Starting phenix.real_space_refine on Thu Feb 5 18:41:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e67_47552/02_2026/9e67_47552.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e67_47552/02_2026/9e67_47552.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/9e67_47552/02_2026/9e67_47552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e67_47552/02_2026/9e67_47552.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e67_47552/02_2026/9e67_47552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e67_47552/02_2026/9e67_47552.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= -0.003 sd= 0.040 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 12502 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 33 residue(s): 0.02s 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: 19033 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: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 256 Unusual residues: {'PTY': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 44 Chain: "B" 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: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 210 Unusual residues: {'PTY': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 40 Chain: "D" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 256 Unusual residues: {'PTY': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 44 Chain: "E" 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: "F" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 256 Unusual residues: {'PTY': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 44 Chain: "G" 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 Time building chain proxies: 4.20, per 1000 atoms: 0.22 Number of scatterers: 19033 At special positions: 0 Unit cell: (109.22, 110.94, 139.32, 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 12502 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 788.6 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 61.7% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 5 through 12 Processing helix chain 'A' and resid 15 through 31 removed outlier: 3.823A pdb=" N ARG A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 68 Processing helix chain 'A' and resid 74 through 109 removed outlier: 3.895A pdb=" N ILE A 78 " --> pdb=" O THR A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 135 Processing helix chain 'A' and resid 141 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 248 removed outlier: 3.559A pdb=" N ALA A 248 " --> pdb=" O TYR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 298 through 320 removed outlier: 3.537A pdb=" N HIS A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 12 Processing helix chain 'B' and resid 15 through 31 removed outlier: 3.821A pdb=" N ARG B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 68 Processing helix chain 'B' and resid 74 through 109 removed outlier: 3.895A pdb=" N ILE B 78 " --> pdb=" O THR B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 135 Processing helix chain 'B' and resid 141 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 248 removed outlier: 3.598A pdb=" N ALA B 248 " --> pdb=" O TYR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 263 Processing helix chain 'B' and resid 298 through 320 removed outlier: 3.528A pdb=" N HIS B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 12 Processing helix chain 'C' and resid 15 through 31 removed outlier: 3.821A pdb=" N ARG C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 68 Processing helix chain 'C' and resid 74 through 109 removed outlier: 3.895A 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 141 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 248 removed outlier: 3.607A pdb=" N ALA C 248 " --> pdb=" O TYR C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 265 Processing helix chain 'C' and resid 298 through 320 removed outlier: 3.528A pdb=" N HIS C 320 " --> pdb=" O ILE C 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 12 Processing helix chain 'D' and resid 15 through 31 removed outlier: 3.816A pdb=" N ARG D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 68 Processing helix chain 'D' and resid 74 through 109 removed outlier: 3.890A pdb=" N ILE D 78 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 135 Processing helix chain 'D' and resid 141 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 248 removed outlier: 3.535A pdb=" N ALA D 248 " --> pdb=" O TYR D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 265 Processing helix chain 'D' and resid 298 through 320 removed outlier: 3.514A pdb=" N HIS D 320 " --> pdb=" O ILE D 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 12 Processing helix chain 'E' and resid 15 through 31 removed outlier: 3.821A pdb=" N ARG E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 68 Processing helix chain 'E' and resid 74 through 109 removed outlier: 3.884A pdb=" N ILE E 78 " --> pdb=" O THR E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 135 Processing helix chain 'E' and resid 141 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 248 removed outlier: 3.564A pdb=" N ALA E 248 " --> pdb=" O TYR E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 265 Processing helix chain 'E' and resid 298 through 320 removed outlier: 3.510A pdb=" N HIS E 320 " --> pdb=" O ILE E 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 12 Processing helix chain 'F' and resid 15 through 31 removed outlier: 3.824A pdb=" N ARG F 31 " --> pdb=" O SER F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 68 Processing helix chain 'F' and resid 74 through 109 removed outlier: 3.890A pdb=" N ILE F 78 " --> pdb=" O THR F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 135 Processing helix chain 'F' and resid 141 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 248 removed outlier: 3.543A pdb=" N ALA F 248 " --> pdb=" O TYR F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 265 Processing helix chain 'F' and resid 298 through 320 removed outlier: 3.529A pdb=" N HIS F 320 " --> pdb=" O ILE F 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 12 Processing helix chain 'G' and resid 15 through 31 removed outlier: 3.820A pdb=" N ARG G 31 " --> pdb=" O SER G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 68 Processing helix chain 'G' and resid 74 through 109 removed outlier: 3.890A pdb=" N ILE G 78 " --> pdb=" O THR G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 135 Processing helix chain 'G' and resid 141 through 160 Processing helix chain 'G' and resid 160 through 176 removed outlier: 3.508A pdb=" N LEU G 164 " --> pdb=" O GLY G 160 " (cutoff:3.500A) 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 248 removed outlier: 3.597A pdb=" N ALA G 248 " --> pdb=" O TYR G 245 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 265 Processing helix chain 'G' and resid 298 through 320 removed outlier: 3.525A pdb=" N HIS G 320 " --> pdb=" O ILE G 316 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 185 removed outlier: 6.540A pdb=" N LYS A 205 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE A 199 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 7.355A 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: 7.326A pdb=" N ILE G 203 " --> pdb=" O ILE G 199 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ILE G 199 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 6.524A 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: 4.000A pdb=" N ARG A 235 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A 280 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N MET A 289 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N PHE A 278 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N TYR A 291 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL A 276 " --> pdb=" O TYR A 291 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 333 removed outlier: 8.442A pdb=" N GLN G 329 " --> pdb=" O SER A 328 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR A 330 " --> pdb=" O GLN G 329 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU G 331 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TYR A 332 " --> pdb=" O LEU G 331 " (cutoff:3.500A) removed outlier: 7.827A 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: 6.525A pdb=" N LYS B 205 " --> pdb=" O ALA B 197 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ILE B 199 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.298A 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: 3.916A pdb=" N ARG B 235 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN B 280 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N MET B 289 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N PHE B 278 " --> pdb=" O MET B 289 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N TYR B 291 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL B 276 " --> pdb=" O TYR B 291 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 184 through 185 removed outlier: 6.572A pdb=" N LYS C 205 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ILE C 199 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 7.345A 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: 3.900A pdb=" N ARG C 235 " --> pdb=" O THR C 294 " (cutoff:3.500A) removed outlier: 6.818A 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: 6.530A pdb=" N LYS D 205 " --> pdb=" O ALA D 197 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ILE D 199 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 7.299A 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: 3.933A pdb=" N ARG D 235 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN D 280 " --> pdb=" O ASN D 287 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N MET D 289 " --> pdb=" O PHE D 278 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N PHE D 278 " --> pdb=" O MET D 289 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N TYR D 291 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 5.563A 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: 6.549A pdb=" N LYS E 205 " --> pdb=" O ALA E 197 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ILE E 199 " --> pdb=" O ILE E 203 " (cutoff:3.500A) removed outlier: 7.343A 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: 3.988A pdb=" N ARG E 235 " --> pdb=" O THR E 294 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN E 280 " --> pdb=" O ASN E 287 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N MET E 289 " --> pdb=" O PHE E 278 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N PHE E 278 " --> pdb=" O MET E 289 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N TYR E 291 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 5.541A 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: 6.549A pdb=" N LYS F 205 " --> pdb=" O ALA F 197 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ILE F 199 " --> pdb=" O ILE F 203 " (cutoff:3.500A) removed outlier: 7.305A 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: 3.937A pdb=" N ARG F 235 " --> pdb=" O THR F 294 " (cutoff:3.500A) removed outlier: 6.815A 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: 3.922A pdb=" N ARG G 235 " --> pdb=" O THR G 294 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN G 287 " --> pdb=" O ASN G 279 " (cutoff:3.500A) 1263 hydrogen bonds defined for protein. 3633 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2891 1.32 - 1.44: 4965 1.44 - 1.56: 11281 1.56 - 1.69: 71 1.69 - 1.81: 126 Bond restraints: 19334 Sorted by residual: bond pdb=" N ARG B 120 " pdb=" CA ARG B 120 " ideal model delta sigma weight residual 1.459 1.405 0.054 1.19e-02 7.06e+03 2.07e+01 bond pdb=" N ARG E 120 " pdb=" CA ARG E 120 " ideal model delta sigma weight residual 1.459 1.408 0.051 1.19e-02 7.06e+03 1.86e+01 bond pdb=" N ARG G 120 " pdb=" CA ARG G 120 " ideal model delta sigma weight residual 1.459 1.407 0.052 1.21e-02 6.83e+03 1.83e+01 bond pdb=" N ARG C 120 " pdb=" CA ARG C 120 " ideal model delta sigma weight residual 1.459 1.409 0.050 1.21e-02 6.83e+03 1.70e+01 bond pdb=" C ARG A 120 " pdb=" O ARG A 120 " ideal model delta sigma weight residual 1.237 1.193 0.043 1.17e-02 7.31e+03 1.37e+01 ... (remaining 19329 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 25629 2.11 - 4.21: 268 4.21 - 6.32: 19 6.32 - 8.43: 9 8.43 - 10.54: 3 Bond angle restraints: 25928 Sorted by residual: angle pdb=" CA ILE B 112 " pdb=" CB ILE B 112 " pdb=" CG1 ILE B 112 " ideal model delta sigma weight residual 110.40 116.32 -5.92 1.70e+00 3.46e-01 1.21e+01 angle pdb=" N ILE A 15 " pdb=" CA ILE A 15 " pdb=" C ILE A 15 " ideal model delta sigma weight residual 111.62 108.88 2.74 7.90e-01 1.60e+00 1.20e+01 angle pdb=" N ILE C 15 " pdb=" CA ILE C 15 " pdb=" C ILE C 15 " ideal model delta sigma weight residual 111.62 108.91 2.71 7.90e-01 1.60e+00 1.18e+01 angle pdb=" N ILE B 15 " pdb=" CA ILE B 15 " pdb=" C ILE B 15 " ideal model delta sigma weight residual 111.62 108.92 2.70 7.90e-01 1.60e+00 1.17e+01 angle pdb=" N ILE D 15 " pdb=" CA ILE D 15 " pdb=" C ILE D 15 " ideal model delta sigma weight residual 111.62 108.93 2.69 7.90e-01 1.60e+00 1.16e+01 ... (remaining 25923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.94: 10376 19.94 - 39.88: 948 39.88 - 59.82: 353 59.82 - 79.75: 61 79.75 - 99.69: 8 Dihedral angle restraints: 11746 sinusoidal: 5047 harmonic: 6699 Sorted by residual: dihedral pdb=" CA GLY D 139 " pdb=" C GLY D 139 " pdb=" N MET D 140 " pdb=" CA MET D 140 " ideal model delta harmonic sigma weight residual 180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" C ILE E 78 " pdb=" N ILE E 78 " pdb=" CA ILE E 78 " pdb=" CB ILE E 78 " ideal model delta harmonic sigma weight residual -122.00 -131.36 9.36 0 2.50e+00 1.60e-01 1.40e+01 dihedral pdb=" CA PHE F 138 " pdb=" C PHE F 138 " pdb=" N GLY F 139 " pdb=" CA GLY F 139 " ideal model delta harmonic sigma weight residual -180.00 -162.15 -17.85 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 11743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1967 0.034 - 0.068: 603 0.068 - 0.103: 288 0.103 - 0.137: 63 0.137 - 0.171: 12 Chirality restraints: 2933 Sorted by residual: chirality pdb=" CA ILE E 78 " pdb=" N ILE E 78 " pdb=" C ILE E 78 " pdb=" CB ILE E 78 " both_signs ideal model delta sigma weight residual False 2.43 2.26 0.17 2.00e-01 2.50e+01 7.32e-01 chirality pdb=" CA ILE F 78 " pdb=" N ILE F 78 " pdb=" C ILE F 78 " pdb=" CB ILE F 78 " both_signs ideal model delta sigma weight residual False 2.43 2.29 0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" CB ILE C 98 " pdb=" CA ILE C 98 " pdb=" CG1 ILE C 98 " pdb=" CG2 ILE C 98 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 2930 not shown) Planarity restraints: 3122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 255 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C VAL C 255 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL C 255 " -0.012 2.00e-02 2.50e+03 pdb=" N GLU C 256 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 255 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" C VAL E 255 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL E 255 " -0.012 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 G 255 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.36e+00 pdb=" C VAL G 255 " 0.032 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: 2.27 - 2.80: 4404 2.80 - 3.32: 17790 3.32 - 3.85: 31326 3.85 - 4.37: 36365 4.37 - 4.90: 62580 Nonbonded interactions: 152465 Sorted by model distance: nonbonded pdb=" OG1 THR G 208 " pdb=" OD1 ASP G 210 " model vdw 2.275 3.040 nonbonded pdb=" OG1 THR D 208 " pdb=" OD1 ASP D 210 " model vdw 2.278 3.040 nonbonded pdb=" OG1 THR C 208 " pdb=" OD1 ASP C 210 " model vdw 2.290 3.040 nonbonded pdb=" OG1 THR E 208 " pdb=" OD1 ASP E 210 " model vdw 2.308 3.040 nonbonded pdb=" OG1 THR A 208 " pdb=" OD1 ASP A 210 " model vdw 2.323 3.040 ... (remaining 152460 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 through 404 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 na \ me C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 o \ r name C5 or name C6 or name C8 or name N1 or name O10 or name O11 or name O12 o \ r 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 through 404 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 na \ me C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 o \ r name C5 or name C6 or name C8 or name N1 or name O10 or name O11 or name O12 o \ r 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 through 404 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 na \ me C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 o \ r name C5 or name C6 or name C8 or name N1 or name O10 or name O11 or name O12 o \ r name O13 or name O14 or name O30 or name O4 or name O7 or name P1 )))) 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 through 404 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 na \ me C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 o \ r name C5 or name C6 or name C8 or name N1 or name O10 or name O11 or name O12 o \ r 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 through 404 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 na \ me C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 o \ r name C5 or name C6 or name C8 or name N1 or name O10 or name O11 or name O12 o \ r 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 through 404 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 na \ me C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 o \ r name C5 or name C6 or name C8 or name N1 or name O10 or name O11 or name O12 o \ r 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 through 404 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 o \ r name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C \ 38 or name C39 or name C5 or name C6 or name C8 or name N1 or name O10 or name O \ 11 or name O12 or name O13 or name O14 or name O30 or name O4 or name 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: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.690 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 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 0.054 19334 Z= 0.188 Angle : 0.551 10.536 25928 Z= 0.315 Chirality : 0.043 0.171 2933 Planarity : 0.004 0.031 3122 Dihedral : 17.896 99.692 7434 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.52 % Allowed : 16.93 % Favored : 81.55 % 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: 1.32 (0.18), residues: 2303 helix: 2.40 (0.14), residues: 1316 sheet: -1.19 (0.28), residues: 357 loop : -1.19 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 120 TYR 0.014 0.001 TYR E 134 PHE 0.011 0.001 PHE D 281 TRP 0.005 0.001 TRP F 201 HIS 0.003 0.001 HIS E 137 Details of bonding type rmsd covalent geometry : bond 0.00312 (19334) covalent geometry : angle 0.55141 (25928) hydrogen bonds : bond 0.10362 ( 1263) hydrogen bonds : angle 5.15024 ( 3633) *********************** 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 350 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 323 time to evaluate : 0.699 Fit side-chains REVERT: A 50 TYR cc_start: 0.9259 (m-10) cc_final: 0.8958 (m-10) REVERT: A 100 GLN cc_start: 0.9038 (pp30) cc_final: 0.8552 (pp30) REVERT: A 116 ARG cc_start: 0.8600 (mtm180) cc_final: 0.8278 (ttm-80) REVERT: A 142 LEU cc_start: 0.8388 (mm) cc_final: 0.8122 (mm) REVERT: B 97 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9317 (tm) REVERT: B 100 GLN cc_start: 0.8997 (pp30) cc_final: 0.8500 (pp30) REVERT: B 116 ARG cc_start: 0.8608 (mtm180) cc_final: 0.8259 (ttm-80) REVERT: B 142 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8235 (mm) REVERT: B 147 THR cc_start: 0.8904 (m) cc_final: 0.8693 (p) REVERT: C 97 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9311 (tm) REVERT: C 100 GLN cc_start: 0.9029 (pp30) cc_final: 0.8752 (pp30) REVERT: C 103 LYS cc_start: 0.9400 (mmtt) cc_final: 0.9181 (mppt) REVERT: C 116 ARG cc_start: 0.8618 (mtm180) cc_final: 0.8284 (ttm-80) REVERT: C 120 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8343 (ttp-110) REVERT: D 50 TYR cc_start: 0.9284 (m-10) cc_final: 0.8986 (m-10) REVERT: D 100 GLN cc_start: 0.9072 (pp30) cc_final: 0.8636 (pp30) REVERT: D 103 LYS cc_start: 0.9390 (mmtt) cc_final: 0.9136 (mmmt) REVERT: D 116 ARG cc_start: 0.8547 (mtm180) cc_final: 0.8225 (ttm-80) REVERT: E 100 GLN cc_start: 0.9039 (pp30) cc_final: 0.8801 (pp30) REVERT: E 103 LYS cc_start: 0.9386 (mmtt) cc_final: 0.9162 (mppt) REVERT: E 116 ARG cc_start: 0.8667 (mtm180) cc_final: 0.8324 (ttm-80) REVERT: E 120 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8331 (ttp-110) REVERT: F 100 GLN cc_start: 0.9060 (pp30) cc_final: 0.8735 (pp30) REVERT: F 103 LYS cc_start: 0.9396 (mmtt) cc_final: 0.9178 (mppt) REVERT: F 116 ARG cc_start: 0.8615 (mtm180) cc_final: 0.8278 (ttm-80) REVERT: G 50 TYR cc_start: 0.9299 (m-10) cc_final: 0.8973 (m-10) REVERT: G 100 GLN cc_start: 0.9005 (pp30) cc_final: 0.8694 (pp30) REVERT: G 103 LYS cc_start: 0.9388 (mmtt) cc_final: 0.9120 (mppt) REVERT: G 116 ARG cc_start: 0.8590 (mtm180) cc_final: 0.8278 (ttm-80) REVERT: G 142 LEU cc_start: 0.8573 (mm) cc_final: 0.8282 (tm) outliers start: 27 outliers final: 2 residues processed: 340 average time/residue: 0.6440 time to fit residues: 245.7474 Evaluate side-chains 295 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 288 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 120 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 5.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 137 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.125479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.065305 restraints weight = 31346.077| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 2.16 r_work: 0.2548 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2420 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19334 Z= 0.119 Angle : 0.616 13.398 25928 Z= 0.292 Chirality : 0.042 0.134 2933 Planarity : 0.003 0.026 3122 Dihedral : 13.958 81.879 3693 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.05 % Allowed : 15.97 % Favored : 79.98 % 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 (0.17), residues: 2303 helix: 2.60 (0.14), residues: 1309 sheet: -0.23 (0.32), residues: 273 loop : -1.36 (0.20), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 120 TYR 0.023 0.001 TYR B 50 PHE 0.011 0.001 PHE G 80 TRP 0.006 0.001 TRP B 184 HIS 0.002 0.000 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00254 (19334) covalent geometry : angle 0.61639 (25928) hydrogen bonds : bond 0.03921 ( 1263) hydrogen bonds : angle 3.85579 ( 3633) *********************** 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 386 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 314 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 100 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8671 (pp30) REVERT: A 116 ARG cc_start: 0.8751 (mtm180) cc_final: 0.8476 (ttm-80) REVERT: A 136 GLU cc_start: 0.8320 (tm-30) cc_final: 0.8013 (pp20) REVERT: A 140 MET cc_start: 0.8954 (mtp) cc_final: 0.8583 (mtp) REVERT: A 318 GLN cc_start: 0.9260 (OUTLIER) cc_final: 0.8984 (mt0) REVERT: B 97 LEU cc_start: 0.9490 (tt) cc_final: 0.9062 (tm) REVERT: B 100 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8622 (pp30) REVERT: B 116 ARG cc_start: 0.8822 (mtm180) cc_final: 0.8463 (ttm-80) REVERT: B 136 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7986 (pp20) REVERT: B 147 THR cc_start: 0.8761 (m) cc_final: 0.8511 (p) REVERT: C 100 GLN cc_start: 0.9089 (pp30) cc_final: 0.8687 (pp30) REVERT: C 116 ARG cc_start: 0.8780 (mtm180) cc_final: 0.8441 (ttm-80) REVERT: C 142 LEU cc_start: 0.8309 (mm) cc_final: 0.7703 (tm) REVERT: C 289 MET cc_start: 0.9477 (OUTLIER) cc_final: 0.9156 (ppp) REVERT: D 97 LEU cc_start: 0.9513 (tt) cc_final: 0.9216 (tm) REVERT: D 99 ASN cc_start: 0.9334 (OUTLIER) cc_final: 0.9120 (m-40) REVERT: D 100 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.8667 (pp30) REVERT: D 116 ARG cc_start: 0.8758 (mtm180) cc_final: 0.8516 (ttm-80) REVERT: D 318 GLN cc_start: 0.9257 (OUTLIER) cc_final: 0.8992 (mt0) REVERT: E 97 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9209 (tm) REVERT: E 100 GLN cc_start: 0.9095 (pp30) cc_final: 0.8788 (pp30) REVERT: E 103 LYS cc_start: 0.9407 (mmtt) cc_final: 0.9188 (mppt) REVERT: E 116 ARG cc_start: 0.8859 (mtm180) cc_final: 0.8458 (ttm-80) REVERT: E 142 LEU cc_start: 0.8219 (mm) cc_final: 0.7633 (tm) REVERT: F 100 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8642 (pp30) REVERT: F 116 ARG cc_start: 0.8752 (mtm180) cc_final: 0.8406 (ttm-80) REVERT: F 142 LEU cc_start: 0.8242 (mm) cc_final: 0.7934 (tm) REVERT: G 100 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8644 (pp30) REVERT: G 116 ARG cc_start: 0.8857 (mtm180) cc_final: 0.8553 (ttm-80) REVERT: G 140 MET cc_start: 0.7711 (mmp) cc_final: 0.7480 (mmm) REVERT: G 142 LEU cc_start: 0.8339 (mm) cc_final: 0.8024 (tm) outliers start: 72 outliers final: 28 residues processed: 354 average time/residue: 0.5918 time to fit residues: 236.0441 Evaluate side-chains 329 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 291 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 318 GLN Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 120 ARG Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 133 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 134 optimal weight: 50.0000 chunk 34 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 182 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 168 optimal weight: 20.0000 chunk 30 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.123795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.063343 restraints weight = 31492.961| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 2.17 r_work: 0.2506 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2377 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 19334 Z= 0.175 Angle : 0.605 11.484 25928 Z= 0.301 Chirality : 0.045 0.174 2933 Planarity : 0.003 0.023 3122 Dihedral : 13.547 70.607 3679 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.99 % Allowed : 16.42 % Favored : 79.58 % 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: 1.61 (0.17), residues: 2303 helix: 2.63 (0.14), residues: 1309 sheet: -0.19 (0.32), residues: 273 loop : -1.49 (0.20), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 120 TYR 0.038 0.001 TYR B 50 PHE 0.014 0.001 PHE C 80 TRP 0.008 0.001 TRP B 184 HIS 0.002 0.001 HIS G 137 Details of bonding type rmsd covalent geometry : bond 0.00406 (19334) covalent geometry : angle 0.60523 (25928) hydrogen bonds : bond 0.04327 ( 1263) hydrogen bonds : angle 3.83276 ( 3633) *********************** 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 375 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 304 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 100 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8684 (pp30) REVERT: A 116 ARG cc_start: 0.8767 (mtm180) cc_final: 0.8473 (ttm-80) REVERT: A 136 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8049 (pp20) REVERT: A 140 MET cc_start: 0.8895 (mtp) cc_final: 0.8297 (mtp) REVERT: A 250 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8509 (mmtp) REVERT: B 97 LEU cc_start: 0.9465 (tt) cc_final: 0.9220 (tm) REVERT: B 100 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8650 (pp30) REVERT: B 116 ARG cc_start: 0.8837 (mtm180) cc_final: 0.8472 (ttm-80) REVERT: B 136 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8009 (pp20) REVERT: B 147 THR cc_start: 0.8733 (m) cc_final: 0.8489 (p) REVERT: B 250 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8389 (mmtp) REVERT: C 100 GLN cc_start: 0.9103 (pp30) cc_final: 0.8692 (pp30) REVERT: C 116 ARG cc_start: 0.8806 (mtm180) cc_final: 0.8465 (ttm-80) REVERT: C 142 LEU cc_start: 0.7991 (mm) cc_final: 0.7511 (tm) REVERT: C 250 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8443 (mmpt) REVERT: D 43 HIS cc_start: 0.8516 (m90) cc_final: 0.7947 (m90) REVERT: D 99 ASN cc_start: 0.9346 (OUTLIER) cc_final: 0.9094 (m-40) REVERT: D 100 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8669 (pp30) REVERT: D 116 ARG cc_start: 0.8795 (mtm180) cc_final: 0.8536 (ttm-80) REVERT: E 97 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9239 (tm) REVERT: E 100 GLN cc_start: 0.9089 (pp30) cc_final: 0.8698 (pp30) REVERT: E 102 GLU cc_start: 0.9131 (tm-30) cc_final: 0.8820 (tm-30) REVERT: E 116 ARG cc_start: 0.8904 (mtm180) cc_final: 0.8520 (ttm-80) REVERT: E 140 MET cc_start: 0.7983 (mmm) cc_final: 0.7728 (mmp) REVERT: E 142 LEU cc_start: 0.8018 (mm) cc_final: 0.7486 (tm) REVERT: E 250 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8477 (mmtm) REVERT: F 100 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8627 (pp30) REVERT: F 116 ARG cc_start: 0.8773 (mtm180) cc_final: 0.8438 (ttm-80) REVERT: F 142 LEU cc_start: 0.8294 (mm) cc_final: 0.7973 (tm) REVERT: F 250 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8481 (mmtm) REVERT: G 100 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8686 (pp30) REVERT: G 116 ARG cc_start: 0.8846 (mtm180) cc_final: 0.8546 (ttm-80) REVERT: G 142 LEU cc_start: 0.8293 (mm) cc_final: 0.7956 (tm) outliers start: 71 outliers final: 26 residues processed: 336 average time/residue: 0.5943 time to fit residues: 224.3232 Evaluate side-chains 341 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 303 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 120 ARG Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 130 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 138 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 68 optimal weight: 50.0000 chunk 125 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 2 optimal weight: 50.0000 chunk 188 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 137 HIS D 43 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.123178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.062618 restraints weight = 31468.887| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 2.16 r_work: 0.2493 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2363 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 19334 Z= 0.206 Angle : 0.640 13.554 25928 Z= 0.316 Chirality : 0.045 0.207 2933 Planarity : 0.003 0.025 3122 Dihedral : 13.491 69.276 3679 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.99 % Allowed : 17.32 % Favored : 78.68 % 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: 1.54 (0.17), residues: 2303 helix: 2.56 (0.14), residues: 1316 sheet: -0.22 (0.32), residues: 273 loop : -1.53 (0.20), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 120 TYR 0.047 0.002 TYR B 50 PHE 0.016 0.002 PHE F 80 TRP 0.007 0.001 TRP E 184 HIS 0.002 0.001 HIS G 137 Details of bonding type rmsd covalent geometry : bond 0.00483 (19334) covalent geometry : angle 0.63955 (25928) hydrogen bonds : bond 0.04580 ( 1263) hydrogen bonds : angle 3.88109 ( 3633) *********************** 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 379 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 308 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 100 GLN cc_start: 0.9098 (OUTLIER) cc_final: 0.8707 (pp30) REVERT: A 116 ARG cc_start: 0.8812 (mtm180) cc_final: 0.8530 (ttm-80) REVERT: A 140 MET cc_start: 0.8501 (mtp) cc_final: 0.8053 (ptp) REVERT: B 97 LEU cc_start: 0.9483 (tt) cc_final: 0.9250 (tm) REVERT: B 100 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8645 (pp30) REVERT: B 116 ARG cc_start: 0.8864 (mtm180) cc_final: 0.8494 (ttm-80) REVERT: B 134 TYR cc_start: 0.8607 (m-10) cc_final: 0.8342 (m-10) REVERT: B 250 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8324 (mmtp) REVERT: C 100 GLN cc_start: 0.9100 (pp30) cc_final: 0.8662 (pp30) REVERT: C 116 ARG cc_start: 0.8818 (mtm180) cc_final: 0.8480 (ttm-80) REVERT: C 142 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7571 (tm) REVERT: C 250 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8478 (mmpt) REVERT: D 43 HIS cc_start: 0.8524 (m-70) cc_final: 0.8053 (m90) REVERT: D 99 ASN cc_start: 0.9336 (OUTLIER) cc_final: 0.9091 (m-40) REVERT: D 100 GLN cc_start: 0.9131 (pp30) cc_final: 0.8693 (pp30) REVERT: D 116 ARG cc_start: 0.8815 (mtm180) cc_final: 0.8553 (ttm-80) REVERT: D 134 TYR cc_start: 0.8881 (m-10) cc_final: 0.8651 (m-10) REVERT: D 140 MET cc_start: 0.8312 (mmp) cc_final: 0.7984 (mmp) REVERT: D 250 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8272 (mmpt) REVERT: E 97 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9285 (tm) REVERT: E 100 GLN cc_start: 0.9119 (pp30) cc_final: 0.8712 (pp30) REVERT: E 102 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8926 (tm-30) REVERT: E 116 ARG cc_start: 0.8924 (mtm180) cc_final: 0.8547 (ttm-80) REVERT: E 250 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8510 (mmtm) REVERT: E 256 GLU cc_start: 0.9239 (OUTLIER) cc_final: 0.8700 (mp0) REVERT: F 63 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.8235 (m-10) REVERT: F 100 GLN cc_start: 0.9106 (pp30) cc_final: 0.8645 (pp30) REVERT: F 116 ARG cc_start: 0.8784 (mtm180) cc_final: 0.8454 (ttm-80) REVERT: F 142 LEU cc_start: 0.8341 (mm) cc_final: 0.7992 (tm) REVERT: F 250 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8488 (mmtm) REVERT: G 63 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.8289 (m-10) REVERT: G 100 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8712 (pp30) REVERT: G 116 ARG cc_start: 0.8849 (mtm180) cc_final: 0.8559 (ttm-80) REVERT: G 142 LEU cc_start: 0.8357 (mm) cc_final: 0.8027 (tm) REVERT: G 250 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8078 (mmpt) outliers start: 71 outliers final: 32 residues processed: 346 average time/residue: 0.6170 time to fit residues: 241.1589 Evaluate side-chains 353 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 306 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain F residue 63 TYR Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain G residue 63 TYR Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 250 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 56 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 202 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.125055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.066433 restraints weight = 31209.864| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 2.19 r_work: 0.2541 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2412 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19334 Z= 0.119 Angle : 0.635 13.761 25928 Z= 0.306 Chirality : 0.043 0.160 2933 Planarity : 0.003 0.021 3122 Dihedral : 13.003 69.304 3675 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.26 % Allowed : 18.73 % Favored : 78.01 % 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: 1.60 (0.17), residues: 2303 helix: 2.65 (0.14), residues: 1309 sheet: -0.18 (0.32), residues: 273 loop : -1.56 (0.19), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 120 TYR 0.049 0.001 TYR G 50 PHE 0.016 0.001 PHE A 80 TRP 0.005 0.001 TRP E 201 HIS 0.002 0.000 HIS E 137 Details of bonding type rmsd covalent geometry : bond 0.00257 (19334) covalent geometry : angle 0.63540 (25928) hydrogen bonds : bond 0.03753 ( 1263) hydrogen bonds : angle 3.71701 ( 3633) *********************** 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 371 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 313 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 100 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8709 (pp30) REVERT: A 116 ARG cc_start: 0.8818 (mtm180) cc_final: 0.8523 (ttm-80) REVERT: A 140 MET cc_start: 0.8631 (mtp) cc_final: 0.8263 (ptp) REVERT: A 250 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8231 (mmpt) REVERT: B 97 LEU cc_start: 0.9486 (tt) cc_final: 0.9266 (tm) REVERT: B 100 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8673 (pp30) REVERT: B 116 ARG cc_start: 0.8838 (mtm180) cc_final: 0.8434 (ttm-80) REVERT: B 250 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8298 (mmtp) REVERT: C 50 TYR cc_start: 0.9163 (m-80) cc_final: 0.8675 (m-80) REVERT: C 100 GLN cc_start: 0.9101 (pp30) cc_final: 0.8690 (pp30) REVERT: C 116 ARG cc_start: 0.8818 (mtm180) cc_final: 0.8476 (ttm-80) REVERT: C 142 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7491 (tm) REVERT: C 250 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8416 (mmpt) REVERT: C 289 MET cc_start: 0.9461 (OUTLIER) cc_final: 0.9217 (ppp) REVERT: D 100 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8724 (pp30) REVERT: D 116 ARG cc_start: 0.8788 (mtm180) cc_final: 0.8512 (ttm-80) REVERT: D 140 MET cc_start: 0.8192 (mmp) cc_final: 0.7802 (mmp) REVERT: D 250 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8183 (mmpt) REVERT: E 50 TYR cc_start: 0.9283 (m-80) cc_final: 0.8793 (m-80) REVERT: E 100 GLN cc_start: 0.9108 (pp30) cc_final: 0.8700 (pp30) REVERT: E 102 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8940 (tm-30) REVERT: E 116 ARG cc_start: 0.8901 (mtm180) cc_final: 0.8492 (ttm-80) REVERT: E 250 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8393 (mmtm) REVERT: E 256 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.8720 (mp0) REVERT: F 99 ASN cc_start: 0.9243 (OUTLIER) cc_final: 0.9006 (m-40) REVERT: F 100 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8634 (pp30) REVERT: F 116 ARG cc_start: 0.8767 (mtm180) cc_final: 0.8431 (ttm-80) REVERT: F 142 LEU cc_start: 0.8308 (mm) cc_final: 0.7986 (tm) REVERT: G 100 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8710 (pp30) REVERT: G 116 ARG cc_start: 0.8852 (mtm180) cc_final: 0.8544 (ttm-80) REVERT: G 140 MET cc_start: 0.8037 (mmm) cc_final: 0.7724 (mmp) REVERT: G 142 LEU cc_start: 0.8297 (mm) cc_final: 0.7964 (tm) REVERT: G 250 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.7889 (mmpt) REVERT: G 318 GLN cc_start: 0.9219 (OUTLIER) cc_final: 0.8936 (mt0) outliers start: 58 outliers final: 24 residues processed: 345 average time/residue: 0.5811 time to fit residues: 226.8998 Evaluate side-chains 343 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 303 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain F residue 99 ASN Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 250 LYS Chi-restraints excluded: chain G residue 318 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 73 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 106 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 228 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.122941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.062310 restraints weight = 31431.455| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 2.16 r_work: 0.2488 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2357 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 19334 Z= 0.233 Angle : 0.690 13.502 25928 Z= 0.339 Chirality : 0.046 0.137 2933 Planarity : 0.003 0.024 3122 Dihedral : 13.250 69.358 3675 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.71 % Allowed : 18.90 % Favored : 77.39 % 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: 1.48 (0.17), residues: 2303 helix: 2.55 (0.14), residues: 1309 sheet: -0.20 (0.32), residues: 273 loop : -1.62 (0.19), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 190 TYR 0.017 0.001 TYR G 291 PHE 0.017 0.002 PHE E 80 TRP 0.009 0.001 TRP B 184 HIS 0.005 0.001 HIS E 137 Details of bonding type rmsd covalent geometry : bond 0.00550 (19334) covalent geometry : angle 0.69041 (25928) hydrogen bonds : bond 0.04723 ( 1263) hydrogen bonds : angle 3.94021 ( 3633) *********************** 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 370 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 304 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: A 100 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8725 (pp30) REVERT: A 116 ARG cc_start: 0.8838 (mtm180) cc_final: 0.8547 (ttm-80) REVERT: A 140 MET cc_start: 0.8350 (mtp) cc_final: 0.7945 (ptp) REVERT: A 250 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8304 (mmpt) REVERT: B 50 TYR cc_start: 0.9252 (m-80) cc_final: 0.8872 (m-80) REVERT: B 97 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9249 (tm) REVERT: B 100 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8684 (pp30) REVERT: B 116 ARG cc_start: 0.8866 (mtm180) cc_final: 0.8492 (ttm-80) REVERT: B 250 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8300 (mmtp) REVERT: C 100 GLN cc_start: 0.9111 (pp30) cc_final: 0.8812 (pp30) REVERT: C 103 LYS cc_start: 0.9461 (mmtt) cc_final: 0.9146 (mppt) REVERT: C 116 ARG cc_start: 0.8833 (mtm180) cc_final: 0.8500 (ttm-80) REVERT: C 142 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7547 (tm) REVERT: C 250 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8466 (mmpt) REVERT: D 99 ASN cc_start: 0.9355 (OUTLIER) cc_final: 0.9109 (m-40) REVERT: D 100 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8705 (pp30) REVERT: D 116 ARG cc_start: 0.8822 (mtm180) cc_final: 0.8548 (ttm-80) REVERT: D 140 MET cc_start: 0.8221 (mmp) cc_final: 0.8000 (mmp) REVERT: D 250 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8294 (mmpt) REVERT: D 333 MET cc_start: 0.9075 (mmm) cc_final: 0.8837 (mmm) REVERT: E 99 ASN cc_start: 0.9230 (OUTLIER) cc_final: 0.8929 (m-40) REVERT: E 100 GLN cc_start: 0.9120 (pp30) cc_final: 0.8725 (pp30) REVERT: E 102 GLU cc_start: 0.9179 (tm-30) cc_final: 0.8973 (tm-30) REVERT: E 116 ARG cc_start: 0.8938 (mtm180) cc_final: 0.8547 (ttm-80) REVERT: E 250 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8500 (mmtm) REVERT: F 100 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8657 (pp30) REVERT: F 116 ARG cc_start: 0.8796 (mtm180) cc_final: 0.8456 (ttm-80) REVERT: F 142 LEU cc_start: 0.8353 (mm) cc_final: 0.8007 (tm) REVERT: G 50 TYR cc_start: 0.9311 (m-80) cc_final: 0.8855 (m-80) REVERT: G 100 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8725 (pp30) REVERT: G 116 ARG cc_start: 0.8864 (mtm180) cc_final: 0.8578 (ttm-80) REVERT: G 140 MET cc_start: 0.8166 (mmm) cc_final: 0.7949 (mmp) REVERT: G 142 LEU cc_start: 0.8410 (mm) cc_final: 0.8047 (tm) REVERT: G 250 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8067 (mmpt) outliers start: 66 outliers final: 27 residues processed: 340 average time/residue: 0.6268 time to fit residues: 239.7062 Evaluate side-chains 347 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 305 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 250 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 118 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 134 optimal weight: 50.0000 chunk 179 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 199 optimal weight: 9.9990 chunk 130 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 318 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.125397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.067079 restraints weight = 31401.672| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 2.24 r_work: 0.2552 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2424 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19334 Z= 0.115 Angle : 0.663 14.475 25928 Z= 0.318 Chirality : 0.043 0.236 2933 Planarity : 0.003 0.020 3122 Dihedral : 12.755 69.746 3675 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.87 % Allowed : 20.02 % Favored : 77.11 % 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: 2.63 (0.14), residues: 1316 sheet: -0.17 (0.32), residues: 273 loop : -1.60 (0.19), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 120 TYR 0.046 0.001 TYR E 50 PHE 0.018 0.001 PHE E 80 TRP 0.006 0.000 TRP E 201 HIS 0.002 0.000 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00246 (19334) covalent geometry : angle 0.66306 (25928) hydrogen bonds : bond 0.03565 ( 1263) hydrogen bonds : angle 3.72065 ( 3633) *********************** 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 367 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 316 time to evaluate : 1.084 Fit side-chains REVERT: A 100 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8746 (pp30) REVERT: A 116 ARG cc_start: 0.8829 (mtm180) cc_final: 0.8507 (ttm-80) REVERT: A 140 MET cc_start: 0.8326 (mtp) cc_final: 0.7974 (ptp) REVERT: A 250 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8335 (mmtm) REVERT: B 97 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9248 (tm) REVERT: B 100 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8680 (pp30) REVERT: B 116 ARG cc_start: 0.8838 (mtm180) cc_final: 0.8422 (ttm-80) REVERT: B 250 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8288 (mmtp) REVERT: C 50 TYR cc_start: 0.9248 (m-80) cc_final: 0.8770 (m-80) REVERT: C 100 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8674 (pp30) REVERT: C 116 ARG cc_start: 0.8813 (mtm180) cc_final: 0.8458 (ttm-80) REVERT: C 142 LEU cc_start: 0.7975 (mm) cc_final: 0.7491 (tm) REVERT: C 250 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8392 (mmpt) REVERT: C 289 MET cc_start: 0.9454 (OUTLIER) cc_final: 0.9235 (ppp) REVERT: D 100 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8721 (pp30) REVERT: D 116 ARG cc_start: 0.8799 (mtm180) cc_final: 0.8505 (ttm-80) REVERT: D 250 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8142 (mmpt) REVERT: E 99 ASN cc_start: 0.9195 (OUTLIER) cc_final: 0.8905 (m-40) REVERT: E 100 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8690 (pp30) REVERT: E 116 ARG cc_start: 0.8892 (mtm180) cc_final: 0.8536 (ttm-80) REVERT: E 120 ARG cc_start: 0.8349 (ttp-110) cc_final: 0.8110 (ttm170) REVERT: E 250 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8363 (mmtm) REVERT: E 256 GLU cc_start: 0.9230 (OUTLIER) cc_final: 0.8720 (mp0) REVERT: F 99 ASN cc_start: 0.9215 (OUTLIER) cc_final: 0.8982 (m-40) REVERT: F 100 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8658 (pp30) REVERT: F 116 ARG cc_start: 0.8768 (mtm180) cc_final: 0.8415 (ttm-80) REVERT: F 142 LEU cc_start: 0.8318 (mm) cc_final: 0.8015 (tm) REVERT: G 50 TYR cc_start: 0.9377 (m-80) cc_final: 0.8899 (m-80) REVERT: G 99 ASN cc_start: 0.9199 (OUTLIER) cc_final: 0.8951 (m-40) REVERT: G 100 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8713 (pp30) REVERT: G 116 ARG cc_start: 0.8839 (mtm180) cc_final: 0.8525 (ttm-80) REVERT: G 142 LEU cc_start: 0.8335 (mm) cc_final: 0.7985 (tm) REVERT: G 250 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.7887 (mmpt) outliers start: 51 outliers final: 23 residues processed: 339 average time/residue: 0.5950 time to fit residues: 228.4732 Evaluate side-chains 350 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 308 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain F residue 99 ASN Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 250 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 82 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 154 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 173 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 17 optimal weight: 0.1980 chunk 37 optimal weight: 5.9990 chunk 212 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.125638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.067179 restraints weight = 31233.751| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 2.20 r_work: 0.2559 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2430 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19334 Z= 0.115 Angle : 0.702 14.951 25928 Z= 0.330 Chirality : 0.043 0.209 2933 Planarity : 0.003 0.023 3122 Dihedral : 12.433 71.372 3675 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.76 % Allowed : 20.81 % Favored : 76.43 % 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: 1.65 (0.17), residues: 2303 helix: 2.69 (0.14), residues: 1316 sheet: -0.09 (0.32), residues: 273 loop : -1.61 (0.19), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 120 TYR 0.057 0.001 TYR D 50 PHE 0.017 0.001 PHE E 80 TRP 0.005 0.001 TRP E 201 HIS 0.001 0.000 HIS E 137 Details of bonding type rmsd covalent geometry : bond 0.00249 (19334) covalent geometry : angle 0.70192 (25928) hydrogen bonds : bond 0.03519 ( 1263) hydrogen bonds : angle 3.66993 ( 3633) *********************** 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 364 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 315 time to evaluate : 0.759 Fit side-chains REVERT: A 50 TYR cc_start: 0.9212 (m-80) cc_final: 0.8893 (m-80) REVERT: A 100 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8761 (pp30) REVERT: A 116 ARG cc_start: 0.8833 (mtm180) cc_final: 0.8464 (ttm-80) REVERT: A 140 MET cc_start: 0.8247 (mtp) cc_final: 0.7921 (ptp) REVERT: A 250 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8331 (mmtm) REVERT: B 50 TYR cc_start: 0.9231 (m-80) cc_final: 0.8789 (m-80) REVERT: B 97 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9257 (tm) REVERT: B 100 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8699 (pp30) REVERT: B 116 ARG cc_start: 0.8834 (mtm180) cc_final: 0.8419 (ttm-80) REVERT: B 250 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8069 (mmpt) REVERT: C 100 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8666 (pp30) REVERT: C 116 ARG cc_start: 0.8796 (mtm180) cc_final: 0.8441 (ttm-80) REVERT: C 142 LEU cc_start: 0.7978 (mm) cc_final: 0.7491 (tm) REVERT: D 100 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8722 (pp30) REVERT: D 116 ARG cc_start: 0.8790 (mtm180) cc_final: 0.8499 (ttm-80) REVERT: D 140 MET cc_start: 0.7776 (mmt) cc_final: 0.7518 (mmm) REVERT: D 250 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8170 (mmpt) REVERT: E 50 TYR cc_start: 0.9313 (m-80) cc_final: 0.8900 (m-80) REVERT: E 99 ASN cc_start: 0.9207 (OUTLIER) cc_final: 0.8917 (m-40) REVERT: E 100 GLN cc_start: 0.9096 (pp30) cc_final: 0.8704 (pp30) REVERT: E 116 ARG cc_start: 0.8911 (mtm180) cc_final: 0.8563 (ttm-80) REVERT: E 120 ARG cc_start: 0.8345 (ttp-110) cc_final: 0.8088 (ttm170) REVERT: E 250 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8363 (mmtm) REVERT: F 99 ASN cc_start: 0.9213 (OUTLIER) cc_final: 0.8989 (m-40) REVERT: F 100 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8722 (pp30) REVERT: F 116 ARG cc_start: 0.8760 (mtm180) cc_final: 0.8418 (ttm-80) REVERT: F 140 MET cc_start: 0.8233 (mmp) cc_final: 0.7226 (mtp) REVERT: F 142 LEU cc_start: 0.8333 (mm) cc_final: 0.7994 (tm) REVERT: G 100 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8718 (pp30) REVERT: G 116 ARG cc_start: 0.8824 (mtm180) cc_final: 0.8490 (ttm-80) REVERT: G 142 LEU cc_start: 0.8299 (mm) cc_final: 0.7918 (tm) REVERT: G 250 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.7824 (mmpt) outliers start: 49 outliers final: 23 residues processed: 336 average time/residue: 0.6241 time to fit residues: 237.2061 Evaluate side-chains 345 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 308 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain F residue 99 ASN Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 250 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 204 optimal weight: 0.0980 chunk 146 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 186 optimal weight: 0.7980 chunk 193 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 197 optimal weight: 0.8980 chunk 167 optimal weight: 50.0000 chunk 96 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.125857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.066057 restraints weight = 31155.995| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 2.17 r_work: 0.2575 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2447 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19334 Z= 0.118 Angle : 0.714 15.230 25928 Z= 0.336 Chirality : 0.044 0.305 2933 Planarity : 0.003 0.022 3122 Dihedral : 12.215 72.722 3675 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.53 % Allowed : 21.60 % Favored : 75.87 % 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: 1.70 (0.18), residues: 2303 helix: 2.72 (0.14), residues: 1316 sheet: -0.04 (0.33), residues: 273 loop : -1.60 (0.20), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 120 TYR 0.055 0.001 TYR C 50 PHE 0.017 0.001 PHE B 80 TRP 0.006 0.001 TRP E 201 HIS 0.001 0.000 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00259 (19334) covalent geometry : angle 0.71384 (25928) hydrogen bonds : bond 0.03437 ( 1263) hydrogen bonds : angle 3.66657 ( 3633) *********************** 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 358 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 313 time to evaluate : 0.751 Fit side-chains REVERT: A 100 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.8756 (pp30) REVERT: A 116 ARG cc_start: 0.8831 (mtm180) cc_final: 0.8436 (ttm-80) REVERT: A 140 MET cc_start: 0.8235 (mtp) cc_final: 0.7939 (ptp) REVERT: A 250 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8360 (mmtm) REVERT: B 50 TYR cc_start: 0.9313 (m-80) cc_final: 0.8842 (m-80) REVERT: B 97 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9267 (tm) REVERT: B 100 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8681 (pp30) REVERT: B 116 ARG cc_start: 0.8852 (mtm180) cc_final: 0.8431 (ttm-80) REVERT: B 250 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8082 (mmpt) REVERT: C 50 TYR cc_start: 0.9199 (m-80) cc_final: 0.8778 (m-80) REVERT: C 100 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8678 (pp30) REVERT: C 107 LYS cc_start: 0.9336 (tmmt) cc_final: 0.9062 (tmmt) REVERT: C 116 ARG cc_start: 0.8790 (mtm180) cc_final: 0.8425 (ttm-80) REVERT: C 142 LEU cc_start: 0.7979 (mm) cc_final: 0.7488 (tm) REVERT: D 100 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8731 (pp30) REVERT: D 116 ARG cc_start: 0.8768 (mtm180) cc_final: 0.8466 (ttm-80) REVERT: D 140 MET cc_start: 0.7734 (mmt) cc_final: 0.7522 (mmm) REVERT: D 250 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8163 (mmpt) REVERT: E 50 TYR cc_start: 0.9368 (m-80) cc_final: 0.8964 (m-80) REVERT: E 100 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8688 (pp30) REVERT: E 116 ARG cc_start: 0.8890 (mtm180) cc_final: 0.8512 (ttm-80) REVERT: E 120 ARG cc_start: 0.8315 (ttp-110) cc_final: 0.8050 (ttm170) REVERT: E 250 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8368 (mmtm) REVERT: F 100 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8704 (pp30) REVERT: F 116 ARG cc_start: 0.8773 (mtm180) cc_final: 0.8427 (ttm-80) REVERT: F 142 LEU cc_start: 0.8400 (mm) cc_final: 0.8047 (tm) REVERT: G 100 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8737 (pp30) REVERT: G 116 ARG cc_start: 0.8811 (mtm180) cc_final: 0.8462 (ttm-80) REVERT: G 142 LEU cc_start: 0.8335 (mm) cc_final: 0.7936 (tm) REVERT: G 250 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.7836 (mmpt) outliers start: 45 outliers final: 21 residues processed: 335 average time/residue: 0.6096 time to fit residues: 230.9860 Evaluate side-chains 345 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 311 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 250 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 23 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 168 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 2 optimal weight: 50.0000 chunk 212 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.124400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.065433 restraints weight = 31344.956| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 2.20 r_work: 0.2516 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2386 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19334 Z= 0.161 Angle : 0.753 15.261 25928 Z= 0.358 Chirality : 0.045 0.275 2933 Planarity : 0.003 0.027 3122 Dihedral : 12.407 73.281 3675 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.14 % Allowed : 22.10 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.17), residues: 2303 helix: 2.62 (0.14), residues: 1323 sheet: -0.05 (0.33), residues: 273 loop : -1.51 (0.19), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 120 TYR 0.066 0.002 TYR D 50 PHE 0.018 0.002 PHE E 80 TRP 0.008 0.001 TRP B 184 HIS 0.001 0.000 HIS G 137 Details of bonding type rmsd covalent geometry : bond 0.00372 (19334) covalent geometry : angle 0.75329 (25928) hydrogen bonds : bond 0.04040 ( 1263) hydrogen bonds : angle 3.79689 ( 3633) ********************** 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 345 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 307 time to evaluate : 0.707 Fit side-chains REVERT: A 100 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8773 (pp30) REVERT: A 116 ARG cc_start: 0.8798 (mtm180) cc_final: 0.8495 (ttm-80) REVERT: A 140 MET cc_start: 0.8316 (mtp) cc_final: 0.8014 (ptp) REVERT: A 250 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8264 (mmpt) REVERT: B 97 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9165 (tm) REVERT: B 100 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8686 (pp30) REVERT: B 116 ARG cc_start: 0.8854 (mtm180) cc_final: 0.8421 (ttm-80) REVERT: B 250 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8276 (mmtp) REVERT: C 50 TYR cc_start: 0.9248 (m-80) cc_final: 0.8856 (m-80) REVERT: C 100 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8692 (pp30) REVERT: C 107 LYS cc_start: 0.9338 (tmmt) cc_final: 0.9076 (tmmt) REVERT: C 116 ARG cc_start: 0.8822 (mtm180) cc_final: 0.8470 (ttm-80) REVERT: C 142 LEU cc_start: 0.8057 (mm) cc_final: 0.7555 (tm) REVERT: D 100 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8748 (pp30) REVERT: D 116 ARG cc_start: 0.8806 (mtm180) cc_final: 0.8504 (ttm-80) REVERT: D 140 MET cc_start: 0.7873 (mmt) cc_final: 0.7659 (mmm) REVERT: D 250 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8212 (mmpt) REVERT: E 50 TYR cc_start: 0.9396 (m-80) cc_final: 0.9027 (m-80) REVERT: E 100 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8703 (pp30) REVERT: E 116 ARG cc_start: 0.8910 (mtm180) cc_final: 0.8541 (ttm-80) REVERT: E 120 ARG cc_start: 0.8334 (ttp-110) cc_final: 0.8064 (ttm170) REVERT: E 250 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8384 (mmtm) REVERT: F 100 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8728 (pp30) REVERT: F 116 ARG cc_start: 0.8766 (mtm180) cc_final: 0.8406 (ttm-80) REVERT: F 142 LEU cc_start: 0.8356 (mm) cc_final: 0.7982 (tm) REVERT: G 100 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8761 (pp30) REVERT: G 116 ARG cc_start: 0.8847 (mtm180) cc_final: 0.8529 (ttm-80) REVERT: G 142 LEU cc_start: 0.8278 (mm) cc_final: 0.7872 (tm) REVERT: G 250 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.7864 (mmpt) outliers start: 38 outliers final: 18 residues processed: 323 average time/residue: 0.6385 time to fit residues: 232.7287 Evaluate side-chains 338 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 307 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 250 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 189 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 chunk 222 optimal weight: 0.7980 chunk 22 optimal weight: 0.0670 chunk 36 optimal weight: 40.0000 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.125697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.066036 restraints weight = 31487.602| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 2.17 r_work: 0.2572 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2445 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19334 Z= 0.120 Angle : 0.747 15.773 25928 Z= 0.351 Chirality : 0.044 0.278 2933 Planarity : 0.003 0.027 3122 Dihedral : 12.138 73.955 3675 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.02 % Allowed : 22.38 % Favored : 75.59 % 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 (0.18), residues: 2303 helix: 2.67 (0.14), residues: 1323 sheet: -0.04 (0.33), residues: 273 loop : -1.52 (0.19), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 120 TYR 0.068 0.001 TYR A 50 PHE 0.022 0.001 PHE E 148 TRP 0.009 0.000 TRP E 201 HIS 0.001 0.000 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00263 (19334) covalent geometry : angle 0.74726 (25928) hydrogen bonds : bond 0.03424 ( 1263) hydrogen bonds : angle 3.66540 ( 3633) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12604.17 seconds wall clock time: 213 minutes 56.43 seconds (12836.43 seconds total)