Starting phenix.real_space_refine on Thu Feb 5 18:40:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e63_47548/02_2026/9e63_47548.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e63_47548/02_2026/9e63_47548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e63_47548/02_2026/9e63_47548.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e63_47548/02_2026/9e63_47548.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e63_47548/02_2026/9e63_47548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e63_47548/02_2026/9e63_47548.map" } resolution = 2.3 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= 0.038 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: 5 Type Number sf(0) Gaussians P 35 5.49 5 S 70 5.16 5 C 12495 2.51 5 N 2982 2.21 5 O 3444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19026 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2509 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 8, 'TRANS': 322} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2509 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 8, 'TRANS': 322} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "C" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2509 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 8, 'TRANS': 322} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "D" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2509 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 8, 'TRANS': 322} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "E" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2509 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 8, 'TRANS': 322} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "F" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2509 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 8, 'TRANS': 322} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "G" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2509 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 8, 'TRANS': 322} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "A" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 250 Unusual residues: {'PTY': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 50 Chain: "B" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 254 Unusual residues: {'PTY': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 46 Chain: "C" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 164 Unusual residues: {'PTY': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Chain: "D" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 209 Unusual residues: {'PTY': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 41 Chain: "E" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 254 Unusual residues: {'PTY': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 46 Chain: "F" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 209 Unusual residues: {'PTY': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 41 Chain: "G" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 123 Unusual residues: {'PTY': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 27 Time building chain proxies: 4.21, per 1000 atoms: 0.22 Number of scatterers: 19026 At special positions: 0 Unit cell: (112.66, 110.94, 141.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 P 35 15.00 O 3444 8.00 N 2982 7.00 C 12495 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 805.2 milliseconds 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4312 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 15 sheets defined 61.4% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 removed outlier: 3.798A pdb=" N LEU A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 31 removed outlier: 3.714A pdb=" N ARG A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 67 removed outlier: 3.776A pdb=" N GLN A 46 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE A 65 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN A 67 " --> pdb=" O TYR A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 109 removed outlier: 3.967A pdb=" N ILE A 78 " --> pdb=" O THR A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 134 Processing helix chain 'A' and resid 143 through 160 Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 219 through 223 Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 244 through 249 removed outlier: 3.668A pdb=" N ALA A 248 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA A 249 " --> pdb=" O GLU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 264 Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'B' and resid 5 through 13 removed outlier: 3.808A pdb=" N LEU B 13 " --> pdb=" O ASN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 31 removed outlier: 3.743A pdb=" N ARG B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 67 removed outlier: 3.778A pdb=" N GLN B 46 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE B 65 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN B 67 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 109 removed outlier: 3.959A pdb=" N ILE B 78 " --> pdb=" O THR B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 134 Processing helix chain 'B' and resid 143 through 160 Processing helix chain 'B' and resid 160 through 176 Processing helix chain 'B' and resid 219 through 223 Processing helix chain 'B' and resid 229 through 232 Processing helix chain 'B' and resid 244 through 249 removed outlier: 3.603A pdb=" N ALA B 248 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ALA B 249 " --> pdb=" O GLU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 264 Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'C' and resid 5 through 13 removed outlier: 3.800A pdb=" N LEU C 13 " --> pdb=" O ASN C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 31 removed outlier: 3.736A pdb=" N ARG C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 67 removed outlier: 3.751A pdb=" N GLN C 46 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE C 65 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN C 67 " --> pdb=" O TYR C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 109 removed outlier: 3.962A pdb=" N ILE C 78 " --> pdb=" O THR C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 134 Processing helix chain 'C' and resid 143 through 160 Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 219 through 223 Processing helix chain 'C' and resid 229 through 232 Processing helix chain 'C' and resid 244 through 249 removed outlier: 3.611A pdb=" N ALA C 248 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ALA C 249 " --> pdb=" O GLU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 264 Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'D' and resid 5 through 13 removed outlier: 3.797A pdb=" N LEU D 13 " --> pdb=" O ASN D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 31 removed outlier: 3.715A pdb=" N ARG D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 67 removed outlier: 3.785A pdb=" N GLN D 46 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE D 65 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN D 67 " --> pdb=" O TYR D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 109 removed outlier: 3.972A pdb=" N ILE D 78 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 134 Processing helix chain 'D' and resid 143 through 160 Processing helix chain 'D' and resid 160 through 176 Processing helix chain 'D' and resid 219 through 223 Processing helix chain 'D' and resid 229 through 232 Processing helix chain 'D' and resid 244 through 249 removed outlier: 3.652A pdb=" N ALA D 248 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ALA D 249 " --> pdb=" O GLU D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 264 Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'E' and resid 5 through 13 removed outlier: 3.798A pdb=" N LEU E 13 " --> pdb=" O ASN E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 31 removed outlier: 3.733A pdb=" N ARG E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 67 removed outlier: 3.777A pdb=" N GLN E 46 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE E 65 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN E 67 " --> pdb=" O TYR E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 109 removed outlier: 3.964A pdb=" N ILE E 78 " --> pdb=" O THR E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 134 Processing helix chain 'E' and resid 143 through 160 Processing helix chain 'E' and resid 160 through 176 Processing helix chain 'E' and resid 219 through 223 Processing helix chain 'E' and resid 229 through 232 Processing helix chain 'E' and resid 244 through 249 removed outlier: 3.596A pdb=" N ALA E 248 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ALA E 249 " --> pdb=" O GLU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 264 Processing helix chain 'E' and resid 298 through 320 Processing helix chain 'F' and resid 5 through 13 removed outlier: 3.806A pdb=" N LEU F 13 " --> pdb=" O ASN F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 31 removed outlier: 3.733A pdb=" N ARG F 31 " --> pdb=" O SER F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 67 removed outlier: 3.762A pdb=" N GLN F 46 " --> pdb=" O PHE F 42 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE F 65 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN F 67 " --> pdb=" O TYR F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 109 removed outlier: 3.963A pdb=" N ILE F 78 " --> pdb=" O THR F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 134 Processing helix chain 'F' and resid 143 through 160 Processing helix chain 'F' and resid 160 through 176 Processing helix chain 'F' and resid 219 through 223 Processing helix chain 'F' and resid 229 through 232 Processing helix chain 'F' and resid 244 through 249 removed outlier: 3.701A pdb=" N ALA F 248 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ALA F 249 " --> pdb=" O GLU F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 264 Processing helix chain 'F' and resid 298 through 320 Processing helix chain 'G' and resid 5 through 13 removed outlier: 3.808A pdb=" N LEU G 13 " --> pdb=" O ASN G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 31 removed outlier: 3.734A pdb=" N ARG G 31 " --> pdb=" O SER G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 67 removed outlier: 3.786A pdb=" N GLN G 46 " --> pdb=" O PHE G 42 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE G 65 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN G 67 " --> pdb=" O TYR G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 109 removed outlier: 3.967A pdb=" N ILE G 78 " --> pdb=" O THR G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 134 Processing helix chain 'G' and resid 143 through 160 Processing helix chain 'G' and resid 160 through 176 Processing helix chain 'G' and resid 219 through 223 Processing helix chain 'G' and resid 229 through 232 Processing helix chain 'G' and resid 244 through 249 removed outlier: 3.685A pdb=" N ALA G 248 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ALA G 249 " --> pdb=" O GLU G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 264 Processing helix chain 'G' and resid 298 through 320 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 185 removed outlier: 6.610A pdb=" N LYS A 205 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ILE A 199 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ILE A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 removed outlier: 7.339A pdb=" N ILE G 203 " --> pdb=" O ILE G 199 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ILE G 199 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LYS G 205 " --> pdb=" O ALA G 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 235 through 243 removed outlier: 3.928A pdb=" N ARG A 235 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN A 287 " --> pdb=" O ASN A 279 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 333 removed outlier: 6.524A pdb=" N GLN B 329 " --> pdb=" O TYR C 332 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN C 329 " --> pdb=" O TYR D 332 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLN F 329 " --> pdb=" O TYR G 332 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N GLN G 329 " --> pdb=" O SER A 328 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR A 330 " --> pdb=" O GLN G 329 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LEU G 331 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TYR A 332 " --> pdb=" O LEU G 331 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N MET G 333 " --> pdb=" O TYR A 332 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 184 through 185 removed outlier: 6.608A pdb=" N LYS B 205 " --> pdb=" O ALA B 197 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ILE B 199 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ILE B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 235 through 243 removed outlier: 3.941A pdb=" N ARG B 235 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN B 287 " --> pdb=" O ASN B 279 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 184 through 185 removed outlier: 6.602A pdb=" N LYS C 205 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ILE C 199 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ILE C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 235 through 243 removed outlier: 3.988A pdb=" N ARG C 235 " --> pdb=" O THR C 294 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASN C 287 " --> pdb=" O ASN C 279 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 184 through 185 removed outlier: 6.576A pdb=" N LYS D 205 " --> pdb=" O ALA D 197 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ILE D 199 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ILE D 203 " --> pdb=" O ILE D 199 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 235 through 243 removed outlier: 3.919A pdb=" N ARG D 235 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN D 280 " --> pdb=" O ASN D 287 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N MET D 289 " --> pdb=" O PHE D 278 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N PHE D 278 " --> pdb=" O MET D 289 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N TYR D 291 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL D 276 " --> pdb=" O TYR D 291 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 184 through 185 removed outlier: 6.560A pdb=" N LYS E 205 " --> pdb=" O ALA E 197 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ILE E 199 " --> pdb=" O ILE E 203 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE E 203 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 235 through 243 removed outlier: 3.926A pdb=" N ARG E 235 " --> pdb=" O THR E 294 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN E 280 " --> pdb=" O ASN E 287 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N MET E 289 " --> pdb=" O PHE E 278 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N PHE E 278 " --> pdb=" O MET E 289 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N TYR E 291 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL E 276 " --> pdb=" O TYR E 291 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 184 through 185 removed outlier: 6.581A pdb=" N LYS F 205 " --> pdb=" O ALA F 197 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ILE F 199 " --> pdb=" O ILE F 203 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ILE F 203 " --> pdb=" O ILE F 199 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 235 through 243 removed outlier: 3.946A pdb=" N ARG F 235 " --> pdb=" O THR F 294 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN F 287 " --> pdb=" O ASN F 279 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 235 through 243 removed outlier: 3.997A pdb=" N ARG G 235 " --> pdb=" O THR G 294 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN G 280 " --> pdb=" O ASN G 287 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N MET G 289 " --> pdb=" O PHE G 278 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N PHE G 278 " --> pdb=" O MET G 289 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N TYR G 291 " --> pdb=" O VAL G 276 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N VAL G 276 " --> pdb=" O TYR G 291 " (cutoff:3.500A) 1223 hydrogen bonds defined for protein. 3510 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: 3.44 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3072 1.32 - 1.44: 4790 1.44 - 1.57: 11269 1.57 - 1.69: 70 1.69 - 1.81: 126 Bond restraints: 19327 Sorted by residual: bond pdb=" SD MET G 158 " pdb=" CE MET G 158 " ideal model delta sigma weight residual 1.791 1.759 0.032 2.50e-02 1.60e+03 1.63e+00 bond pdb=" CB MET B 172 " pdb=" CG MET B 172 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.01e+00 bond pdb=" CG LYS F 123 " pdb=" CD LYS F 123 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.43e-01 bond pdb=" CG LYS C 123 " pdb=" CD LYS C 123 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 7.87e-01 bond pdb=" CG LYS D 123 " pdb=" CD LYS D 123 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 7.83e-01 ... (remaining 19322 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 25700 2.32 - 4.64: 182 4.64 - 6.96: 25 6.96 - 9.28: 11 9.28 - 11.60: 3 Bond angle restraints: 25921 Sorted by residual: angle pdb=" CA LEU G 154 " pdb=" CB LEU G 154 " pdb=" CG LEU G 154 " ideal model delta sigma weight residual 116.30 127.90 -11.60 3.50e+00 8.16e-02 1.10e+01 angle pdb=" CA LEU D 154 " pdb=" CB LEU D 154 " pdb=" CG LEU D 154 " ideal model delta sigma weight residual 116.30 127.17 -10.87 3.50e+00 8.16e-02 9.64e+00 angle pdb=" CA LEU C 154 " pdb=" CB LEU C 154 " pdb=" CG LEU C 154 " ideal model delta sigma weight residual 116.30 126.90 -10.60 3.50e+00 8.16e-02 9.17e+00 angle pdb=" CB MET B 172 " pdb=" CG MET B 172 " pdb=" SD MET B 172 " ideal model delta sigma weight residual 112.70 121.70 -9.00 3.00e+00 1.11e-01 9.00e+00 angle pdb=" CA TRP G 184 " pdb=" CB TRP G 184 " pdb=" CG TRP G 184 " ideal model delta sigma weight residual 113.60 118.98 -5.38 1.90e+00 2.77e-01 8.03e+00 ... (remaining 25916 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.98: 10604 25.98 - 51.95: 954 51.95 - 77.93: 142 77.93 - 103.90: 32 103.90 - 129.88: 7 Dihedral angle restraints: 11739 sinusoidal: 5040 harmonic: 6699 Sorted by residual: dihedral pdb=" N1 PTY E 404 " pdb=" C2 PTY E 404 " pdb=" C3 PTY E 404 " pdb=" O11 PTY E 404 " ideal model delta sinusoidal sigma weight residual 65.33 -164.79 -129.88 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" N1 PTY A 401 " pdb=" C2 PTY A 401 " pdb=" C3 PTY A 401 " pdb=" O11 PTY A 401 " ideal model delta sinusoidal sigma weight residual 65.33 -168.44 -126.23 1 3.00e+01 1.11e-03 1.70e+01 dihedral pdb=" N1 PTY F 403 " pdb=" C2 PTY F 403 " pdb=" C3 PTY F 403 " pdb=" O11 PTY F 403 " ideal model delta sinusoidal sigma weight residual 65.33 -169.34 -125.33 1 3.00e+01 1.11e-03 1.68e+01 ... (remaining 11736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1796 0.031 - 0.062: 705 0.062 - 0.092: 308 0.092 - 0.123: 86 0.123 - 0.154: 38 Chirality restraints: 2933 Sorted by residual: chirality pdb=" CA ILE G 206 " pdb=" N ILE G 206 " pdb=" C ILE G 206 " pdb=" CB ILE G 206 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA ILE E 206 " pdb=" N ILE E 206 " pdb=" C ILE E 206 " pdb=" CB ILE E 206 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" CA ILE A 206 " pdb=" N ILE A 206 " pdb=" C ILE A 206 " pdb=" CB ILE A 206 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.71e-01 ... (remaining 2930 not shown) Planarity restraints: 3122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 255 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.86e+00 pdb=" C VAL E 255 " 0.034 2.00e-02 2.50e+03 pdb=" O VAL E 255 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU E 256 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 255 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.73e+00 pdb=" C VAL D 255 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL D 255 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU D 256 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 255 " -0.010 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C VAL G 255 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL G 255 " -0.012 2.00e-02 2.50e+03 pdb=" N GLU G 256 " -0.011 2.00e-02 2.50e+03 ... (remaining 3119 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4123 2.79 - 3.32: 17817 3.32 - 3.84: 31044 3.84 - 4.37: 37166 4.37 - 4.90: 62019 Nonbonded interactions: 152169 Sorted by model distance: nonbonded pdb=" OG1 THR E 208 " pdb=" OD1 ASP E 210 " model vdw 2.261 3.040 nonbonded pdb=" OG1 THR F 208 " pdb=" OD1 ASP F 210 " model vdw 2.289 3.040 nonbonded pdb=" OG1 THR G 208 " pdb=" OD1 ASP G 210 " model vdw 2.315 3.040 nonbonded pdb=" OG1 THR B 208 " pdb=" OD1 ASP B 210 " model vdw 2.315 3.040 nonbonded pdb=" OG1 THR D 208 " pdb=" OD1 ASP D 210 " model vdw 2.315 3.040 ... (remaining 152164 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 4 through 334 or (resid 401 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C5 or name C6 or name C8 or name N1 or name O10 or name \ O11 or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or na \ me P1 )) or (resid 402 and (name C1 or name C11 or name C12 or name C13 or name \ C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or na \ me C20 or name C21 or name C22 or name C23 or name C3 or name C30 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C3 \ 8 or name C39 or name C5 or name C6 or name C8 or name N1 or name O10 or name O1 \ 1 or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name \ P1 )) or (resid 403 and (name C1 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or name \ C20 or name C21 or name C3 or name C30 or name C31 or name C32 or name C33 or na \ me C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 o \ r name C41 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 o \ r name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 \ )))) selection = (chain 'B' and (resid 4 through 334 or (resid 401 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C5 or name C6 or name C8 or name N1 or name O10 or name \ O11 or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or na \ me P1 )) or (resid 402 and (name C1 or name C11 or name C12 or name C13 or name \ C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or na \ me C20 or name C21 or name C22 or name C23 or name C3 or name C30 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C3 \ 8 or name C39 or name C5 or name C6 or name C8 or name N1 or name O10 or name O1 \ 1 or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name \ P1 )) or (resid 403 and (name C1 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or name \ C20 or name C21 or name C3 or name C30 or name C31 or name C32 or name C33 or na \ me C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 o \ r name C41 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 o \ r name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 \ )))) selection = (chain 'C' and (resid 4 through 334 or (resid 401 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C5 or name C6 or name C8 or name N1 or name O10 or name \ O11 or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or na \ me P1 )) or (resid 402 and (name C1 or name C11 or name C12 or name C13 or name \ C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or na \ me C20 or name C21 or name C22 or name C23 or name C3 or name C30 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C3 \ 8 or name C39 or name C5 or name C6 or name C8 or name N1 or name O10 or name O1 \ 1 or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name \ P1 )) or resid 403)) selection = (chain 'D' and (resid 4 through 334 or (resid 401 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C5 or name C6 or name C8 or name N1 or name O10 or name \ O11 or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or na \ me P1 )) or (resid 402 and (name C1 or name C11 or name C12 or name C13 or name \ C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or na \ me C20 or name C21 or name C22 or name C23 or name C3 or name C30 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C3 \ 8 or name C39 or name C5 or name C6 or name C8 or name N1 or name O10 or name O1 \ 1 or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name \ P1 )) or (resid 403 and (name C1 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or name \ C20 or name C21 or name C3 or name C30 or name C31 or name C32 or name C33 or na \ me C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 o \ r name C41 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 o \ r name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 \ )))) selection = (chain 'E' and (resid 4 through 334 or (resid 401 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C5 or name C6 or name C8 or name N1 or name O10 or name \ O11 or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or na \ me P1 )) or (resid 402 and (name C1 or name C11 or name C12 or name C13 or name \ C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or na \ me C20 or name C21 or name C22 or name C23 or name C3 or name C30 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C3 \ 8 or name C39 or name C5 or name C6 or name C8 or name N1 or name O10 or name O1 \ 1 or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name \ P1 )) or (resid 403 and (name C1 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or name \ C20 or name C21 or name C3 or name C30 or name C31 or name C32 or name C33 or na \ me C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 o \ r name C41 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 o \ r name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 \ )))) selection = (chain 'F' and (resid 4 through 334 or (resid 401 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C5 or name C6 or name C8 or name N1 or name O10 or name \ O11 or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or na \ me P1 )) or (resid 402 and (name C1 or name C11 or name C12 or name C13 or name \ C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or na \ me C20 or name C21 or name C22 or name C23 or name C3 or name C30 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C3 \ 8 or name C39 or name C5 or name C6 or name C8 or name N1 or name O10 or name O1 \ 1 or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name \ P1 )) or (resid 403 and (name C1 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or name \ C20 or name C21 or name C25 or name C26 or name C3 or name C30 or name C31 or na \ me C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 o \ r name C39 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 o \ r name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 \ )))) selection = (chain 'G' and (resid 4 through 334 or (resid 401 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C5 or name C6 or name C8 or name N1 or name O10 or name \ O11 or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or na \ me P1 )) or resid 402 or (resid 403 and (name C1 or name C11 or name C12 or name \ C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or \ name C2 or name C20 or name C21 or name C3 or name C30 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C \ 39 or name C40 or name C41 or name C5 or name C6 or name C8 or name N1 or name O \ 10 or name O11 or name O12 or name O13 or name O14 or name O30 or name O4 or nam \ e O7 or name P1 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.150 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.500 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9106 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19327 Z= 0.154 Angle : 0.562 11.603 25921 Z= 0.300 Chirality : 0.042 0.154 2933 Planarity : 0.004 0.032 3122 Dihedral : 19.566 129.880 7427 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.84 % Allowed : 22.10 % Favored : 77.05 % 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: 0.78 (0.17), residues: 2303 helix: 1.88 (0.14), residues: 1281 sheet: -1.05 (0.28), residues: 350 loop : -1.25 (0.21), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 202 TYR 0.012 0.001 TYR F 291 PHE 0.012 0.001 PHE D 281 TRP 0.012 0.001 TRP D 184 HIS 0.001 0.000 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00331 (19327) covalent geometry : angle 0.56190 (25921) hydrogen bonds : bond 0.12280 ( 1223) hydrogen bonds : angle 5.71694 ( 3510) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 397 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.9058 (m-10) cc_final: 0.8791 (m-10) REVERT: A 92 ILE cc_start: 0.9483 (mm) cc_final: 0.9280 (mm) REVERT: A 93 LYS cc_start: 0.8312 (mmtt) cc_final: 0.7737 (mttt) REVERT: A 103 LYS cc_start: 0.9392 (mmtt) cc_final: 0.9147 (mptt) REVERT: A 104 GLN cc_start: 0.9011 (tt0) cc_final: 0.8549 (tm-30) REVERT: A 107 LYS cc_start: 0.9212 (tttt) cc_final: 0.8761 (tmmt) REVERT: A 116 ARG cc_start: 0.8728 (mtp180) cc_final: 0.8426 (ttm-80) REVERT: B 50 TYR cc_start: 0.9089 (m-10) cc_final: 0.8775 (m-10) REVERT: B 81 ILE cc_start: 0.9048 (mm) cc_final: 0.8779 (mp) REVERT: B 92 ILE cc_start: 0.9499 (mm) cc_final: 0.9266 (mm) REVERT: B 93 LYS cc_start: 0.8319 (mmtt) cc_final: 0.7949 (mttt) REVERT: B 103 LYS cc_start: 0.9365 (mmtt) cc_final: 0.9113 (mptt) REVERT: B 104 GLN cc_start: 0.8955 (tt0) cc_final: 0.8367 (tm-30) REVERT: B 107 LYS cc_start: 0.9259 (tttt) cc_final: 0.8833 (tmmt) REVERT: B 116 ARG cc_start: 0.8727 (mtp180) cc_final: 0.8403 (mtp85) REVERT: C 81 ILE cc_start: 0.9076 (mm) cc_final: 0.8840 (mm) REVERT: C 92 ILE cc_start: 0.9508 (mm) cc_final: 0.9300 (mm) REVERT: C 93 LYS cc_start: 0.8284 (mmtt) cc_final: 0.8051 (mttt) REVERT: C 103 LYS cc_start: 0.9348 (mmtt) cc_final: 0.9138 (mppt) REVERT: C 104 GLN cc_start: 0.8871 (tt0) cc_final: 0.8373 (tm-30) REVERT: C 107 LYS cc_start: 0.9234 (tttt) cc_final: 0.8838 (tmmt) REVERT: C 116 ARG cc_start: 0.8712 (mtp180) cc_final: 0.8471 (mmm-85) REVERT: D 50 TYR cc_start: 0.9098 (m-10) cc_final: 0.8838 (m-10) REVERT: D 93 LYS cc_start: 0.8399 (mmtt) cc_final: 0.7918 (mttt) REVERT: D 97 LEU cc_start: 0.9598 (tt) cc_final: 0.9385 (tt) REVERT: D 103 LYS cc_start: 0.9362 (mmtt) cc_final: 0.9135 (mppt) REVERT: D 104 GLN cc_start: 0.8942 (tt0) cc_final: 0.8541 (tm-30) REVERT: D 107 LYS cc_start: 0.9208 (tttt) cc_final: 0.8753 (tmmt) REVERT: D 116 ARG cc_start: 0.8724 (mtp180) cc_final: 0.8429 (mmm-85) REVERT: D 120 ARG cc_start: 0.8470 (ttm170) cc_final: 0.8208 (mtm-85) REVERT: E 50 TYR cc_start: 0.9112 (m-10) cc_final: 0.8817 (m-10) REVERT: E 93 LYS cc_start: 0.8293 (mmtt) cc_final: 0.7818 (mmtp) REVERT: E 96 LEU cc_start: 0.9180 (tp) cc_final: 0.8937 (mm) REVERT: E 103 LYS cc_start: 0.9310 (mmtt) cc_final: 0.9039 (mppt) REVERT: E 104 GLN cc_start: 0.8822 (tm130) cc_final: 0.8483 (tm-30) REVERT: E 107 LYS cc_start: 0.9160 (tttt) cc_final: 0.8719 (tmmt) REVERT: E 116 ARG cc_start: 0.8693 (mtp180) cc_final: 0.8479 (mmm-85) REVERT: F 50 TYR cc_start: 0.9032 (m-10) cc_final: 0.8800 (m-10) REVERT: F 92 ILE cc_start: 0.9520 (mm) cc_final: 0.9316 (mm) REVERT: F 103 LYS cc_start: 0.9319 (mmtt) cc_final: 0.9031 (mptt) REVERT: F 104 GLN cc_start: 0.8874 (tt0) cc_final: 0.8551 (tm-30) REVERT: F 105 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8472 (tp40) REVERT: F 107 LYS cc_start: 0.9207 (tttt) cc_final: 0.8772 (tmmt) REVERT: F 116 ARG cc_start: 0.8644 (mtp180) cc_final: 0.8408 (mtp85) REVERT: F 120 ARG cc_start: 0.8374 (ttm170) cc_final: 0.8071 (mtm-85) REVERT: G 50 TYR cc_start: 0.9048 (m-10) cc_final: 0.8780 (m-80) REVERT: G 93 LYS cc_start: 0.8293 (mmtt) cc_final: 0.7911 (mttt) REVERT: G 103 LYS cc_start: 0.9375 (mmtt) cc_final: 0.9141 (mptt) REVERT: G 107 LYS cc_start: 0.9257 (tttt) cc_final: 0.8849 (tmmt) outliers start: 15 outliers final: 13 residues processed: 410 average time/residue: 0.6002 time to fit residues: 275.3437 Evaluate side-chains 379 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 366 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 136 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.0470 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.1980 chunk 200 optimal weight: 50.0000 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 43 HIS C 46 GLN D 280 GLN F 43 HIS ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.128726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.066818 restraints weight = 28729.669| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 2.03 r_work: 0.2515 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2391 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19327 Z= 0.120 Angle : 0.529 8.310 25921 Z= 0.275 Chirality : 0.042 0.180 2933 Planarity : 0.003 0.026 3122 Dihedral : 17.006 117.294 3695 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.82 % Allowed : 22.16 % Favored : 74.02 % 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: 1.63 (0.18), residues: 2303 helix: 2.72 (0.14), residues: 1295 sheet: -0.85 (0.28), residues: 329 loop : -1.24 (0.21), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 116 TYR 0.016 0.001 TYR A 174 PHE 0.012 0.001 PHE A 80 TRP 0.009 0.001 TRP C 184 HIS 0.004 0.001 HIS G 43 Details of bonding type rmsd covalent geometry : bond 0.00258 (19327) covalent geometry : angle 0.52885 (25921) hydrogen bonds : bond 0.04316 ( 1223) hydrogen bonds : angle 3.76832 ( 3510) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 394 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.9052 (m-10) cc_final: 0.8772 (m-10) REVERT: A 93 LYS cc_start: 0.8307 (mmtt) cc_final: 0.7620 (mttt) REVERT: A 103 LYS cc_start: 0.9409 (mmtt) cc_final: 0.8986 (mmtm) REVERT: A 104 GLN cc_start: 0.9206 (tt0) cc_final: 0.8577 (tm-30) REVERT: A 107 LYS cc_start: 0.9328 (tttt) cc_final: 0.8815 (tmmt) REVERT: A 116 ARG cc_start: 0.9111 (mtp180) cc_final: 0.8720 (ttm-80) REVERT: B 50 TYR cc_start: 0.9059 (m-10) cc_final: 0.8787 (m-10) REVERT: B 103 LYS cc_start: 0.9384 (mmtt) cc_final: 0.8970 (mmtm) REVERT: B 104 GLN cc_start: 0.9122 (tt0) cc_final: 0.8475 (tm-30) REVERT: B 107 LYS cc_start: 0.9366 (tttt) cc_final: 0.8867 (tmmt) REVERT: B 116 ARG cc_start: 0.8967 (mtp180) cc_final: 0.8652 (mtp85) REVERT: B 140 MET cc_start: 0.7208 (tpp) cc_final: 0.6958 (tpp) REVERT: C 46 GLN cc_start: 0.9119 (tt0) cc_final: 0.8686 (tm-30) REVERT: C 93 LYS cc_start: 0.8562 (mmtt) cc_final: 0.7613 (mttt) REVERT: C 103 LYS cc_start: 0.9374 (mmtt) cc_final: 0.9056 (mptt) REVERT: C 104 GLN cc_start: 0.9097 (tt0) cc_final: 0.8583 (tm-30) REVERT: C 107 LYS cc_start: 0.9315 (tttt) cc_final: 0.8872 (tmmt) REVERT: C 116 ARG cc_start: 0.9122 (mtp180) cc_final: 0.8794 (mmm-85) REVERT: C 140 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.6652 (mpp) REVERT: C 158 MET cc_start: 0.9066 (mmm) cc_final: 0.8842 (mtp) REVERT: C 172 MET cc_start: 0.8754 (tmm) cc_final: 0.8521 (tmm) REVERT: D 50 TYR cc_start: 0.9071 (m-10) cc_final: 0.8821 (m-10) REVERT: D 93 LYS cc_start: 0.8373 (mmtt) cc_final: 0.7627 (mttt) REVERT: D 103 LYS cc_start: 0.9397 (mmtt) cc_final: 0.9075 (mppt) REVERT: D 104 GLN cc_start: 0.9141 (tt0) cc_final: 0.8520 (tm-30) REVERT: D 107 LYS cc_start: 0.9320 (tttt) cc_final: 0.8774 (tmmt) REVERT: D 116 ARG cc_start: 0.9079 (mtp180) cc_final: 0.8700 (mmm-85) REVERT: D 120 ARG cc_start: 0.8352 (ttm170) cc_final: 0.8128 (mtm-85) REVERT: D 134 TYR cc_start: 0.8428 (m-10) cc_final: 0.8151 (m-10) REVERT: E 50 TYR cc_start: 0.9083 (m-10) cc_final: 0.8770 (m-10) REVERT: E 68 TYR cc_start: 0.8171 (m-10) cc_final: 0.7936 (m-10) REVERT: E 92 ILE cc_start: 0.9449 (mm) cc_final: 0.9234 (mm) REVERT: E 103 LYS cc_start: 0.9310 (mmtt) cc_final: 0.8977 (mptt) REVERT: E 104 GLN cc_start: 0.8945 (tm130) cc_final: 0.8440 (tm-30) REVERT: E 107 LYS cc_start: 0.9270 (tttt) cc_final: 0.8754 (tmmt) REVERT: E 116 ARG cc_start: 0.9087 (mtp180) cc_final: 0.8751 (mmm-85) REVERT: F 50 TYR cc_start: 0.9056 (m-10) cc_final: 0.8833 (m-10) REVERT: F 93 LYS cc_start: 0.8378 (mmtt) cc_final: 0.7862 (mmtt) REVERT: F 103 LYS cc_start: 0.9350 (mmtt) cc_final: 0.8995 (mptt) REVERT: F 104 GLN cc_start: 0.9049 (tt0) cc_final: 0.8634 (tm-30) REVERT: F 107 LYS cc_start: 0.9325 (tttt) cc_final: 0.8795 (tmmt) REVERT: F 116 ARG cc_start: 0.9113 (mtp180) cc_final: 0.8766 (mmm-85) REVERT: F 120 ARG cc_start: 0.8315 (ttm170) cc_final: 0.8072 (mtm-85) REVERT: G 50 TYR cc_start: 0.9034 (m-10) cc_final: 0.8662 (m-80) REVERT: G 103 LYS cc_start: 0.9378 (mmtt) cc_final: 0.9068 (mptt) REVERT: G 104 GLN cc_start: 0.9015 (tm-30) cc_final: 0.8618 (tm-30) REVERT: G 107 LYS cc_start: 0.9369 (tttt) cc_final: 0.8879 (tmmt) outliers start: 68 outliers final: 21 residues processed: 432 average time/residue: 0.5975 time to fit residues: 289.0874 Evaluate side-chains 401 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 379 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 148 PHE Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 136 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 67 optimal weight: 40.0000 chunk 145 optimal weight: 0.9990 chunk 165 optimal weight: 40.0000 chunk 205 optimal weight: 4.9990 chunk 134 optimal weight: 50.0000 chunk 13 optimal weight: 2.9990 chunk 100 optimal weight: 40.0000 chunk 160 optimal weight: 1.9990 chunk 34 optimal weight: 50.0000 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN B 100 GLN C 46 GLN C 280 GLN D 100 GLN D 280 GLN E 318 GLN G 100 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.126110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.063688 restraints weight = 28879.799| |-----------------------------------------------------------------------------| r_work (start): 0.2617 rms_B_bonded: 2.02 r_work: 0.2445 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2320 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 19327 Z= 0.208 Angle : 0.586 14.482 25921 Z= 0.300 Chirality : 0.044 0.157 2933 Planarity : 0.003 0.027 3122 Dihedral : 16.884 111.704 3695 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.04 % Favored : 96.66 % Rotamer: Outliers : 4.33 % Allowed : 24.35 % Favored : 71.32 % 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: 1.66 (0.17), residues: 2303 helix: 2.64 (0.14), residues: 1309 sheet: -0.07 (0.33), residues: 259 loop : -1.42 (0.19), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 116 TYR 0.016 0.001 TYR B 174 PHE 0.016 0.002 PHE F 47 TRP 0.012 0.001 TRP C 184 HIS 0.004 0.001 HIS D 320 Details of bonding type rmsd covalent geometry : bond 0.00486 (19327) covalent geometry : angle 0.58584 (25921) hydrogen bonds : bond 0.05102 ( 1223) hydrogen bonds : angle 3.73244 ( 3510) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 400 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 HIS cc_start: 0.8636 (m-70) cc_final: 0.8357 (m-70) REVERT: A 50 TYR cc_start: 0.9104 (m-10) cc_final: 0.8810 (m-10) REVERT: A 93 LYS cc_start: 0.8386 (mmtt) cc_final: 0.7801 (mttt) REVERT: A 103 LYS cc_start: 0.9438 (mmtt) cc_final: 0.9024 (mmtm) REVERT: A 104 GLN cc_start: 0.9210 (tt0) cc_final: 0.8591 (tm-30) REVERT: A 107 LYS cc_start: 0.9379 (tttt) cc_final: 0.8898 (tmmt) REVERT: A 116 ARG cc_start: 0.9135 (mtp180) cc_final: 0.8922 (mmm-85) REVERT: B 50 TYR cc_start: 0.9071 (m-10) cc_final: 0.8754 (m-10) REVERT: B 103 LYS cc_start: 0.9387 (mmtt) cc_final: 0.9053 (mptt) REVERT: B 104 GLN cc_start: 0.9124 (tt0) cc_final: 0.8496 (tm-30) REVERT: B 107 LYS cc_start: 0.9380 (tttt) cc_final: 0.8878 (tmmt) REVERT: B 116 ARG cc_start: 0.8998 (mtp180) cc_final: 0.8703 (mtp85) REVERT: B 140 MET cc_start: 0.7451 (tpp) cc_final: 0.7101 (tpp) REVERT: C 50 TYR cc_start: 0.9147 (m-80) cc_final: 0.8725 (m-10) REVERT: C 93 LYS cc_start: 0.8607 (mmtt) cc_final: 0.7942 (mttt) REVERT: C 103 LYS cc_start: 0.9405 (mmtt) cc_final: 0.9082 (mptt) REVERT: C 104 GLN cc_start: 0.9130 (tt0) cc_final: 0.8535 (tm-30) REVERT: C 107 LYS cc_start: 0.9360 (tttt) cc_final: 0.8901 (tmmt) REVERT: C 116 ARG cc_start: 0.9134 (mtp180) cc_final: 0.8871 (mmm-85) REVERT: C 158 MET cc_start: 0.9123 (mmm) cc_final: 0.8919 (mtp) REVERT: C 176 ASP cc_start: 0.8517 (t70) cc_final: 0.8250 (t0) REVERT: D 50 TYR cc_start: 0.9128 (m-10) cc_final: 0.8825 (m-10) REVERT: D 103 LYS cc_start: 0.9410 (mmtt) cc_final: 0.9079 (mptt) REVERT: D 104 GLN cc_start: 0.9182 (tt0) cc_final: 0.8590 (tm-30) REVERT: D 107 LYS cc_start: 0.9382 (tttt) cc_final: 0.8885 (tmmt) REVERT: D 116 ARG cc_start: 0.9099 (mtp180) cc_final: 0.8736 (mmm-85) REVERT: D 120 ARG cc_start: 0.8402 (ttm170) cc_final: 0.8196 (mtm-85) REVERT: E 50 TYR cc_start: 0.9121 (m-10) cc_final: 0.8803 (m-10) REVERT: E 68 TYR cc_start: 0.8198 (m-10) cc_final: 0.7916 (m-10) REVERT: E 93 LYS cc_start: 0.8632 (mmtt) cc_final: 0.7904 (mmmt) REVERT: E 103 LYS cc_start: 0.9353 (mmtt) cc_final: 0.9014 (mptt) REVERT: E 104 GLN cc_start: 0.9010 (tm130) cc_final: 0.8494 (tm-30) REVERT: E 107 LYS cc_start: 0.9325 (tttt) cc_final: 0.8835 (tmmt) REVERT: E 116 ARG cc_start: 0.9153 (mtp180) cc_final: 0.8768 (mmm-85) REVERT: F 50 TYR cc_start: 0.9081 (m-10) cc_final: 0.8780 (m-10) REVERT: F 103 LYS cc_start: 0.9365 (mmtt) cc_final: 0.9024 (mptt) REVERT: F 104 GLN cc_start: 0.9093 (tt0) cc_final: 0.8687 (tm-30) REVERT: F 107 LYS cc_start: 0.9376 (tttt) cc_final: 0.8881 (tmmt) REVERT: F 116 ARG cc_start: 0.9143 (mtp180) cc_final: 0.8811 (mmm-85) REVERT: F 120 ARG cc_start: 0.8374 (ttm170) cc_final: 0.8126 (mtm-85) REVERT: F 271 ARG cc_start: 0.9342 (OUTLIER) cc_final: 0.8900 (mtp85) REVERT: G 50 TYR cc_start: 0.9044 (m-10) cc_final: 0.8668 (m-80) REVERT: G 103 LYS cc_start: 0.9399 (mmtt) cc_final: 0.9090 (mptt) REVERT: G 104 GLN cc_start: 0.9076 (tm-30) cc_final: 0.8663 (tm-30) REVERT: G 107 LYS cc_start: 0.9385 (tttt) cc_final: 0.8934 (tmmt) outliers start: 77 outliers final: 26 residues processed: 428 average time/residue: 0.6021 time to fit residues: 289.0414 Evaluate side-chains 405 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 378 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain C residue 63 TYR Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 63 TYR Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 148 PHE Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain F residue 63 TYR Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 271 ARG Chi-restraints excluded: chain G residue 63 TYR Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 136 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 181 optimal weight: 0.7980 chunk 150 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 193 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 166 optimal weight: 50.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN B 100 GLN C 100 GLN C 280 GLN D 100 GLN D 280 GLN E 100 GLN F 100 GLN G 100 GLN G 105 GLN G 318 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.128245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.067815 restraints weight = 28953.717| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 2.12 r_work: 0.2506 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2380 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 19327 Z= 0.110 Angle : 0.554 13.717 25921 Z= 0.275 Chirality : 0.042 0.303 2933 Planarity : 0.003 0.029 3122 Dihedral : 15.936 96.100 3677 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.78 % Favored : 96.92 % Rotamer: Outliers : 4.33 % Allowed : 24.30 % Favored : 71.37 % 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: 1.70 (0.17), residues: 2303 helix: 2.71 (0.14), residues: 1309 sheet: -0.13 (0.33), residues: 259 loop : -1.46 (0.19), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 116 TYR 0.018 0.001 TYR B 174 PHE 0.013 0.001 PHE F 47 TRP 0.009 0.001 TRP C 184 HIS 0.003 0.001 HIS D 137 Details of bonding type rmsd covalent geometry : bond 0.00226 (19327) covalent geometry : angle 0.55414 (25921) hydrogen bonds : bond 0.03883 ( 1223) hydrogen bonds : angle 3.45736 ( 3510) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 383 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LYS cc_start: 0.9406 (mmtt) cc_final: 0.9038 (mptt) REVERT: A 104 GLN cc_start: 0.9233 (tt0) cc_final: 0.8609 (tm-30) REVERT: A 107 LYS cc_start: 0.9372 (tttt) cc_final: 0.8878 (tmmt) REVERT: A 116 ARG cc_start: 0.9138 (mtp180) cc_final: 0.8925 (mmm-85) REVERT: B 50 TYR cc_start: 0.9095 (m-10) cc_final: 0.8775 (m-10) REVERT: B 103 LYS cc_start: 0.9379 (mmtt) cc_final: 0.9031 (mptt) REVERT: B 104 GLN cc_start: 0.9119 (tt0) cc_final: 0.8533 (tm-30) REVERT: B 107 LYS cc_start: 0.9365 (tttt) cc_final: 0.8851 (tmmt) REVERT: B 116 ARG cc_start: 0.8995 (mtp180) cc_final: 0.8784 (mtp85) REVERT: C 50 TYR cc_start: 0.9182 (m-80) cc_final: 0.8750 (m-10) REVERT: C 103 LYS cc_start: 0.9389 (mmtt) cc_final: 0.9051 (mptt) REVERT: C 104 GLN cc_start: 0.9129 (tt0) cc_final: 0.8504 (tm-30) REVERT: C 107 LYS cc_start: 0.9349 (tttt) cc_final: 0.8916 (tmmt) REVERT: C 116 ARG cc_start: 0.9124 (mtp180) cc_final: 0.8807 (mmm-85) REVERT: C 158 MET cc_start: 0.9072 (mmm) cc_final: 0.8852 (mtp) REVERT: C 176 ASP cc_start: 0.8314 (t70) cc_final: 0.8059 (t0) REVERT: D 50 TYR cc_start: 0.9198 (m-10) cc_final: 0.8886 (m-10) REVERT: D 103 LYS cc_start: 0.9391 (mmtt) cc_final: 0.9032 (mppt) REVERT: D 104 GLN cc_start: 0.9181 (tt0) cc_final: 0.8611 (tm-30) REVERT: D 107 LYS cc_start: 0.9365 (tttt) cc_final: 0.8852 (tmmt) REVERT: D 116 ARG cc_start: 0.9078 (mtp180) cc_final: 0.8715 (mmm-85) REVERT: D 120 ARG cc_start: 0.8378 (ttm170) cc_final: 0.8150 (mtm-85) REVERT: D 333 MET cc_start: 0.8981 (mmm) cc_final: 0.8757 (mmm) REVERT: E 50 TYR cc_start: 0.9175 (m-10) cc_final: 0.8836 (m-10) REVERT: E 103 LYS cc_start: 0.9349 (mmtt) cc_final: 0.9007 (mptt) REVERT: E 104 GLN cc_start: 0.9022 (tm130) cc_final: 0.8504 (tm-30) REVERT: E 107 LYS cc_start: 0.9314 (tttt) cc_final: 0.8812 (tmmt) REVERT: E 116 ARG cc_start: 0.9138 (mtp180) cc_final: 0.8812 (mmm-85) REVERT: F 50 TYR cc_start: 0.9119 (m-10) cc_final: 0.8804 (m-10) REVERT: F 103 LYS cc_start: 0.9356 (mmtt) cc_final: 0.9007 (mppt) REVERT: F 104 GLN cc_start: 0.9075 (tt0) cc_final: 0.8678 (tm-30) REVERT: F 107 LYS cc_start: 0.9352 (tttt) cc_final: 0.8851 (tmmt) REVERT: F 116 ARG cc_start: 0.9129 (mtp180) cc_final: 0.8803 (mmm-85) REVERT: F 120 ARG cc_start: 0.8309 (ttm170) cc_final: 0.8064 (mtm-85) REVERT: F 271 ARG cc_start: 0.9333 (OUTLIER) cc_final: 0.8919 (mtp85) REVERT: G 50 TYR cc_start: 0.9111 (m-10) cc_final: 0.8729 (m-80) REVERT: G 103 LYS cc_start: 0.9370 (mmtt) cc_final: 0.9049 (mptt) REVERT: G 104 GLN cc_start: 0.9092 (tm-30) cc_final: 0.8683 (tm-30) REVERT: G 107 LYS cc_start: 0.9371 (tttt) cc_final: 0.8902 (tmmt) REVERT: G 116 ARG cc_start: 0.8923 (mmm-85) cc_final: 0.8679 (mmm-85) REVERT: G 120 ARG cc_start: 0.8274 (ttm170) cc_final: 0.8026 (mtm-85) outliers start: 77 outliers final: 20 residues processed: 412 average time/residue: 0.6037 time to fit residues: 278.0355 Evaluate side-chains 392 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 371 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain C residue 63 TYR Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain E residue 63 TYR Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 148 PHE Chi-restraints excluded: chain F residue 63 TYR Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 271 ARG Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 126 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 1 optimal weight: 50.0000 chunk 71 optimal weight: 10.0000 chunk 162 optimal weight: 0.9980 chunk 180 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 117 optimal weight: 0.3980 chunk 83 optimal weight: 0.3980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN A 137 HIS B 100 GLN B 280 GLN C 46 GLN C 100 GLN C 137 HIS D 100 GLN D 280 GLN E 100 GLN E 318 GLN F 100 GLN F 137 HIS G 100 GLN ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.127337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.066883 restraints weight = 28729.326| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 2.10 r_work: 0.2484 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2359 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19327 Z= 0.131 Angle : 0.578 13.602 25921 Z= 0.289 Chirality : 0.043 0.287 2933 Planarity : 0.003 0.024 3122 Dihedral : 15.493 82.598 3674 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.17 % Favored : 96.53 % Rotamer: Outliers : 3.37 % Allowed : 25.87 % Favored : 70.75 % 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: 1.71 (0.17), residues: 2303 helix: 2.75 (0.14), residues: 1295 sheet: -0.09 (0.33), residues: 259 loop : -1.44 (0.19), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 116 TYR 0.028 0.001 TYR A 50 PHE 0.011 0.001 PHE F 47 TRP 0.009 0.001 TRP G 184 HIS 0.004 0.001 HIS G 137 Details of bonding type rmsd covalent geometry : bond 0.00288 (19327) covalent geometry : angle 0.57843 (25921) hydrogen bonds : bond 0.04202 ( 1223) hydrogen bonds : angle 3.47461 ( 3510) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 377 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.9084 (m-80) cc_final: 0.8606 (m-80) REVERT: A 103 LYS cc_start: 0.9427 (mmtt) cc_final: 0.9063 (mptt) REVERT: A 104 GLN cc_start: 0.9245 (tt0) cc_final: 0.8622 (tm-30) REVERT: A 107 LYS cc_start: 0.9379 (tttt) cc_final: 0.8897 (tmmt) REVERT: A 116 ARG cc_start: 0.9156 (mtp180) cc_final: 0.8883 (mmm-85) REVERT: A 120 ARG cc_start: 0.8359 (mtm-85) cc_final: 0.8062 (mmm-85) REVERT: A 140 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.6668 (mmt) REVERT: B 50 TYR cc_start: 0.9094 (m-10) cc_final: 0.8757 (m-10) REVERT: B 103 LYS cc_start: 0.9381 (mmtt) cc_final: 0.9031 (mptt) REVERT: B 104 GLN cc_start: 0.9131 (tt0) cc_final: 0.8551 (tm-30) REVERT: B 107 LYS cc_start: 0.9376 (tttt) cc_final: 0.8863 (tmmt) REVERT: B 116 ARG cc_start: 0.9006 (mtp180) cc_final: 0.8719 (mtp85) REVERT: C 50 TYR cc_start: 0.9139 (m-80) cc_final: 0.8911 (m-80) REVERT: C 103 LYS cc_start: 0.9394 (mmtt) cc_final: 0.9046 (mptt) REVERT: C 104 GLN cc_start: 0.9146 (tt0) cc_final: 0.8604 (tm-30) REVERT: C 107 LYS cc_start: 0.9367 (tttt) cc_final: 0.8939 (tmmt) REVERT: C 116 ARG cc_start: 0.9147 (mtp180) cc_final: 0.8836 (mmm-85) REVERT: C 158 MET cc_start: 0.9149 (mmm) cc_final: 0.8916 (mtp) REVERT: D 50 TYR cc_start: 0.9184 (m-10) cc_final: 0.8829 (m-10) REVERT: D 103 LYS cc_start: 0.9397 (mmtt) cc_final: 0.9024 (mppt) REVERT: D 104 GLN cc_start: 0.9197 (tt0) cc_final: 0.8641 (tm-30) REVERT: D 107 LYS cc_start: 0.9378 (tttt) cc_final: 0.8871 (tmmt) REVERT: D 116 ARG cc_start: 0.9087 (mtp180) cc_final: 0.8772 (mmm-85) REVERT: D 120 ARG cc_start: 0.8418 (ttm170) cc_final: 0.8178 (mtm-85) REVERT: D 333 MET cc_start: 0.8970 (mmm) cc_final: 0.8709 (mmm) REVERT: E 50 TYR cc_start: 0.9161 (m-10) cc_final: 0.8805 (m-10) REVERT: E 103 LYS cc_start: 0.9354 (mmtt) cc_final: 0.9008 (mptt) REVERT: E 104 GLN cc_start: 0.9039 (tm130) cc_final: 0.8530 (tm-30) REVERT: E 107 LYS cc_start: 0.9321 (tttt) cc_final: 0.8833 (tmmt) REVERT: E 116 ARG cc_start: 0.9148 (mtp180) cc_final: 0.8828 (mmm-85) REVERT: F 50 TYR cc_start: 0.9099 (m-10) cc_final: 0.8731 (m-10) REVERT: F 103 LYS cc_start: 0.9388 (mmtt) cc_final: 0.9022 (mppt) REVERT: F 104 GLN cc_start: 0.9094 (tt0) cc_final: 0.8700 (tm-30) REVERT: F 107 LYS cc_start: 0.9364 (tttt) cc_final: 0.8866 (tmmt) REVERT: F 116 ARG cc_start: 0.9135 (mtp180) cc_final: 0.8821 (mmm-85) REVERT: F 120 ARG cc_start: 0.8346 (ttm170) cc_final: 0.8041 (mtm-85) REVERT: F 271 ARG cc_start: 0.9335 (OUTLIER) cc_final: 0.8916 (mtp85) REVERT: G 50 TYR cc_start: 0.9114 (m-10) cc_final: 0.8774 (m-10) REVERT: G 103 LYS cc_start: 0.9377 (mmtt) cc_final: 0.9042 (mptt) REVERT: G 104 GLN cc_start: 0.9119 (tm-30) cc_final: 0.8704 (tm-30) REVERT: G 107 LYS cc_start: 0.9380 (tttt) cc_final: 0.8917 (tmmt) REVERT: G 116 ARG cc_start: 0.8931 (mmm-85) cc_final: 0.8701 (mmm-85) outliers start: 60 outliers final: 20 residues processed: 397 average time/residue: 0.6545 time to fit residues: 290.7775 Evaluate side-chains 387 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 365 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain E residue 63 TYR Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 148 PHE Chi-restraints excluded: chain F residue 63 TYR Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 271 ARG Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 126 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 18 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 2 optimal weight: 50.0000 chunk 189 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 163 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 198 optimal weight: 40.0000 chunk 6 optimal weight: 8.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 100 GLN B 43 HIS B 100 GLN B 280 GLN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN D 100 GLN E 100 GLN F 100 GLN G 43 HIS ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.125028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.063200 restraints weight = 28726.484| |-----------------------------------------------------------------------------| r_work (start): 0.2602 rms_B_bonded: 1.99 r_work: 0.2430 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2303 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 19327 Z= 0.246 Angle : 0.651 13.328 25921 Z= 0.329 Chirality : 0.047 0.348 2933 Planarity : 0.003 0.025 3122 Dihedral : 15.879 81.994 3674 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.30 % Favored : 96.40 % Rotamer: Outliers : 3.94 % Allowed : 25.93 % Favored : 70.13 % 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: 1.59 (0.17), residues: 2303 helix: 2.65 (0.14), residues: 1295 sheet: -0.25 (0.32), residues: 273 loop : -1.47 (0.19), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 116 TYR 0.022 0.001 TYR A 50 PHE 0.013 0.002 PHE F 281 TRP 0.013 0.001 TRP F 184 HIS 0.004 0.001 HIS B 320 Details of bonding type rmsd covalent geometry : bond 0.00580 (19327) covalent geometry : angle 0.65148 (25921) hydrogen bonds : bond 0.05315 ( 1223) hydrogen bonds : angle 3.68148 ( 3510) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 370 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.9079 (m-80) cc_final: 0.8561 (m-80) REVERT: A 103 LYS cc_start: 0.9447 (mmtt) cc_final: 0.9125 (mptt) REVERT: A 104 GLN cc_start: 0.9217 (tt0) cc_final: 0.8616 (tm-30) REVERT: A 107 LYS cc_start: 0.9450 (tttt) cc_final: 0.8981 (tmmt) REVERT: A 116 ARG cc_start: 0.9145 (mtp180) cc_final: 0.8862 (mmm-85) REVERT: A 120 ARG cc_start: 0.8283 (mtm-85) cc_final: 0.8072 (mmm-85) REVERT: B 50 TYR cc_start: 0.9088 (m-10) cc_final: 0.8720 (m-10) REVERT: B 80 PHE cc_start: 0.8840 (t80) cc_final: 0.8518 (t80) REVERT: B 103 LYS cc_start: 0.9398 (mmtt) cc_final: 0.9066 (mptt) REVERT: B 104 GLN cc_start: 0.9123 (tt0) cc_final: 0.8544 (tm-30) REVERT: B 107 LYS cc_start: 0.9427 (tttt) cc_final: 0.8938 (tmmt) REVERT: B 116 ARG cc_start: 0.9002 (mtp180) cc_final: 0.8766 (mtp85) REVERT: C 93 LYS cc_start: 0.8889 (mmtt) cc_final: 0.8353 (mttm) REVERT: C 103 LYS cc_start: 0.9418 (mmtt) cc_final: 0.9084 (mptt) REVERT: C 104 GLN cc_start: 0.9136 (tt0) cc_final: 0.8667 (tm-30) REVERT: C 107 LYS cc_start: 0.9409 (tttt) cc_final: 0.8986 (tmmt) REVERT: C 116 ARG cc_start: 0.9126 (mtp180) cc_final: 0.8715 (mmm-85) REVERT: C 158 MET cc_start: 0.9135 (mmm) cc_final: 0.8921 (mtp) REVERT: D 50 TYR cc_start: 0.9171 (m-10) cc_final: 0.8789 (m-10) REVERT: D 103 LYS cc_start: 0.9437 (mmtt) cc_final: 0.9088 (mptt) REVERT: D 104 GLN cc_start: 0.9194 (tt0) cc_final: 0.8660 (tm-30) REVERT: D 107 LYS cc_start: 0.9436 (tttt) cc_final: 0.8946 (tmmt) REVERT: D 116 ARG cc_start: 0.9072 (mtp180) cc_final: 0.8710 (mmm-85) REVERT: D 120 ARG cc_start: 0.8436 (ttm170) cc_final: 0.8230 (mtm-85) REVERT: E 50 TYR cc_start: 0.9181 (m-10) cc_final: 0.8809 (m-10) REVERT: E 103 LYS cc_start: 0.9400 (mmtt) cc_final: 0.9085 (mptt) REVERT: E 104 GLN cc_start: 0.9061 (tm130) cc_final: 0.8291 (tm-30) REVERT: E 107 LYS cc_start: 0.9388 (tttt) cc_final: 0.8901 (tmmt) REVERT: E 116 ARG cc_start: 0.9156 (mtp180) cc_final: 0.8792 (mmm-85) REVERT: F 50 TYR cc_start: 0.9110 (m-10) cc_final: 0.8706 (m-10) REVERT: F 103 LYS cc_start: 0.9411 (mmtt) cc_final: 0.9055 (mptt) REVERT: F 104 GLN cc_start: 0.9102 (tt0) cc_final: 0.8725 (tm-30) REVERT: F 107 LYS cc_start: 0.9392 (tttt) cc_final: 0.8891 (tmmt) REVERT: F 116 ARG cc_start: 0.9148 (mtp180) cc_final: 0.8844 (mmm-85) REVERT: F 120 ARG cc_start: 0.8334 (ttm170) cc_final: 0.8080 (mtm-85) REVERT: F 271 ARG cc_start: 0.9335 (OUTLIER) cc_final: 0.8885 (mtp85) REVERT: G 50 TYR cc_start: 0.9125 (m-10) cc_final: 0.8746 (m-10) REVERT: G 100 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8249 (pp30) REVERT: G 103 LYS cc_start: 0.9408 (mmtt) cc_final: 0.9056 (mmtm) REVERT: G 104 GLN cc_start: 0.9087 (tm-30) cc_final: 0.8413 (tm-30) REVERT: G 107 LYS cc_start: 0.9428 (tttt) cc_final: 0.8978 (tmmt) REVERT: G 116 ARG cc_start: 0.8930 (mmm-85) cc_final: 0.8594 (mmm-85) outliers start: 70 outliers final: 23 residues processed: 393 average time/residue: 0.6527 time to fit residues: 286.8127 Evaluate side-chains 388 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 363 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 63 TYR Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 63 TYR Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 271 ARG Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 131 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 9.9990 chunk 35 optimal weight: 50.0000 chunk 211 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 152 optimal weight: 0.6980 chunk 196 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 100 GLN B 100 GLN C 100 GLN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN E 100 GLN F 100 GLN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.127584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.067506 restraints weight = 28816.693| |-----------------------------------------------------------------------------| r_work (start): 0.2689 rms_B_bonded: 2.13 r_work: 0.2511 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2386 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19327 Z= 0.111 Angle : 0.611 14.470 25921 Z= 0.297 Chirality : 0.044 0.353 2933 Planarity : 0.003 0.023 3122 Dihedral : 14.985 86.051 3674 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.17 % Favored : 96.53 % Rotamer: Outliers : 2.53 % Allowed : 26.60 % Favored : 70.87 % 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: 1.55 (0.17), residues: 2303 helix: 2.71 (0.14), residues: 1302 sheet: -0.96 (0.28), residues: 329 loop : -1.42 (0.20), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 116 TYR 0.022 0.001 TYR A 174 PHE 0.010 0.001 PHE F 47 TRP 0.010 0.001 TRP C 184 HIS 0.002 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00232 (19327) covalent geometry : angle 0.61111 (25921) hydrogen bonds : bond 0.03807 ( 1223) hydrogen bonds : angle 3.45420 ( 3510) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 375 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.9052 (m-80) cc_final: 0.8499 (m-80) REVERT: A 103 LYS cc_start: 0.9422 (mmtt) cc_final: 0.9075 (mptt) REVERT: A 104 GLN cc_start: 0.9219 (tt0) cc_final: 0.8621 (tm-30) REVERT: A 107 LYS cc_start: 0.9394 (tttt) cc_final: 0.8912 (tmmt) REVERT: A 116 ARG cc_start: 0.9157 (mtp180) cc_final: 0.8894 (mmm-85) REVERT: A 120 ARG cc_start: 0.8275 (mtm-85) cc_final: 0.7991 (mmm-85) REVERT: B 50 TYR cc_start: 0.9077 (m-10) cc_final: 0.8690 (m-10) REVERT: B 103 LYS cc_start: 0.9377 (mmtt) cc_final: 0.9034 (mptt) REVERT: B 104 GLN cc_start: 0.9112 (tt0) cc_final: 0.8547 (tm-30) REVERT: B 107 LYS cc_start: 0.9407 (tttt) cc_final: 0.8906 (tmmt) REVERT: B 116 ARG cc_start: 0.8990 (mtp180) cc_final: 0.8784 (mtp85) REVERT: C 46 GLN cc_start: 0.9187 (tt0) cc_final: 0.8460 (tm-30) REVERT: C 50 TYR cc_start: 0.9209 (m-80) cc_final: 0.8924 (m-80) REVERT: C 103 LYS cc_start: 0.9395 (mmtt) cc_final: 0.9036 (mptt) REVERT: C 104 GLN cc_start: 0.9115 (tt0) cc_final: 0.8668 (tm-30) REVERT: C 107 LYS cc_start: 0.9390 (tttt) cc_final: 0.8950 (tmmt) REVERT: C 116 ARG cc_start: 0.9127 (mtp180) cc_final: 0.8870 (mmm-85) REVERT: C 158 MET cc_start: 0.9152 (mmm) cc_final: 0.8922 (mtp) REVERT: D 50 TYR cc_start: 0.9149 (m-10) cc_final: 0.8739 (m-10) REVERT: D 103 LYS cc_start: 0.9422 (mmtt) cc_final: 0.9053 (mppt) REVERT: D 104 GLN cc_start: 0.9205 (tt0) cc_final: 0.8674 (tm-30) REVERT: D 107 LYS cc_start: 0.9409 (tttt) cc_final: 0.8905 (tmmt) REVERT: D 116 ARG cc_start: 0.9067 (mtp180) cc_final: 0.8762 (mmm-85) REVERT: D 120 ARG cc_start: 0.8440 (ttm170) cc_final: 0.8155 (mtm-85) REVERT: E 50 TYR cc_start: 0.9170 (m-10) cc_final: 0.8773 (m-10) REVERT: E 103 LYS cc_start: 0.9362 (mmtt) cc_final: 0.9023 (mptt) REVERT: E 104 GLN cc_start: 0.9045 (tm130) cc_final: 0.8327 (tm-30) REVERT: E 107 LYS cc_start: 0.9363 (tttt) cc_final: 0.8874 (tmmt) REVERT: E 116 ARG cc_start: 0.9160 (mtp180) cc_final: 0.8824 (mmm-85) REVERT: F 50 TYR cc_start: 0.9068 (m-10) cc_final: 0.8672 (m-10) REVERT: F 103 LYS cc_start: 0.9401 (mmtt) cc_final: 0.9021 (mppt) REVERT: F 104 GLN cc_start: 0.9089 (tt0) cc_final: 0.8746 (tm-30) REVERT: F 107 LYS cc_start: 0.9366 (tttt) cc_final: 0.8881 (tmmt) REVERT: F 116 ARG cc_start: 0.9128 (mtp180) cc_final: 0.8830 (mmm-85) REVERT: F 120 ARG cc_start: 0.8318 (ttm170) cc_final: 0.8046 (mtm-85) REVERT: F 333 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8327 (mtm) REVERT: G 50 TYR cc_start: 0.9122 (m-10) cc_final: 0.8782 (m-10) REVERT: G 100 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8484 (pp30) REVERT: G 103 LYS cc_start: 0.9386 (mmtt) cc_final: 0.9038 (mptt) REVERT: G 104 GLN cc_start: 0.9094 (tm-30) cc_final: 0.8721 (tm-30) REVERT: G 107 LYS cc_start: 0.9410 (tttt) cc_final: 0.8963 (tmmt) outliers start: 45 outliers final: 15 residues processed: 394 average time/residue: 0.6760 time to fit residues: 296.9204 Evaluate side-chains 381 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 364 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain E residue 63 TYR Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 148 PHE Chi-restraints excluded: chain F residue 63 TYR Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 333 MET Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 100 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 49 optimal weight: 0.9990 chunk 51 optimal weight: 0.2980 chunk 145 optimal weight: 5.9990 chunk 121 optimal weight: 0.0770 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 83 optimal weight: 0.0020 chunk 6 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 overall best weight: 0.4148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN B 100 GLN C 100 GLN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN E 100 GLN E 318 GLN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 GLN G 105 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.128884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.069161 restraints weight = 28601.481| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 2.19 r_work: 0.2524 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2399 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 19327 Z= 0.100 Angle : 0.621 18.171 25921 Z= 0.295 Chirality : 0.044 0.353 2933 Planarity : 0.003 0.030 3122 Dihedral : 14.225 89.091 3674 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.39 % Favored : 96.31 % Rotamer: Outliers : 2.08 % Allowed : 27.67 % Favored : 70.25 % 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: 1.75 (0.17), residues: 2303 helix: 2.76 (0.14), residues: 1302 sheet: -0.04 (0.33), residues: 259 loop : -1.45 (0.19), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 116 TYR 0.018 0.001 TYR A 50 PHE 0.009 0.001 PHE B 47 TRP 0.007 0.001 TRP A 184 HIS 0.003 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00198 (19327) covalent geometry : angle 0.62055 (25921) hydrogen bonds : bond 0.03414 ( 1223) hydrogen bonds : angle 3.35227 ( 3510) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 377 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.9064 (m-80) cc_final: 0.8541 (m-80) REVERT: A 93 LYS cc_start: 0.8770 (mmtt) cc_final: 0.8304 (mttm) REVERT: A 103 LYS cc_start: 0.9391 (mmtt) cc_final: 0.9007 (mptt) REVERT: A 104 GLN cc_start: 0.9228 (tt0) cc_final: 0.8637 (tm-30) REVERT: A 107 LYS cc_start: 0.9366 (tttt) cc_final: 0.8877 (tmmt) REVERT: A 116 ARG cc_start: 0.9138 (mtp180) cc_final: 0.8894 (mmm-85) REVERT: A 120 ARG cc_start: 0.8227 (mtm-85) cc_final: 0.7989 (mmm-85) REVERT: A 162 ASP cc_start: 0.8657 (m-30) cc_final: 0.8183 (m-30) REVERT: B 50 TYR cc_start: 0.9000 (m-10) cc_final: 0.8623 (m-10) REVERT: B 103 LYS cc_start: 0.9360 (mmtt) cc_final: 0.8991 (mptt) REVERT: B 104 GLN cc_start: 0.9096 (tt0) cc_final: 0.8547 (tm-30) REVERT: B 107 LYS cc_start: 0.9394 (tttt) cc_final: 0.8895 (tmmt) REVERT: B 116 ARG cc_start: 0.8939 (mtp180) cc_final: 0.8657 (mtp85) REVERT: C 103 LYS cc_start: 0.9369 (mmtt) cc_final: 0.9001 (mptt) REVERT: C 104 GLN cc_start: 0.9115 (tt0) cc_final: 0.8678 (tm-30) REVERT: C 107 LYS cc_start: 0.9373 (tttt) cc_final: 0.8924 (tmmt) REVERT: C 116 ARG cc_start: 0.9097 (mtp180) cc_final: 0.8762 (mmm-85) REVERT: C 140 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7033 (mtp) REVERT: C 158 MET cc_start: 0.9070 (mmm) cc_final: 0.8845 (mtp) REVERT: D 50 TYR cc_start: 0.9126 (m-10) cc_final: 0.8739 (m-10) REVERT: D 96 LEU cc_start: 0.9473 (mm) cc_final: 0.9135 (pt) REVERT: D 103 LYS cc_start: 0.9375 (mmtt) cc_final: 0.8996 (mppt) REVERT: D 104 GLN cc_start: 0.9192 (tt0) cc_final: 0.8652 (tm-30) REVERT: D 107 LYS cc_start: 0.9385 (tttt) cc_final: 0.8867 (tmmt) REVERT: D 116 ARG cc_start: 0.9076 (mtp180) cc_final: 0.8785 (mmm-85) REVERT: E 50 TYR cc_start: 0.9132 (m-10) cc_final: 0.8782 (m-10) REVERT: E 96 LEU cc_start: 0.9503 (mm) cc_final: 0.9196 (pt) REVERT: E 102 GLU cc_start: 0.8952 (tt0) cc_final: 0.8728 (tt0) REVERT: E 103 LYS cc_start: 0.9346 (mmtt) cc_final: 0.8998 (mptt) REVERT: E 104 GLN cc_start: 0.9057 (tm130) cc_final: 0.8250 (tm-30) REVERT: E 105 GLN cc_start: 0.8923 (tp40) cc_final: 0.8711 (tp40) REVERT: E 107 LYS cc_start: 0.9338 (tttt) cc_final: 0.8827 (tmmt) REVERT: E 116 ARG cc_start: 0.9121 (mtp180) cc_final: 0.8797 (mmm-85) REVERT: F 50 TYR cc_start: 0.9074 (m-10) cc_final: 0.8705 (m-10) REVERT: F 96 LEU cc_start: 0.9479 (mm) cc_final: 0.9113 (pt) REVERT: F 100 GLN cc_start: 0.8618 (pp30) cc_final: 0.8190 (pp30) REVERT: F 103 LYS cc_start: 0.9363 (mmtt) cc_final: 0.8917 (mmtm) REVERT: F 104 GLN cc_start: 0.9088 (tt0) cc_final: 0.8722 (tm-30) REVERT: F 107 LYS cc_start: 0.9339 (tttt) cc_final: 0.8836 (tmmt) REVERT: F 116 ARG cc_start: 0.9079 (mtp180) cc_final: 0.8740 (mmm-85) REVERT: G 50 TYR cc_start: 0.9119 (m-10) cc_final: 0.8758 (m-10) REVERT: G 103 LYS cc_start: 0.9342 (mmtt) cc_final: 0.8962 (mptt) REVERT: G 104 GLN cc_start: 0.9085 (tm-30) cc_final: 0.8719 (tm-30) REVERT: G 107 LYS cc_start: 0.9373 (tttt) cc_final: 0.8917 (tmmt) outliers start: 37 outliers final: 12 residues processed: 396 average time/residue: 0.6520 time to fit residues: 288.0487 Evaluate side-chains 377 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 364 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain E residue 63 TYR Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 148 PHE Chi-restraints excluded: chain F residue 63 TYR Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 124 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 112 optimal weight: 0.8980 chunk 201 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 194 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 204 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 100 GLN B 100 GLN B 280 GLN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN D 100 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN E 318 GLN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 GLN G 105 GLN G 280 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.127759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.066996 restraints weight = 28333.477| |-----------------------------------------------------------------------------| r_work (start): 0.2670 rms_B_bonded: 2.11 r_work: 0.2487 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2361 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19327 Z= 0.116 Angle : 0.637 16.692 25921 Z= 0.304 Chirality : 0.046 0.372 2933 Planarity : 0.003 0.030 3122 Dihedral : 14.113 89.952 3674 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.26 % Favored : 96.44 % Rotamer: Outliers : 1.57 % Allowed : 28.52 % Favored : 69.91 % 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: 1.72 (0.17), residues: 2303 helix: 2.74 (0.14), residues: 1302 sheet: -0.00 (0.33), residues: 259 loop : -1.49 (0.19), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 116 TYR 0.030 0.001 TYR B 63 PHE 0.009 0.001 PHE G 281 TRP 0.009 0.001 TRP A 184 HIS 0.003 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00251 (19327) covalent geometry : angle 0.63695 (25921) hydrogen bonds : bond 0.03771 ( 1223) hydrogen bonds : angle 3.39357 ( 3510) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 369 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.9095 (m-80) cc_final: 0.8569 (m-80) REVERT: A 103 LYS cc_start: 0.9384 (mmtt) cc_final: 0.8985 (mptt) REVERT: A 104 GLN cc_start: 0.9215 (tt0) cc_final: 0.8630 (tm-30) REVERT: A 107 LYS cc_start: 0.9371 (tttt) cc_final: 0.8882 (tmmt) REVERT: A 116 ARG cc_start: 0.9118 (mtp180) cc_final: 0.8853 (mmm-85) REVERT: A 120 ARG cc_start: 0.8149 (mtm-85) cc_final: 0.7836 (mmm-85) REVERT: B 50 TYR cc_start: 0.9007 (m-10) cc_final: 0.8619 (m-10) REVERT: B 96 LEU cc_start: 0.9496 (mm) cc_final: 0.9205 (pt) REVERT: B 103 LYS cc_start: 0.9354 (mmtt) cc_final: 0.8984 (mptt) REVERT: B 104 GLN cc_start: 0.9085 (tt0) cc_final: 0.8550 (tm-30) REVERT: B 107 LYS cc_start: 0.9392 (tttt) cc_final: 0.8879 (tmmt) REVERT: B 116 ARG cc_start: 0.8915 (mtp180) cc_final: 0.8645 (mtp85) REVERT: C 46 GLN cc_start: 0.9100 (tt0) cc_final: 0.8491 (tm-30) REVERT: C 103 LYS cc_start: 0.9364 (mmtt) cc_final: 0.8993 (mptt) REVERT: C 104 GLN cc_start: 0.9079 (tt0) cc_final: 0.8659 (tm-30) REVERT: C 107 LYS cc_start: 0.9386 (tttt) cc_final: 0.8937 (tmmt) REVERT: C 116 ARG cc_start: 0.9037 (mtp180) cc_final: 0.8767 (mmm-85) REVERT: C 158 MET cc_start: 0.9093 (mmm) cc_final: 0.8865 (mtp) REVERT: D 50 TYR cc_start: 0.9121 (m-10) cc_final: 0.8741 (m-10) REVERT: D 96 LEU cc_start: 0.9464 (mm) cc_final: 0.9137 (pt) REVERT: D 103 LYS cc_start: 0.9377 (mmtt) cc_final: 0.8989 (mppt) REVERT: D 104 GLN cc_start: 0.9187 (tt0) cc_final: 0.8672 (tm-30) REVERT: D 107 LYS cc_start: 0.9391 (tttt) cc_final: 0.8875 (tmmt) REVERT: D 116 ARG cc_start: 0.9002 (mtp180) cc_final: 0.8687 (mmm-85) REVERT: E 50 TYR cc_start: 0.9156 (m-10) cc_final: 0.8807 (m-10) REVERT: E 97 LEU cc_start: 0.9401 (tm) cc_final: 0.9171 (tt) REVERT: E 100 GLN cc_start: 0.8651 (pp30) cc_final: 0.8233 (pp30) REVERT: E 103 LYS cc_start: 0.9322 (mmtt) cc_final: 0.8965 (mptt) REVERT: E 104 GLN cc_start: 0.9066 (tm130) cc_final: 0.8276 (tm-30) REVERT: E 107 LYS cc_start: 0.9330 (tttt) cc_final: 0.8828 (tmmt) REVERT: E 116 ARG cc_start: 0.9079 (mtp180) cc_final: 0.8767 (mmm-85) REVERT: F 50 TYR cc_start: 0.9068 (m-10) cc_final: 0.8704 (m-10) REVERT: F 96 LEU cc_start: 0.9471 (mm) cc_final: 0.9130 (pt) REVERT: F 103 LYS cc_start: 0.9361 (mmtt) cc_final: 0.8953 (mmtm) REVERT: F 104 GLN cc_start: 0.9097 (tt0) cc_final: 0.8726 (tm-30) REVERT: F 107 LYS cc_start: 0.9329 (tttt) cc_final: 0.8839 (tmmt) REVERT: F 116 ARG cc_start: 0.8972 (mtp180) cc_final: 0.8737 (mmm-85) REVERT: G 50 TYR cc_start: 0.9128 (m-10) cc_final: 0.8758 (m-10) REVERT: G 96 LEU cc_start: 0.9464 (mm) cc_final: 0.9139 (pt) REVERT: G 103 LYS cc_start: 0.9351 (mmtt) cc_final: 0.8892 (mmtm) REVERT: G 104 GLN cc_start: 0.9099 (tm-30) cc_final: 0.8726 (tm-30) REVERT: G 107 LYS cc_start: 0.9377 (tttt) cc_final: 0.8920 (tmmt) REVERT: G 116 ARG cc_start: 0.8894 (mmm-85) cc_final: 0.8377 (mmm-85) outliers start: 28 outliers final: 10 residues processed: 379 average time/residue: 0.6884 time to fit residues: 291.0010 Evaluate side-chains 378 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 368 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain E residue 63 TYR Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 148 PHE Chi-restraints excluded: chain F residue 63 TYR Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain G residue 82 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 175 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 230 optimal weight: 0.6980 chunk 132 optimal weight: 0.0040 chunk 73 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 154 optimal weight: 0.7980 chunk 189 optimal weight: 3.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 100 GLN B 100 GLN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN D 100 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN F 100 GLN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 HIS G 105 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.127203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.065226 restraints weight = 28367.195| |-----------------------------------------------------------------------------| r_work (start): 0.2648 rms_B_bonded: 2.00 r_work: 0.2481 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2355 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19327 Z= 0.128 Angle : 0.654 15.031 25921 Z= 0.312 Chirality : 0.046 0.381 2933 Planarity : 0.003 0.030 3122 Dihedral : 14.072 89.535 3673 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.21 % Favored : 96.48 % Rotamer: Outliers : 1.41 % Allowed : 28.97 % Favored : 69.63 % 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: 1.73 (0.17), residues: 2303 helix: 2.70 (0.14), residues: 1309 sheet: -0.03 (0.33), residues: 259 loop : -1.42 (0.19), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 116 TYR 0.021 0.001 TYR C 174 PHE 0.010 0.001 PHE G 281 TRP 0.009 0.001 TRP G 184 HIS 0.002 0.001 HIS G 320 Details of bonding type rmsd covalent geometry : bond 0.00284 (19327) covalent geometry : angle 0.65356 (25921) hydrogen bonds : bond 0.03988 ( 1223) hydrogen bonds : angle 3.43983 ( 3510) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 370 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.9102 (m-80) cc_final: 0.8552 (m-10) REVERT: A 103 LYS cc_start: 0.9394 (mmtt) cc_final: 0.9031 (mptt) REVERT: A 104 GLN cc_start: 0.9205 (tt0) cc_final: 0.8624 (tm-30) REVERT: A 107 LYS cc_start: 0.9392 (tttt) cc_final: 0.8909 (tmmt) REVERT: A 116 ARG cc_start: 0.9114 (mtp180) cc_final: 0.8769 (mmm-85) REVERT: A 120 ARG cc_start: 0.8196 (mtm-85) cc_final: 0.7949 (mmm-85) REVERT: B 50 TYR cc_start: 0.9032 (m-10) cc_final: 0.8646 (m-10) REVERT: B 96 LEU cc_start: 0.9491 (mm) cc_final: 0.9206 (pt) REVERT: B 103 LYS cc_start: 0.9362 (mmtt) cc_final: 0.8991 (mptt) REVERT: B 104 GLN cc_start: 0.9100 (tt0) cc_final: 0.8552 (tm-30) REVERT: B 107 LYS cc_start: 0.9409 (tttt) cc_final: 0.8908 (tmmt) REVERT: B 116 ARG cc_start: 0.8902 (mtp180) cc_final: 0.8626 (mtp85) REVERT: C 46 GLN cc_start: 0.9124 (tt0) cc_final: 0.8478 (tm-30) REVERT: C 103 LYS cc_start: 0.9374 (mmtt) cc_final: 0.8998 (mptt) REVERT: C 104 GLN cc_start: 0.9078 (tt0) cc_final: 0.8636 (tm-30) REVERT: C 107 LYS cc_start: 0.9385 (tttt) cc_final: 0.8937 (tmmt) REVERT: C 116 ARG cc_start: 0.9027 (mtp180) cc_final: 0.8745 (mmm-85) REVERT: C 140 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7285 (mtp) REVERT: C 158 MET cc_start: 0.9114 (mmm) cc_final: 0.8903 (mtp) REVERT: D 50 TYR cc_start: 0.9133 (m-10) cc_final: 0.8749 (m-10) REVERT: D 96 LEU cc_start: 0.9443 (mm) cc_final: 0.9131 (pt) REVERT: D 103 LYS cc_start: 0.9399 (mmtt) cc_final: 0.8996 (mppt) REVERT: D 104 GLN cc_start: 0.9186 (tt0) cc_final: 0.8673 (tm-30) REVERT: D 107 LYS cc_start: 0.9394 (tttt) cc_final: 0.8883 (tmmt) REVERT: D 116 ARG cc_start: 0.8988 (mtp180) cc_final: 0.8662 (mmm-85) REVERT: E 50 TYR cc_start: 0.9164 (m-10) cc_final: 0.8810 (m-10) REVERT: E 96 LEU cc_start: 0.9484 (mm) cc_final: 0.9132 (pt) REVERT: E 97 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9189 (tt) REVERT: E 100 GLN cc_start: 0.8658 (pp30) cc_final: 0.8223 (pp30) REVERT: E 103 LYS cc_start: 0.9344 (mmtt) cc_final: 0.8995 (mptt) REVERT: E 104 GLN cc_start: 0.9077 (tm130) cc_final: 0.8405 (tm-30) REVERT: E 107 LYS cc_start: 0.9335 (tttt) cc_final: 0.8855 (tmmt) REVERT: E 116 ARG cc_start: 0.9056 (mtp180) cc_final: 0.8731 (mmm-85) REVERT: F 50 TYR cc_start: 0.9072 (m-10) cc_final: 0.8685 (m-10) REVERT: F 96 LEU cc_start: 0.9479 (mm) cc_final: 0.9144 (pt) REVERT: F 103 LYS cc_start: 0.9371 (mmtt) cc_final: 0.8923 (mmtm) REVERT: F 104 GLN cc_start: 0.9106 (tt0) cc_final: 0.8721 (tm-30) REVERT: F 107 LYS cc_start: 0.9329 (tttt) cc_final: 0.8806 (tmmt) REVERT: F 116 ARG cc_start: 0.8981 (mtp180) cc_final: 0.8745 (mmm-85) REVERT: G 50 TYR cc_start: 0.9162 (m-10) cc_final: 0.8794 (m-10) REVERT: G 96 LEU cc_start: 0.9473 (mm) cc_final: 0.9144 (pt) REVERT: G 103 LYS cc_start: 0.9362 (mmtt) cc_final: 0.8966 (mptt) REVERT: G 104 GLN cc_start: 0.9095 (tm-30) cc_final: 0.8729 (tm-30) REVERT: G 107 LYS cc_start: 0.9387 (tttt) cc_final: 0.8934 (tmmt) REVERT: G 116 ARG cc_start: 0.8874 (mmm-85) cc_final: 0.8292 (mmm-85) REVERT: G 120 ARG cc_start: 0.8269 (mtm-85) cc_final: 0.7868 (mmm-85) outliers start: 25 outliers final: 12 residues processed: 382 average time/residue: 0.6619 time to fit residues: 282.4087 Evaluate side-chains 378 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 364 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain E residue 63 TYR Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 148 PHE Chi-restraints excluded: chain F residue 63 TYR Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 126 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 0.9980 chunk 69 optimal weight: 50.0000 chunk 42 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 153 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 chunk 121 optimal weight: 0.0060 chunk 186 optimal weight: 0.1980 chunk 24 optimal weight: 0.9980 chunk 80 optimal weight: 0.0770 chunk 152 optimal weight: 0.7980 overall best weight: 0.3954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 100 GLN B 100 GLN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN D 105 GLN D 280 GLN E 105 GLN F 100 GLN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 GLN G 105 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.128964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.068018 restraints weight = 28345.916| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 1.99 r_work: 0.2551 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2427 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19327 Z= 0.100 Angle : 0.632 14.991 25921 Z= 0.300 Chirality : 0.045 0.380 2933 Planarity : 0.002 0.027 3122 Dihedral : 13.617 89.861 3673 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.13 % Favored : 96.57 % Rotamer: Outliers : 1.41 % Allowed : 28.85 % Favored : 69.74 % 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: 1.75 (0.17), residues: 2303 helix: 2.74 (0.14), residues: 1309 sheet: -0.02 (0.33), residues: 259 loop : -1.43 (0.19), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 116 TYR 0.020 0.001 TYR B 174 PHE 0.009 0.001 PHE B 47 TRP 0.006 0.001 TRP A 184 HIS 0.003 0.001 HIS G 137 Details of bonding type rmsd covalent geometry : bond 0.00202 (19327) covalent geometry : angle 0.63155 (25921) hydrogen bonds : bond 0.03331 ( 1223) hydrogen bonds : angle 3.31424 ( 3510) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11366.71 seconds wall clock time: 193 minutes 15.53 seconds (11595.53 seconds total)