4 LMT C1103 " ideal model delta sigma weight residual 117.09 107.29 9.80 3.00e+00 1.11e-01 1.07e+01 angle pdb=" C2 LMT D1103 " pdb=" C3 LMT D1103 " pdb=" C4 LMT D1103 " ideal model delta sigma weight residual 117.09 107.32 9.77 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C2 LMT B1103 " pdb=" C3 LMT B1103 " pdb=" C4 LMT B1103 " ideal model delta sigma weight residual 117.09 107.32 9.77 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C2 LMT A1103 " pdb=" C3 LMT A1103 " pdb=" C4 LMT A1103 " ideal model delta sigma weight residual 117.09 107.32 9.77 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C32 POV C1101 " pdb=" C31 POV C1101 " pdb=" O31 POV C1101 " ideal model delta sigma weight residual 110.66 120.20 -9.54 3.00e+00 1.11e-01 1.01e+01 ... (remaining 21619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.08: 8762 13.08 - 26.16: 478 26.16 - 39.25: 144 39.25 - 52.33: 36 52.33 - 65.41: 12 Dihedral angle restraints: 9432 sinusoidal: 3624 harmonic: 5808 Sorted by residual: dihedral pdb=" CA PHE B 291 " pdb=" C PHE B 291 " pdb=" N ASN B 292 " pdb=" CA ASN B 292 " ideal model delta harmonic sigma weight residual 180.00 157.91 22.09 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA PHE A 291 " pdb=" C PHE A 291 " pdb=" N ASN A 292 " pdb=" CA ASN A 292 " ideal model delta harmonic sigma weight residual 180.00 157.96 22.04 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA PHE C 291 " pdb=" C PHE C 291 " pdb=" N ASN C 292 " pdb=" CA ASN C 292 " ideal model delta harmonic sigma weight residual 180.00 157.98 22.02 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 9429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1744 0.050 - 0.100: 646 0.100 - 0.149: 119 0.149 - 0.199: 23 0.199 - 0.249: 12 Chirality restraints: 2544 Sorted by residual: chirality pdb=" C5' LMT C1103 " pdb=" C4' LMT C1103 " pdb=" C6' LMT C1103 " pdb=" O5' LMT C1103 " both_signs ideal model delta sigma weight residual False -2.51 -2.26 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C5' LMT D1103 " pdb=" C4' LMT D1103 " pdb=" C6' LMT D1103 " pdb=" O5' LMT D1103 " both_signs ideal model delta sigma weight residual False -2.51 -2.26 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C5' LMT B1103 " pdb=" C4' LMT B1103 " pdb=" C6' LMT B1103 " pdb=" O5' LMT B1103 " both_signs ideal model delta sigma weight residual False -2.51 -2.26 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 2541 not shown) Planarity restraints: 2668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 189 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.42e+00 pdb=" C ARG A 189 " 0.036 2.00e-02 2.50e+03 pdb=" O ARG A 189 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE A 190 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 189 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.39e+00 pdb=" C ARG D 189 " 0.036 2.00e-02 2.50e+03 pdb=" O ARG D 189 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE D 190 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 189 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.39e+00 pdb=" C ARG C 189 " -0.036 2.00e-02 2.50e+03 pdb=" O ARG C 189 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE C 190 " 0.012 2.00e-02 2.50e+03 ... (remaining 2665 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.64: 184 2.64 - 3.27: 15967 3.27 - 3.89: 28913 3.89 - 4.52: 38133 4.52 - 5.14: 59827 Nonbonded interactions: 143024 Sorted by model distance: nonbonded pdb=" OD1 ASP G 58 " pdb="CA CA G 202 " model vdw 2.016 2.510 nonbonded pdb=" OD1 ASP H 58 " pdb="CA CA H 202 " model vdw 2.016 2.510 nonbonded pdb=" OD1 ASP F 58 " pdb="CA CA F 202 " model vdw 2.019 2.510 nonbonded pdb=" OD1 ASP E 58 " pdb="CA CA E 202 " model vdw 2.020 2.510 nonbonded pdb=" OD1 ASP F 20 " pdb=" OD1 ASP F 24 " model vdw 2.129 3.040 ... (remaining 143019 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 386) selection = (chain 'B' and resid 9 through 386) selection = (chain 'C' and resid 9 through 386) selection = (chain 'D' and resid 9 through 386) } 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: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.720 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 : 0.008 0.128 16008 Z= 0.374 Angle : 1.070 9.797 21624 Z= 0.557 Chirality : 0.054 0.249 2544 Planarity : 0.006 0.050 2668 Dihedral : 10.143 65.411 5672 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: -4.29 (0.14), residues: 2000 helix: -2.92 (0.09), residues: 1560 sheet: None (None), residues: 0 loop : -1.45 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 159 TYR 0.013 0.003 TYR C 253 PHE 0.032 0.003 PHE D 291 TRP 0.027 0.003 TRP D 221 HIS 0.006 0.002 HIS C 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00839 / 0.37 (16004) covalent geometry : angle 1.06998 / 0.56 (21624) hydrogen bonds : bond 0.14535 / 9.89 ( 940) hydrogen bonds : angle 5.67581 / 4.03 ( 2796) Misc. bond : bond 0.00244 / 0.12 ( 4) *********************** 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 490 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 490 time to evaluate : 0.495 Fit side-chains REVERT: A 293 LYS cc_start: 0.8811 (tptt) cc_final: 0.8561 (tttt) REVERT: A 326 TYR cc_start: 0.8302 (t80) cc_final: 0.8064 (t80) REVERT: A 349 ASN cc_start: 0.8927 (t0) cc_final: 0.8637 (t0) REVERT: B 200 MET cc_start: 0.8186 (ttm) cc_final: 0.7956 (ttm) REVERT: B 293 LYS cc_start: 0.8804 (tptt) cc_final: 0.8550 (tttt) REVERT: B 320 GLN cc_start: 0.7828 (tt0) cc_final: 0.7605 (tt0) REVERT: B 326 TYR cc_start: 0.8269 (t80) cc_final: 0.7982 (t80) REVERT: B 349 ASN cc_start: 0.8913 (t0) cc_final: 0.8631 (t0) REVERT: C 200 MET cc_start: 0.8174 (ttm) cc_final: 0.7940 (ttm) REVERT: C 293 LYS cc_start: 0.8801 (tptt) cc_final: 0.8507 (tttt) REVERT: C 326 TYR cc_start: 0.8266 (t80) cc_final: 0.8023 (t80) REVERT: C 349 ASN cc_start: 0.8909 (t0) cc_final: 0.8624 (t0) REVERT: D 200 MET cc_start: 0.8183 (ttm) cc_final: 0.7938 (ttm) REVERT: D 293 LYS cc_start: 0.8807 (tptt) cc_final: 0.8554 (tttt) REVERT: D 320 GLN cc_start: 0.7866 (tt0) cc_final: 0.7426 (tt0) REVERT: D 326 TYR cc_start: 0.8311 (t80) cc_final: 0.8069 (t80) REVERT: D 349 ASN cc_start: 0.8919 (t0) cc_final: 0.8626 (t0) outliers start: 0 outliers final: 0 residues processed: 490 average time/residue: 0.1346 time to fit residues: 94.6831 Evaluate side-chains 263 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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: 6.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 ASN A 297 HIS A 320 GLN B 201 ASN B 297 HIS C 201 ASN C 320 GLN D 201 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.147764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120586 restraints weight = 22499.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.121374 restraints weight = 16734.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.121562 restraints weight = 13434.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.122458 restraints weight = 10987.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.122580 restraints weight = 9955.073| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16008 Z= 0.117 Angle : 0.540 6.994 21624 Z= 0.280 Chirality : 0.037 0.186 2544 Planarity : 0.004 0.026 2668 Dihedral : 7.386 63.831 2280 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.52 % Allowed : 8.31 % Favored : 90.17 % 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: -1.58 (0.17), residues: 2000 helix: -0.88 (0.12), residues: 1524 sheet: None (None), residues: 0 loop : -1.01 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 90 TYR 0.010 0.001 TYR B 179 PHE 0.012 0.001 PHE F 12 TRP 0.015 0.001 TRP D 221 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (16004) covalent geometry : angle 0.54014 / 0.28 (21624) hydrogen bonds : bond 0.04251 / 2.83 ( 940) hydrogen bonds : angle 3.51604 / 2.47 ( 2796) Misc. bond : bond 0.00057 / 0.03 ( 4) *********************** 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 380 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 357 time to evaluate : 0.570 Fit side-chains REVERT: A 156 MET cc_start: 0.9129 (mmm) cc_final: 0.8926 (mtt) REVERT: A 179 TYR cc_start: 0.8530 (m-80) cc_final: 0.8290 (m-80) REVERT: A 213 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8477 (tt) REVERT: A 293 LYS cc_start: 0.8752 (tptt) cc_final: 0.8456 (tttt) REVERT: B 156 MET cc_start: 0.9140 (mmm) cc_final: 0.8935 (mtt) REVERT: B 179 TYR cc_start: 0.8527 (m-80) cc_final: 0.8299 (m-80) REVERT: B 213 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8512 (tt) REVERT: B 293 LYS cc_start: 0.8739 (tptt) cc_final: 0.8442 (tttt) REVERT: C 179 TYR cc_start: 0.8536 (m-80) cc_final: 0.8296 (m-80) REVERT: C 213 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8489 (tt) REVERT: C 293 LYS cc_start: 0.8813 (tptt) cc_final: 0.8519 (tttt) REVERT: D 179 TYR cc_start: 0.8535 (m-80) cc_final: 0.8293 (m-80) REVERT: D 213 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8491 (tt) REVERT: D 293 LYS cc_start: 0.8810 (tptt) cc_final: 0.8550 (tttt) REVERT: E 71 MET cc_start: 0.8797 (tpp) cc_final: 0.8586 (tpp) REVERT: F 71 MET cc_start: 0.8747 (tpp) cc_final: 0.8538 (tpp) REVERT: G 71 MET cc_start: 0.8756 (tpp) cc_final: 0.8541 (tpp) REVERT: H 71 MET cc_start: 0.8755 (tpp) cc_final: 0.8544 (tpp) outliers start: 23 outliers final: 15 residues processed: 372 average time/residue: 0.1057 time to fit residues: 59.9670 Evaluate side-chains 323 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 304 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 213 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 5 optimal weight: 0.5980 chunk 152 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 182 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 297 HIS D 297 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.146621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.119919 restraints weight = 22705.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.120466 restraints weight = 15476.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.120799 restraints weight = 13523.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.121594 restraints weight = 10998.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.124655 restraints weight = 9857.837| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16008 Z= 0.120 Angle : 0.504 7.489 21624 Z= 0.258 Chirality : 0.037 0.144 2544 Planarity : 0.003 0.027 2668 Dihedral : 6.550 57.005 2280 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.57 % Allowed : 12.07 % Favored : 85.36 % 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: -0.01 (0.19), residues: 2000 helix: 0.24 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.36 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 90 TYR 0.015 0.001 TYR H 99 PHE 0.009 0.001 PHE A 291 TRP 0.013 0.001 TRP A 221 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (16004) covalent geometry : angle 0.50421 / 0.26 (21624) hydrogen bonds : bond 0.03776 / 2.50 ( 940) hydrogen bonds : angle 3.15146 / 2.20 ( 2796) Misc. bond : bond 0.00050 / 0.02 ( 4) *********************** 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 363 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 324 time to evaluate : 0.478 Fit side-chains REVERT: A 206 ARG cc_start: 0.6476 (mtt180) cc_final: 0.6054 (ttp80) REVERT: A 293 LYS cc_start: 0.8748 (tptt) cc_final: 0.8513 (tttt) REVERT: B 206 ARG cc_start: 0.6487 (mtt180) cc_final: 0.6084 (ttp80) REVERT: B 293 LYS cc_start: 0.8749 (tptt) cc_final: 0.8509 (tttt) REVERT: B 374 MET cc_start: 0.7074 (tpp) cc_final: 0.6821 (tpp) REVERT: C 206 ARG cc_start: 0.6506 (mtt180) cc_final: 0.6093 (ttp80) REVERT: C 293 LYS cc_start: 0.8735 (tptt) cc_final: 0.8500 (tttt) REVERT: D 206 ARG cc_start: 0.6459 (mtt180) cc_final: 0.6039 (ttp80) REVERT: E 71 MET cc_start: 0.8760 (tpp) cc_final: 0.8548 (tpp) REVERT: E 137 ASN cc_start: 0.7114 (m110) cc_final: 0.6903 (m110) REVERT: F 71 MET cc_start: 0.8751 (tpp) cc_final: 0.8547 (tpp) REVERT: F 137 ASN cc_start: 0.7104 (m110) cc_final: 0.6899 (m110) REVERT: G 71 MET cc_start: 0.8725 (tpp) cc_final: 0.8513 (tpp) REVERT: G 137 ASN cc_start: 0.7078 (m110) cc_final: 0.6860 (m110) REVERT: H 71 MET cc_start: 0.8749 (tpp) cc_final: 0.8543 (tpp) REVERT: H 137 ASN cc_start: 0.7075 (m110) cc_final: 0.6860 (m110) outliers start: 39 outliers final: 27 residues processed: 346 average time/residue: 0.1107 time to fit residues: 58.2821 Evaluate side-chains 315 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 288 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 91 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 42 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 13 optimal weight: 0.2980 chunk 105 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 358 HIS C 358 HIS D 358 HIS E 42 ASN E 53 ASN F 42 ASN F 53 ASN G 42 ASN G 53 ASN H 42 ASN H 53 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.149305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.122414 restraints weight = 22584.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.122939 restraints weight = 15658.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.123222 restraints weight = 13925.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.124010 restraints weight = 11320.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.124474 restraints weight = 10100.830| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16008 Z= 0.108 Angle : 0.488 6.643 21624 Z= 0.252 Chirality : 0.037 0.150 2544 Planarity : 0.003 0.041 2668 Dihedral : 6.192 59.273 2280 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.77 % Allowed : 13.19 % Favored : 84.04 % 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 (0.19), residues: 2000 helix: 0.82 (0.13), residues: 1508 sheet: None (None), residues: 0 loop : -0.09 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 90 TYR 0.013 0.001 TYR G 99 PHE 0.008 0.001 PHE C 291 TRP 0.010 0.001 TRP A 221 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (16004) covalent geometry : angle 0.48823 / 0.25 (21624) hydrogen bonds : bond 0.03473 / 2.30 ( 940) hydrogen bonds : angle 2.96768 / 2.06 ( 2796) Misc. bond : bond 0.00040 / 0.02 ( 4) *********************** 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 362 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 320 time to evaluate : 0.501 Fit side-chains REVERT: A 206 ARG cc_start: 0.6509 (mtt180) cc_final: 0.6186 (tmm160) REVERT: A 293 LYS cc_start: 0.8812 (tptt) cc_final: 0.8607 (tttt) REVERT: B 206 ARG cc_start: 0.6549 (mtt180) cc_final: 0.6220 (tmm160) REVERT: C 206 ARG cc_start: 0.6554 (mtt180) cc_final: 0.6218 (tmm160) REVERT: C 293 LYS cc_start: 0.8796 (tptt) cc_final: 0.8590 (tttt) REVERT: D 206 ARG cc_start: 0.6539 (mtt180) cc_final: 0.6207 (tmm160) outliers start: 42 outliers final: 23 residues processed: 333 average time/residue: 0.1118 time to fit residues: 56.5528 Evaluate side-chains 310 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 287 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 319 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 22 optimal weight: 0.1980 chunk 120 optimal weight: 0.7980 chunk 189 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 chunk 117 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 42 ASN F 42 ASN G 42 ASN H 42 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.148768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.121468 restraints weight = 22848.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.123215 restraints weight = 14926.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.123349 restraints weight = 13253.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.124118 restraints weight = 10592.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.124242 restraints weight = 9632.281| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16008 Z= 0.104 Angle : 0.487 8.297 21624 Z= 0.250 Chirality : 0.037 0.159 2544 Planarity : 0.003 0.038 2668 Dihedral : 5.905 54.121 2280 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.03 % Allowed : 13.52 % Favored : 83.44 % 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: 1.39 (0.19), residues: 2000 helix: 1.20 (0.14), residues: 1512 sheet: None (None), residues: 0 loop : 0.31 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 37 TYR 0.023 0.002 TYR H 138 PHE 0.007 0.001 PHE C 291 TRP 0.010 0.001 TRP A 221 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (16004) covalent geometry : angle 0.48710 / 0.25 (21624) hydrogen bonds : bond 0.03311 / 2.17 ( 940) hydrogen bonds : angle 2.84525 / 1.97 ( 2796) Misc. bond : bond 0.00037 / 0.02 ( 4) *********************** 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 347 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 301 time to evaluate : 0.617 Fit side-chains REVERT: A 149 GLU cc_start: 0.8091 (pt0) cc_final: 0.7744 (tt0) REVERT: A 156 MET cc_start: 0.8890 (mmm) cc_final: 0.8683 (mtt) REVERT: A 281 LEU cc_start: 0.7698 (tt) cc_final: 0.7345 (tp) REVERT: A 293 LYS cc_start: 0.8823 (tptt) cc_final: 0.8594 (tttt) REVERT: B 149 GLU cc_start: 0.8082 (pt0) cc_final: 0.7730 (tt0) REVERT: B 156 MET cc_start: 0.8891 (mmm) cc_final: 0.8683 (mtt) REVERT: C 149 GLU cc_start: 0.8074 (pt0) cc_final: 0.7757 (tt0) REVERT: C 293 LYS cc_start: 0.8816 (tptt) cc_final: 0.8585 (tttt) REVERT: D 289 LEU cc_start: 0.7396 (mm) cc_final: 0.6859 (tt) REVERT: E 71 MET cc_start: 0.8816 (tpp) cc_final: 0.8560 (tpp) REVERT: F 71 MET cc_start: 0.8814 (tpp) cc_final: 0.8559 (tpp) REVERT: G 71 MET cc_start: 0.8805 (tpp) cc_final: 0.8546 (tpp) REVERT: G 144 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.7008 (tpp) REVERT: H 71 MET cc_start: 0.8807 (tpp) cc_final: 0.8548 (tpp) REVERT: H 144 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6972 (tpp) outliers start: 46 outliers final: 25 residues processed: 320 average time/residue: 0.1118 time to fit residues: 54.3188 Evaluate side-chains 304 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 277 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 291 PHE Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain H residue 144 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 16 optimal weight: 0.0040 chunk 100 optimal weight: 3.9990 chunk 51 optimal weight: 0.0770 chunk 61 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 139 optimal weight: 6.9990 overall best weight: 0.4750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 42 ASN F 42 ASN G 42 ASN H 42 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.149208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.123333 restraints weight = 22679.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.122860 restraints weight = 17008.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.123314 restraints weight = 13438.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.124512 restraints weight = 11360.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.124595 restraints weight = 10102.771| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16008 Z= 0.095 Angle : 0.462 7.592 21624 Z= 0.242 Chirality : 0.036 0.147 2544 Planarity : 0.003 0.042 2668 Dihedral : 5.564 55.696 2280 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.50 % Allowed : 14.25 % Favored : 82.26 % 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: 1.82 (0.20), residues: 2000 helix: 1.54 (0.14), residues: 1520 sheet: None (None), residues: 0 loop : 0.35 (0.32), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 37 TYR 0.019 0.001 TYR H 138 PHE 0.005 0.001 PHE D 291 TRP 0.008 0.001 TRP A 221 HIS 0.004 0.001 HIS C 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (16004) covalent geometry : angle 0.46209 / 0.24 (21624) hydrogen bonds : bond 0.03047 / 1.99 ( 940) hydrogen bonds : angle 2.68977 / 1.86 ( 2796) Misc. bond : bond 0.00027 / 0.01 ( 4) *********************** 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 361 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 308 time to evaluate : 0.637 Fit side-chains REVERT: A 156 MET cc_start: 0.8981 (mmm) cc_final: 0.8626 (mtt) REVERT: A 281 LEU cc_start: 0.7548 (tt) cc_final: 0.7232 (tp) REVERT: A 289 LEU cc_start: 0.7359 (mm) cc_final: 0.6791 (tt) REVERT: A 293 LYS cc_start: 0.8824 (tptt) cc_final: 0.8587 (tttt) REVERT: B 289 LEU cc_start: 0.7375 (mm) cc_final: 0.6794 (tt) REVERT: C 289 LEU cc_start: 0.7488 (mm) cc_final: 0.6882 (tt) REVERT: C 293 LYS cc_start: 0.8796 (tptt) cc_final: 0.8562 (tttt) REVERT: D 289 LEU cc_start: 0.7515 (mm) cc_final: 0.6895 (tt) REVERT: E 108 VAL cc_start: 0.7719 (p) cc_final: 0.7304 (t) REVERT: F 99 TYR cc_start: 0.8275 (m-80) cc_final: 0.8063 (m-80) REVERT: F 108 VAL cc_start: 0.7436 (p) cc_final: 0.7138 (t) REVERT: G 108 VAL cc_start: 0.7405 (p) cc_final: 0.7142 (t) REVERT: H 99 TYR cc_start: 0.8238 (m-80) cc_final: 0.8036 (m-80) REVERT: H 108 VAL cc_start: 0.7445 (p) cc_final: 0.7199 (t) outliers start: 53 outliers final: 33 residues processed: 325 average time/residue: 0.1057 time to fit residues: 53.5059 Evaluate side-chains 321 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 288 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 291 PHE Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 91 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 194 optimal weight: 0.2980 chunk 198 optimal weight: 8.9990 chunk 153 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 182 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 42 ASN H 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.148163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.121755 restraints weight = 22685.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.122791 restraints weight = 15056.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.122957 restraints weight = 13658.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.123717 restraints weight = 10548.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.123944 restraints weight = 9154.508| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16008 Z= 0.105 Angle : 0.483 8.396 21624 Z= 0.249 Chirality : 0.036 0.133 2544 Planarity : 0.003 0.042 2668 Dihedral : 5.450 54.738 2280 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.69 % Allowed : 14.58 % Favored : 81.73 % 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: 2.16 (0.19), residues: 2000 helix: 1.77 (0.13), residues: 1524 sheet: None (None), residues: 0 loop : 0.53 (0.32), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 37 TYR 0.017 0.002 TYR H 138 PHE 0.013 0.001 PHE C 70 TRP 0.010 0.001 TRP A 221 HIS 0.004 0.001 HIS C 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (16004) covalent geometry : angle 0.48276 / 0.25 (21624) hydrogen bonds : bond 0.03103 / 2.02 ( 940) hydrogen bonds : angle 2.66218 / 1.84 ( 2796) Misc. bond : bond 0.00033 / 0.02 ( 4) *********************** 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 353 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 297 time to evaluate : 0.556 Fit side-chains REVERT: A 156 MET cc_start: 0.9019 (mmm) cc_final: 0.8715 (mtt) REVERT: A 281 LEU cc_start: 0.7608 (tt) cc_final: 0.7280 (tp) REVERT: A 289 LEU cc_start: 0.7430 (mm) cc_final: 0.6818 (tt) REVERT: B 289 LEU cc_start: 0.7474 (mm) cc_final: 0.6864 (tt) REVERT: C 289 LEU cc_start: 0.7470 (mm) cc_final: 0.6855 (tt) REVERT: C 343 LYS cc_start: 0.8558 (mttt) cc_final: 0.8177 (mttp) REVERT: D 289 LEU cc_start: 0.7434 (mm) cc_final: 0.6822 (tt) REVERT: E 71 MET cc_start: 0.8844 (tpp) cc_final: 0.8615 (tpp) REVERT: E 108 VAL cc_start: 0.7485 (p) cc_final: 0.7284 (t) REVERT: E 144 MET cc_start: 0.7841 (tmm) cc_final: 0.7549 (tmm) REVERT: F 71 MET cc_start: 0.8812 (tpp) cc_final: 0.8581 (tpp) REVERT: F 93 ASP cc_start: 0.7080 (t0) cc_final: 0.6808 (t0) REVERT: F 144 MET cc_start: 0.7853 (tmm) cc_final: 0.7552 (tmm) REVERT: G 71 MET cc_start: 0.8808 (tpp) cc_final: 0.8574 (tpp) REVERT: G 144 MET cc_start: 0.7838 (tmm) cc_final: 0.7526 (tmm) REVERT: H 71 MET cc_start: 0.8817 (tpp) cc_final: 0.8586 (tpp) REVERT: H 99 TYR cc_start: 0.8256 (m-80) cc_final: 0.8044 (m-80) REVERT: H 144 MET cc_start: 0.7841 (tmm) cc_final: 0.7527 (tmm) outliers start: 56 outliers final: 43 residues processed: 322 average time/residue: 0.1054 time to fit residues: 52.4874 Evaluate side-chains 333 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 290 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 291 PHE Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 42 ASN Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 42 ASN Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 137 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 8.9990 chunk 196 optimal weight: 0.7980 chunk 190 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 197 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 80 HIS D 107 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.147479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.121745 restraints weight = 22804.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.121425 restraints weight = 16844.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.122286 restraints weight = 13582.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.122881 restraints weight = 11340.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.123096 restraints weight = 9974.356| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16008 Z= 0.111 Angle : 0.485 7.515 21624 Z= 0.253 Chirality : 0.036 0.135 2544 Planarity : 0.004 0.044 2668 Dihedral : 5.410 50.871 2280 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.97 % Allowed : 15.11 % Favored : 81.93 % 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: 2.41 (0.19), residues: 2000 helix: 1.92 (0.13), residues: 1528 sheet: None (None), residues: 0 loop : 0.71 (0.32), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 90 TYR 0.017 0.001 TYR H 138 PHE 0.011 0.001 PHE C 70 TRP 0.010 0.001 TRP A 221 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (16004) covalent geometry : angle 0.48501 / 0.25 (21624) hydrogen bonds : bond 0.03185 / 2.07 ( 940) hydrogen bonds : angle 2.67410 / 1.85 ( 2796) Misc. bond : bond 0.00037 / 0.02 ( 4) *********************** 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 347 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 302 time to evaluate : 0.550 Fit side-chains REVERT: A 156 MET cc_start: 0.9023 (mmm) cc_final: 0.8745 (mtt) REVERT: A 281 LEU cc_start: 0.7616 (tt) cc_final: 0.7268 (tp) REVERT: A 289 LEU cc_start: 0.7426 (mm) cc_final: 0.6830 (tt) REVERT: A 321 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7909 (mm-30) REVERT: B 289 LEU cc_start: 0.7440 (mm) cc_final: 0.6834 (tt) REVERT: B 321 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7858 (mm-30) REVERT: C 289 LEU cc_start: 0.7445 (mm) cc_final: 0.6849 (tt) REVERT: C 343 LYS cc_start: 0.8537 (mttt) cc_final: 0.8238 (mtmm) REVERT: D 289 LEU cc_start: 0.7391 (mm) cc_final: 0.6782 (tt) REVERT: D 319 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8752 (tp) REVERT: D 321 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7876 (mm-30) REVERT: E 71 MET cc_start: 0.8811 (tpp) cc_final: 0.8590 (tpp) REVERT: F 71 MET cc_start: 0.8834 (tpp) cc_final: 0.8614 (tpp) REVERT: F 93 ASP cc_start: 0.7137 (t0) cc_final: 0.6862 (t0) REVERT: G 71 MET cc_start: 0.8827 (tpp) cc_final: 0.8602 (tpp) REVERT: H 71 MET cc_start: 0.8833 (tpp) cc_final: 0.8610 (tpp) outliers start: 45 outliers final: 41 residues processed: 324 average time/residue: 0.1048 time to fit residues: 52.3566 Evaluate side-chains 326 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 284 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 291 PHE Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 137 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 93 optimal weight: 0.0020 chunk 167 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 chunk 86 optimal weight: 0.0370 chunk 71 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 121 optimal weight: 0.5980 overall best weight: 0.3666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 HIS A 107 GLN A 358 HIS B 80 HIS B 107 GLN C 80 HIS C 107 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.152139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.126635 restraints weight = 22977.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.126443 restraints weight = 16872.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.127264 restraints weight = 14154.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.127987 restraints weight = 10958.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.128205 restraints weight = 9653.593| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16008 Z= 0.096 Angle : 0.480 7.780 21624 Z= 0.247 Chirality : 0.035 0.133 2544 Planarity : 0.004 0.050 2668 Dihedral : 5.155 46.865 2280 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.51 % Allowed : 15.83 % Favored : 81.66 % 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: 2.76 (0.20), residues: 2000 helix: 2.21 (0.13), residues: 1528 sheet: None (None), residues: 0 loop : 0.69 (0.32), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 90 TYR 0.016 0.002 TYR G 138 PHE 0.015 0.001 PHE G 141 TRP 0.009 0.001 TRP A 221 HIS 0.004 0.001 HIS C 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 (16004) covalent geometry : angle 0.48016 / 0.25 (21624) hydrogen bonds : bond 0.02889 / 1.87 ( 940) hydrogen bonds : angle 2.54356 / 1.76 ( 2796) Misc. bond : bond 0.00022 / 0.01 ( 4) *********************** 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 359 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 321 time to evaluate : 0.572 Fit side-chains REVERT: A 281 LEU cc_start: 0.7573 (tt) cc_final: 0.7207 (tp) REVERT: A 289 LEU cc_start: 0.7410 (mm) cc_final: 0.6793 (tt) REVERT: A 321 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7851 (mm-30) REVERT: B 289 LEU cc_start: 0.7402 (mm) cc_final: 0.6806 (tt) REVERT: B 321 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7805 (mm-30) REVERT: C 289 LEU cc_start: 0.7412 (mm) cc_final: 0.6839 (tt) REVERT: C 343 LYS cc_start: 0.8582 (mttt) cc_final: 0.8259 (mtmm) REVERT: D 289 LEU cc_start: 0.7418 (mm) cc_final: 0.6771 (tt) REVERT: D 321 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7828 (mm-30) REVERT: H 99 TYR cc_start: 0.8258 (m-80) cc_final: 0.7859 (m-80) outliers start: 38 outliers final: 28 residues processed: 332 average time/residue: 0.1093 time to fit residues: 55.6144 Evaluate side-chains 326 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 298 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 291 PHE Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 17 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 94 optimal weight: 0.0170 chunk 195 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 chunk 155 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 40 optimal weight: 0.0770 chunk 190 optimal weight: 4.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 364 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.150126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.123735 restraints weight = 22704.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.124835 restraints weight = 14779.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.125646 restraints weight = 13139.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.126250 restraints weight = 10166.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.126607 restraints weight = 8499.659| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16008 Z= 0.101 Angle : 0.487 7.771 21624 Z= 0.252 Chirality : 0.035 0.134 2544 Planarity : 0.004 0.052 2668 Dihedral : 5.095 44.968 2280 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.98 % Allowed : 16.42 % Favored : 81.60 % 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: 2.78 (0.20), residues: 2000 helix: 2.21 (0.13), residues: 1552 sheet: None (None), residues: 0 loop : 0.63 (0.33), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 90 TYR 0.017 0.002 TYR H 138 PHE 0.023 0.001 PHE F 141 TRP 0.011 0.001 TRP B 221 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (16004) covalent geometry : angle 0.48739 / 0.25 (21624) hydrogen bonds : bond 0.02914 / 1.90 ( 940) hydrogen bonds : angle 2.53869 / 1.76 ( 2796) Misc. bond : bond 0.00025 / 0.01 ( 4) ********************** 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 337 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 307 time to evaluate : 0.562 Fit side-chains REVERT: A 281 LEU cc_start: 0.7584 (tt) cc_final: 0.7318 (tp) REVERT: A 289 LEU cc_start: 0.7398 (mm) cc_final: 0.6819 (tt) REVERT: A 321 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7820 (mm-30) REVERT: B 289 LEU cc_start: 0.7368 (mm) cc_final: 0.6805 (tt) REVERT: B 296 LYS cc_start: 0.8648 (tttp) cc_final: 0.8436 (tptm) REVERT: B 321 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7866 (mm-30) REVERT: C 289 LEU cc_start: 0.7413 (mm) cc_final: 0.6863 (tt) REVERT: C 343 LYS cc_start: 0.8549 (mttt) cc_final: 0.8216 (mtmm) REVERT: D 289 LEU cc_start: 0.7406 (mm) cc_final: 0.6788 (tt) REVERT: D 321 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7890 (mm-30) outliers start: 30 outliers final: 30 residues processed: 315 average time/residue: 0.1112 time to fit residues: 53.3791 Evaluate side-chains 327 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 297 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 291 PHE Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 137 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 97 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 194 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 180 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.147871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.122349 restraints weight = 22717.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.122082 restraints weight = 16696.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.122447 restraints weight = 13966.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.124911 restraints weight = 10906.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.124890 restraints weight = 8323.260| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16008 Z= 0.119 Angle : 0.510 7.620 21624 Z= 0.262 Chirality : 0.037 0.138 2544 Planarity : 0.004 0.053 2668 Dihedral : 5.234 45.899 2280 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.18 % Allowed : 17.22 % Favored : 80.61 % 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: 2.88 (0.19), residues: 2000 helix: 2.28 (0.13), residues: 1532 sheet: None (None), residues: 0 loop : 0.75 (0.32), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 90 TYR 0.017 0.002 TYR F 99 PHE 0.026 0.001 PHE E 141 TRP 0.011 0.001 TRP D 221 HIS 0.003 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (16004) covalent geometry : angle 0.50960 / 0.26 (21624) hydrogen bonds : bond 0.03285 / 2.15 ( 940) hydrogen bonds : angle 2.66473 / 1.85 ( 2796) Misc. bond : bond 0.00041 / 0.02 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2371.36 seconds wall clock time: 42 minutes 3.10 seconds (2523.10 seconds total)