Starting phenix.real_space_refine on Sun Feb 8 07:32:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mu6_48621/02_2026/9mu6_48621.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mu6_48621/02_2026/9mu6_48621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mu6_48621/02_2026/9mu6_48621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mu6_48621/02_2026/9mu6_48621.map" model { file = "/net/cci-nas-00/data/ceres_data/9mu6_48621/02_2026/9mu6_48621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mu6_48621/02_2026/9mu6_48621.cif" } resolution = 3.66 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= 0.004 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 312 5.16 5 C 27435 2.51 5 N 7491 2.21 5 O 7896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.05s 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: 43134 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1797 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1797 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1797 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1797 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1797 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1797 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1803 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Chain: "H" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1797 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1797 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1797 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1797 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1797 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1797 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1797 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1797 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1797 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1797 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1797 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1797 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1797 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "U" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1797 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "V" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1797 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "W" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1797 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "X" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1797 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 11.81, per 1000 atoms: 0.27 Number of scatterers: 43134 At special positions: 0 Unit cell: (146.533, 146.533, 146.533, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 312 16.00 O 7896 8.00 N 7491 7.00 C 27435 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: 3.70 Conformation dependent library (CDL) restraints added in 2.0 seconds 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10368 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 120 sheets defined 40.2% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 245 through 262 removed outlier: 3.889A pdb=" N LEU A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 292 removed outlier: 5.801A pdb=" N ASP A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA A 286 " --> pdb=" O GLN A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 311 Processing helix chain 'A' and resid 354 through 371 removed outlier: 3.578A pdb=" N ARG A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 460 Processing helix chain 'A' and resid 462 through 467 Processing helix chain 'B' and resid 245 through 262 removed outlier: 3.889A pdb=" N LEU B 249 " --> pdb=" O ASN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 292 removed outlier: 5.802A pdb=" N ASP B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA B 286 " --> pdb=" O GLN B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 311 Processing helix chain 'B' and resid 354 through 371 removed outlier: 3.577A pdb=" N ARG B 371 " --> pdb=" O ASP B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 460 Processing helix chain 'B' and resid 462 through 467 Processing helix chain 'C' and resid 245 through 262 removed outlier: 3.889A pdb=" N LEU C 249 " --> pdb=" O ASN C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 292 removed outlier: 5.802A pdb=" N ASP C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA C 286 " --> pdb=" O GLN C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 311 Processing helix chain 'C' and resid 354 through 371 removed outlier: 3.578A pdb=" N ARG C 371 " --> pdb=" O ASP C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 460 Processing helix chain 'C' and resid 462 through 467 Processing helix chain 'D' and resid 245 through 262 removed outlier: 3.888A pdb=" N LEU D 249 " --> pdb=" O ASN D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 292 removed outlier: 5.802A pdb=" N ASP D 285 " --> pdb=" O LYS D 281 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA D 286 " --> pdb=" O GLN D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 354 through 371 removed outlier: 3.578A pdb=" N ARG D 371 " --> pdb=" O ASP D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 460 Processing helix chain 'D' and resid 462 through 467 Processing helix chain 'E' and resid 245 through 262 removed outlier: 3.888A pdb=" N LEU E 249 " --> pdb=" O ASN E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 292 removed outlier: 5.801A pdb=" N ASP E 285 " --> pdb=" O LYS E 281 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA E 286 " --> pdb=" O GLN E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 311 Processing helix chain 'E' and resid 354 through 371 removed outlier: 3.578A pdb=" N ARG E 371 " --> pdb=" O ASP E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 460 Processing helix chain 'E' and resid 462 through 467 Processing helix chain 'F' and resid 245 through 262 removed outlier: 3.889A pdb=" N LEU F 249 " --> pdb=" O ASN F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 292 removed outlier: 5.801A pdb=" N ASP F 285 " --> pdb=" O LYS F 281 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA F 286 " --> pdb=" O GLN F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 311 Processing helix chain 'F' and resid 354 through 371 removed outlier: 3.579A pdb=" N ARG F 371 " --> pdb=" O ASP F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 443 through 460 Processing helix chain 'F' and resid 462 through 467 Processing helix chain 'G' and resid 245 through 262 removed outlier: 3.889A pdb=" N LEU G 249 " --> pdb=" O ASN G 245 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 292 removed outlier: 5.801A pdb=" N ASP G 285 " --> pdb=" O LYS G 281 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ALA G 286 " --> pdb=" O GLN G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 311 Processing helix chain 'G' and resid 354 through 371 removed outlier: 3.578A pdb=" N ARG G 371 " --> pdb=" O ASP G 367 " (cutoff:3.500A) Processing helix chain 'G' and resid 443 through 460 Processing helix chain 'G' and resid 462 through 467 Processing helix chain 'H' and resid 245 through 262 removed outlier: 3.889A pdb=" N LEU H 249 " --> pdb=" O ASN H 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 292 removed outlier: 5.801A pdb=" N ASP H 285 " --> pdb=" O LYS H 281 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA H 286 " --> pdb=" O GLN H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 311 Processing helix chain 'H' and resid 354 through 371 removed outlier: 3.579A pdb=" N ARG H 371 " --> pdb=" O ASP H 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 460 Processing helix chain 'H' and resid 462 through 467 Processing helix chain 'I' and resid 245 through 262 removed outlier: 3.889A pdb=" N LEU I 249 " --> pdb=" O ASN I 245 " (cutoff:3.500A) Processing helix chain 'I' and resid 273 through 292 removed outlier: 5.801A pdb=" N ASP I 285 " --> pdb=" O LYS I 281 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA I 286 " --> pdb=" O GLN I 282 " (cutoff:3.500A) Processing helix chain 'I' and resid 298 through 311 Processing helix chain 'I' and resid 354 through 371 removed outlier: 3.578A pdb=" N ARG I 371 " --> pdb=" O ASP I 367 " (cutoff:3.500A) Processing helix chain 'I' and resid 443 through 460 Processing helix chain 'I' and resid 462 through 467 Processing helix chain 'J' and resid 245 through 262 removed outlier: 3.889A pdb=" N LEU J 249 " --> pdb=" O ASN J 245 " (cutoff:3.500A) Processing helix chain 'J' and resid 273 through 292 removed outlier: 5.801A pdb=" N ASP J 285 " --> pdb=" O LYS J 281 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA J 286 " --> pdb=" O GLN J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 298 through 311 Processing helix chain 'J' and resid 354 through 371 removed outlier: 3.578A pdb=" N ARG J 371 " --> pdb=" O ASP J 367 " (cutoff:3.500A) Processing helix chain 'J' and resid 443 through 460 Processing helix chain 'J' and resid 462 through 467 Processing helix chain 'K' and resid 245 through 262 removed outlier: 3.888A pdb=" N LEU K 249 " --> pdb=" O ASN K 245 " (cutoff:3.500A) Processing helix chain 'K' and resid 273 through 292 removed outlier: 5.802A pdb=" N ASP K 285 " --> pdb=" O LYS K 281 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA K 286 " --> pdb=" O GLN K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 298 through 311 Processing helix chain 'K' and resid 354 through 371 removed outlier: 3.578A pdb=" N ARG K 371 " --> pdb=" O ASP K 367 " (cutoff:3.500A) Processing helix chain 'K' and resid 443 through 460 Processing helix chain 'K' and resid 462 through 467 Processing helix chain 'L' and resid 245 through 262 removed outlier: 3.889A pdb=" N LEU L 249 " --> pdb=" O ASN L 245 " (cutoff:3.500A) Processing helix chain 'L' and resid 273 through 292 removed outlier: 5.801A pdb=" N ASP L 285 " --> pdb=" O LYS L 281 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ALA L 286 " --> pdb=" O GLN L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 311 Processing helix chain 'L' and resid 354 through 371 removed outlier: 3.578A pdb=" N ARG L 371 " --> pdb=" O ASP L 367 " (cutoff:3.500A) Processing helix chain 'L' and resid 443 through 460 Processing helix chain 'L' and resid 462 through 467 Processing helix chain 'M' and resid 245 through 262 removed outlier: 3.888A pdb=" N LEU M 249 " --> pdb=" O ASN M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 273 through 292 removed outlier: 5.801A pdb=" N ASP M 285 " --> pdb=" O LYS M 281 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ALA M 286 " --> pdb=" O GLN M 282 " (cutoff:3.500A) Processing helix chain 'M' and resid 298 through 311 Processing helix chain 'M' and resid 354 through 371 removed outlier: 3.578A pdb=" N ARG M 371 " --> pdb=" O ASP M 367 " (cutoff:3.500A) Processing helix chain 'M' and resid 443 through 460 Processing helix chain 'M' and resid 462 through 467 Processing helix chain 'N' and resid 245 through 262 removed outlier: 3.890A pdb=" N LEU N 249 " --> pdb=" O ASN N 245 " (cutoff:3.500A) Processing helix chain 'N' and resid 273 through 292 removed outlier: 5.801A pdb=" N ASP N 285 " --> pdb=" O LYS N 281 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA N 286 " --> pdb=" O GLN N 282 " (cutoff:3.500A) Processing helix chain 'N' and resid 298 through 311 Processing helix chain 'N' and resid 354 through 371 removed outlier: 3.578A pdb=" N ARG N 371 " --> pdb=" O ASP N 367 " (cutoff:3.500A) Processing helix chain 'N' and resid 443 through 460 Processing helix chain 'N' and resid 462 through 467 Processing helix chain 'O' and resid 245 through 262 removed outlier: 3.889A pdb=" N LEU O 249 " --> pdb=" O ASN O 245 " (cutoff:3.500A) Processing helix chain 'O' and resid 273 through 292 removed outlier: 5.801A pdb=" N ASP O 285 " --> pdb=" O LYS O 281 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA O 286 " --> pdb=" O GLN O 282 " (cutoff:3.500A) Processing helix chain 'O' and resid 298 through 311 Processing helix chain 'O' and resid 354 through 371 removed outlier: 3.578A pdb=" N ARG O 371 " --> pdb=" O ASP O 367 " (cutoff:3.500A) Processing helix chain 'O' and resid 443 through 460 Processing helix chain 'O' and resid 462 through 467 Processing helix chain 'P' and resid 245 through 262 removed outlier: 3.889A pdb=" N LEU P 249 " --> pdb=" O ASN P 245 " (cutoff:3.500A) Processing helix chain 'P' and resid 273 through 292 removed outlier: 5.801A pdb=" N ASP P 285 " --> pdb=" O LYS P 281 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA P 286 " --> pdb=" O GLN P 282 " (cutoff:3.500A) Processing helix chain 'P' and resid 298 through 311 Processing helix chain 'P' and resid 354 through 371 removed outlier: 3.577A pdb=" N ARG P 371 " --> pdb=" O ASP P 367 " (cutoff:3.500A) Processing helix chain 'P' and resid 443 through 460 Processing helix chain 'P' and resid 462 through 467 Processing helix chain 'Q' and resid 245 through 262 removed outlier: 3.889A pdb=" N LEU Q 249 " --> pdb=" O ASN Q 245 " (cutoff:3.500A) Processing helix chain 'Q' and resid 273 through 292 removed outlier: 5.801A pdb=" N ASP Q 285 " --> pdb=" O LYS Q 281 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA Q 286 " --> pdb=" O GLN Q 282 " (cutoff:3.500A) Processing helix chain 'Q' and resid 298 through 311 Processing helix chain 'Q' and resid 354 through 371 removed outlier: 3.578A pdb=" N ARG Q 371 " --> pdb=" O ASP Q 367 " (cutoff:3.500A) Processing helix chain 'Q' and resid 443 through 460 Processing helix chain 'Q' and resid 462 through 467 Processing helix chain 'R' and resid 245 through 262 removed outlier: 3.889A pdb=" N LEU R 249 " --> pdb=" O ASN R 245 " (cutoff:3.500A) Processing helix chain 'R' and resid 273 through 292 removed outlier: 5.801A pdb=" N ASP R 285 " --> pdb=" O LYS R 281 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA R 286 " --> pdb=" O GLN R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 298 through 311 Processing helix chain 'R' and resid 354 through 371 removed outlier: 3.578A pdb=" N ARG R 371 " --> pdb=" O ASP R 367 " (cutoff:3.500A) Processing helix chain 'R' and resid 443 through 460 Processing helix chain 'R' and resid 462 through 467 Processing helix chain 'S' and resid 245 through 262 removed outlier: 3.889A pdb=" N LEU S 249 " --> pdb=" O ASN S 245 " (cutoff:3.500A) Processing helix chain 'S' and resid 273 through 292 removed outlier: 5.802A pdb=" N ASP S 285 " --> pdb=" O LYS S 281 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA S 286 " --> pdb=" O GLN S 282 " (cutoff:3.500A) Processing helix chain 'S' and resid 298 through 311 Processing helix chain 'S' and resid 354 through 371 removed outlier: 3.578A pdb=" N ARG S 371 " --> pdb=" O ASP S 367 " (cutoff:3.500A) Processing helix chain 'S' and resid 443 through 460 Processing helix chain 'S' and resid 462 through 467 Processing helix chain 'T' and resid 245 through 262 removed outlier: 3.889A pdb=" N LEU T 249 " --> pdb=" O ASN T 245 " (cutoff:3.500A) Processing helix chain 'T' and resid 273 through 292 removed outlier: 5.801A pdb=" N ASP T 285 " --> pdb=" O LYS T 281 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA T 286 " --> pdb=" O GLN T 282 " (cutoff:3.500A) Processing helix chain 'T' and resid 298 through 311 Processing helix chain 'T' and resid 354 through 371 removed outlier: 3.578A pdb=" N ARG T 371 " --> pdb=" O ASP T 367 " (cutoff:3.500A) Processing helix chain 'T' and resid 443 through 460 Processing helix chain 'T' and resid 462 through 467 Processing helix chain 'U' and resid 245 through 262 removed outlier: 3.889A pdb=" N LEU U 249 " --> pdb=" O ASN U 245 " (cutoff:3.500A) Processing helix chain 'U' and resid 273 through 292 removed outlier: 5.801A pdb=" N ASP U 285 " --> pdb=" O LYS U 281 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA U 286 " --> pdb=" O GLN U 282 " (cutoff:3.500A) Processing helix chain 'U' and resid 298 through 311 Processing helix chain 'U' and resid 354 through 371 removed outlier: 3.578A pdb=" N ARG U 371 " --> pdb=" O ASP U 367 " (cutoff:3.500A) Processing helix chain 'U' and resid 443 through 460 Processing helix chain 'U' and resid 462 through 467 Processing helix chain 'V' and resid 245 through 262 removed outlier: 3.888A pdb=" N LEU V 249 " --> pdb=" O ASN V 245 " (cutoff:3.500A) Processing helix chain 'V' and resid 273 through 292 removed outlier: 5.802A pdb=" N ASP V 285 " --> pdb=" O LYS V 281 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA V 286 " --> pdb=" O GLN V 282 " (cutoff:3.500A) Processing helix chain 'V' and resid 298 through 311 Processing helix chain 'V' and resid 354 through 371 removed outlier: 3.578A pdb=" N ARG V 371 " --> pdb=" O ASP V 367 " (cutoff:3.500A) Processing helix chain 'V' and resid 443 through 460 Processing helix chain 'V' and resid 462 through 467 Processing helix chain 'W' and resid 245 through 262 removed outlier: 3.889A pdb=" N LEU W 249 " --> pdb=" O ASN W 245 " (cutoff:3.500A) Processing helix chain 'W' and resid 273 through 292 removed outlier: 5.801A pdb=" N ASP W 285 " --> pdb=" O LYS W 281 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ALA W 286 " --> pdb=" O GLN W 282 " (cutoff:3.500A) Processing helix chain 'W' and resid 298 through 311 Processing helix chain 'W' and resid 354 through 371 removed outlier: 3.578A pdb=" N ARG W 371 " --> pdb=" O ASP W 367 " (cutoff:3.500A) Processing helix chain 'W' and resid 443 through 460 Processing helix chain 'W' and resid 462 through 467 Processing helix chain 'X' and resid 245 through 262 removed outlier: 3.888A pdb=" N LEU X 249 " --> pdb=" O ASN X 245 " (cutoff:3.500A) Processing helix chain 'X' and resid 273 through 292 removed outlier: 5.801A pdb=" N ASP X 285 " --> pdb=" O LYS X 281 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA X 286 " --> pdb=" O GLN X 282 " (cutoff:3.500A) Processing helix chain 'X' and resid 298 through 311 Processing helix chain 'X' and resid 354 through 371 removed outlier: 3.579A pdb=" N ARG X 371 " --> pdb=" O ASP X 367 " (cutoff:3.500A) Processing helix chain 'X' and resid 443 through 460 Processing helix chain 'X' and resid 462 through 467 Processing sheet with id=AA1, first strand: chain 'A' and resid 407 through 408 removed outlier: 3.501A pdb=" N MET A 431 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET B 396 " --> pdb=" O PHE A 268 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 318 through 319 removed outlier: 3.945A pdb=" N VAL A 318 " --> pdb=" O VAL A 325 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 347 Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 337 Processing sheet with id=AA5, first strand: chain 'A' and resid 396 through 397 removed outlier: 3.690A pdb=" N MET A 396 " --> pdb=" O PHE C 268 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET C 431 " --> pdb=" O VAL C 271 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 417 through 421 removed outlier: 3.872A pdb=" N ARG A 417 " --> pdb=" O ARG A 428 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 removed outlier: 3.501A pdb=" N MET B 431 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET C 396 " --> pdb=" O PHE B 268 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 318 through 319 removed outlier: 3.946A pdb=" N VAL B 318 " --> pdb=" O VAL B 325 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 346 through 347 Processing sheet with id=AB1, first strand: chain 'B' and resid 336 through 337 Processing sheet with id=AB2, first strand: chain 'B' and resid 417 through 421 removed outlier: 3.872A pdb=" N ARG B 417 " --> pdb=" O ARG B 428 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 318 through 319 removed outlier: 3.946A pdb=" N VAL C 318 " --> pdb=" O VAL C 325 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 346 through 347 Processing sheet with id=AB5, first strand: chain 'C' and resid 336 through 337 Processing sheet with id=AB6, first strand: chain 'C' and resid 417 through 421 removed outlier: 3.872A pdb=" N ARG C 417 " --> pdb=" O ARG C 428 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 407 through 408 removed outlier: 3.502A pdb=" N MET D 431 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET E 396 " --> pdb=" O PHE D 268 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 318 through 319 removed outlier: 3.945A pdb=" N VAL D 318 " --> pdb=" O VAL D 325 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 346 through 347 Processing sheet with id=AC1, first strand: chain 'D' and resid 336 through 337 Processing sheet with id=AC2, first strand: chain 'D' and resid 396 through 397 removed outlier: 3.705A pdb=" N MET D 396 " --> pdb=" O PHE F 268 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET F 431 " --> pdb=" O VAL F 271 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 417 through 421 removed outlier: 3.872A pdb=" N ARG D 417 " --> pdb=" O ARG D 428 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 407 through 408 removed outlier: 3.501A pdb=" N MET E 431 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET F 396 " --> pdb=" O PHE E 268 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 318 through 319 removed outlier: 3.945A pdb=" N VAL E 318 " --> pdb=" O VAL E 325 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 346 through 347 Processing sheet with id=AC7, first strand: chain 'E' and resid 336 through 337 Processing sheet with id=AC8, first strand: chain 'E' and resid 417 through 421 removed outlier: 3.872A pdb=" N ARG E 417 " --> pdb=" O ARG E 428 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 318 through 319 removed outlier: 3.945A pdb=" N VAL F 318 " --> pdb=" O VAL F 325 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 346 through 347 Processing sheet with id=AD2, first strand: chain 'F' and resid 336 through 337 Processing sheet with id=AD3, first strand: chain 'F' and resid 417 through 421 removed outlier: 3.872A pdb=" N ARG F 417 " --> pdb=" O ARG F 428 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 407 through 408 removed outlier: 3.502A pdb=" N MET G 431 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET H 396 " --> pdb=" O PHE G 268 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 318 through 319 removed outlier: 3.945A pdb=" N VAL G 318 " --> pdb=" O VAL G 325 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 346 through 347 Processing sheet with id=AD7, first strand: chain 'G' and resid 336 through 337 Processing sheet with id=AD8, first strand: chain 'G' and resid 396 through 397 removed outlier: 3.711A pdb=" N MET G 396 " --> pdb=" O PHE I 268 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET I 431 " --> pdb=" O VAL I 271 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 417 through 421 removed outlier: 3.872A pdb=" N ARG G 417 " --> pdb=" O ARG G 428 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 407 through 408 removed outlier: 3.502A pdb=" N MET H 431 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET I 396 " --> pdb=" O PHE H 268 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 318 through 319 removed outlier: 3.944A pdb=" N VAL H 318 " --> pdb=" O VAL H 325 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 346 through 347 Processing sheet with id=AE4, first strand: chain 'H' and resid 336 through 337 Processing sheet with id=AE5, first strand: chain 'H' and resid 417 through 421 removed outlier: 3.871A pdb=" N ARG H 417 " --> pdb=" O ARG H 428 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 318 through 319 removed outlier: 3.945A pdb=" N VAL I 318 " --> pdb=" O VAL I 325 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 346 through 347 Processing sheet with id=AE8, first strand: chain 'I' and resid 336 through 337 Processing sheet with id=AE9, first strand: chain 'I' and resid 417 through 421 removed outlier: 3.872A pdb=" N ARG I 417 " --> pdb=" O ARG I 428 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 407 through 408 removed outlier: 3.501A pdb=" N MET J 431 " --> pdb=" O VAL J 271 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET K 396 " --> pdb=" O PHE J 268 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 318 through 319 removed outlier: 3.945A pdb=" N VAL J 318 " --> pdb=" O VAL J 325 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 346 through 347 Processing sheet with id=AF4, first strand: chain 'J' and resid 336 through 337 Processing sheet with id=AF5, first strand: chain 'J' and resid 396 through 397 removed outlier: 3.703A pdb=" N MET J 396 " --> pdb=" O PHE L 268 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET L 431 " --> pdb=" O VAL L 271 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 417 through 421 removed outlier: 3.871A pdb=" N ARG J 417 " --> pdb=" O ARG J 428 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 407 through 408 removed outlier: 3.502A pdb=" N MET K 431 " --> pdb=" O VAL K 271 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET L 396 " --> pdb=" O PHE K 268 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 318 through 319 removed outlier: 3.945A pdb=" N VAL K 318 " --> pdb=" O VAL K 325 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 346 through 347 Processing sheet with id=AG1, first strand: chain 'K' and resid 336 through 337 Processing sheet with id=AG2, first strand: chain 'K' and resid 417 through 421 removed outlier: 3.871A pdb=" N ARG K 417 " --> pdb=" O ARG K 428 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 318 through 319 removed outlier: 3.945A pdb=" N VAL L 318 " --> pdb=" O VAL L 325 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 346 through 347 Processing sheet with id=AG5, first strand: chain 'L' and resid 336 through 337 Processing sheet with id=AG6, first strand: chain 'L' and resid 417 through 421 removed outlier: 3.871A pdb=" N ARG L 417 " --> pdb=" O ARG L 428 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 407 through 408 removed outlier: 3.501A pdb=" N MET M 431 " --> pdb=" O VAL M 271 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET N 396 " --> pdb=" O PHE M 268 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'M' and resid 318 through 319 removed outlier: 3.945A pdb=" N VAL M 318 " --> pdb=" O VAL M 325 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'M' and resid 346 through 347 Processing sheet with id=AH1, first strand: chain 'M' and resid 336 through 337 Processing sheet with id=AH2, first strand: chain 'M' and resid 396 through 397 removed outlier: 3.689A pdb=" N MET M 396 " --> pdb=" O PHE O 268 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET O 431 " --> pdb=" O VAL O 271 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'M' and resid 417 through 421 removed outlier: 3.872A pdb=" N ARG M 417 " --> pdb=" O ARG M 428 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'N' and resid 407 through 408 removed outlier: 3.502A pdb=" N MET N 431 " --> pdb=" O VAL N 271 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET O 396 " --> pdb=" O PHE N 268 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'N' and resid 318 through 319 removed outlier: 3.945A pdb=" N VAL N 318 " --> pdb=" O VAL N 325 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'N' and resid 346 through 347 Processing sheet with id=AH7, first strand: chain 'N' and resid 336 through 337 Processing sheet with id=AH8, first strand: chain 'N' and resid 417 through 421 removed outlier: 3.871A pdb=" N ARG N 417 " --> pdb=" O ARG N 428 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'O' and resid 318 through 319 removed outlier: 3.945A pdb=" N VAL O 318 " --> pdb=" O VAL O 325 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'O' and resid 346 through 347 Processing sheet with id=AI2, first strand: chain 'O' and resid 336 through 337 Processing sheet with id=AI3, first strand: chain 'O' and resid 417 through 421 removed outlier: 3.872A pdb=" N ARG O 417 " --> pdb=" O ARG O 428 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'P' and resid 407 through 408 removed outlier: 3.501A pdb=" N MET P 431 " --> pdb=" O VAL P 271 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET Q 396 " --> pdb=" O PHE P 268 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'P' and resid 318 through 319 removed outlier: 3.944A pdb=" N VAL P 318 " --> pdb=" O VAL P 325 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'P' and resid 346 through 347 Processing sheet with id=AI7, first strand: chain 'P' and resid 336 through 337 Processing sheet with id=AI8, first strand: chain 'P' and resid 396 through 397 removed outlier: 3.687A pdb=" N MET P 396 " --> pdb=" O PHE R 268 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET R 431 " --> pdb=" O VAL R 271 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'P' and resid 417 through 421 removed outlier: 3.871A pdb=" N ARG P 417 " --> pdb=" O ARG P 428 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'Q' and resid 407 through 408 removed outlier: 3.501A pdb=" N MET Q 431 " --> pdb=" O VAL Q 271 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET R 396 " --> pdb=" O PHE Q 268 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'Q' and resid 318 through 319 removed outlier: 3.945A pdb=" N VAL Q 318 " --> pdb=" O VAL Q 325 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'Q' and resid 346 through 347 Processing sheet with id=AJ4, first strand: chain 'Q' and resid 336 through 337 Processing sheet with id=AJ5, first strand: chain 'Q' and resid 417 through 421 removed outlier: 3.871A pdb=" N ARG Q 417 " --> pdb=" O ARG Q 428 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'R' and resid 318 through 319 removed outlier: 3.945A pdb=" N VAL R 318 " --> pdb=" O VAL R 325 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'R' and resid 346 through 347 Processing sheet with id=AJ8, first strand: chain 'R' and resid 336 through 337 Processing sheet with id=AJ9, first strand: chain 'R' and resid 417 through 421 removed outlier: 3.871A pdb=" N ARG R 417 " --> pdb=" O ARG R 428 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'S' and resid 407 through 408 removed outlier: 3.501A pdb=" N MET S 431 " --> pdb=" O VAL S 271 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET T 396 " --> pdb=" O PHE S 268 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'S' and resid 318 through 319 removed outlier: 3.945A pdb=" N VAL S 318 " --> pdb=" O VAL S 325 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'S' and resid 346 through 347 Processing sheet with id=AK4, first strand: chain 'S' and resid 336 through 337 Processing sheet with id=AK5, first strand: chain 'S' and resid 396 through 397 removed outlier: 3.696A pdb=" N MET S 396 " --> pdb=" O PHE U 268 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET U 431 " --> pdb=" O VAL U 271 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'S' and resid 417 through 421 removed outlier: 3.872A pdb=" N ARG S 417 " --> pdb=" O ARG S 428 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'T' and resid 407 through 408 removed outlier: 3.501A pdb=" N MET T 431 " --> pdb=" O VAL T 271 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET U 396 " --> pdb=" O PHE T 268 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'T' and resid 318 through 319 removed outlier: 3.944A pdb=" N VAL T 318 " --> pdb=" O VAL T 325 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'T' and resid 346 through 347 Processing sheet with id=AL1, first strand: chain 'T' and resid 336 through 337 Processing sheet with id=AL2, first strand: chain 'T' and resid 417 through 421 removed outlier: 3.872A pdb=" N ARG T 417 " --> pdb=" O ARG T 428 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'U' and resid 318 through 319 removed outlier: 3.945A pdb=" N VAL U 318 " --> pdb=" O VAL U 325 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'U' and resid 346 through 347 Processing sheet with id=AL5, first strand: chain 'U' and resid 336 through 337 Processing sheet with id=AL6, first strand: chain 'U' and resid 417 through 421 removed outlier: 3.872A pdb=" N ARG U 417 " --> pdb=" O ARG U 428 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'V' and resid 407 through 408 removed outlier: 3.502A pdb=" N MET V 431 " --> pdb=" O VAL V 271 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET W 396 " --> pdb=" O PHE V 268 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'V' and resid 318 through 319 removed outlier: 3.944A pdb=" N VAL V 318 " --> pdb=" O VAL V 325 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'V' and resid 346 through 347 Processing sheet with id=AM1, first strand: chain 'V' and resid 336 through 337 Processing sheet with id=AM2, first strand: chain 'V' and resid 396 through 397 removed outlier: 3.693A pdb=" N MET V 396 " --> pdb=" O PHE X 268 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET X 431 " --> pdb=" O VAL X 271 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'V' and resid 417 through 421 removed outlier: 3.871A pdb=" N ARG V 417 " --> pdb=" O ARG V 428 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'W' and resid 407 through 408 removed outlier: 3.502A pdb=" N MET W 431 " --> pdb=" O VAL W 271 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET X 396 " --> pdb=" O PHE W 268 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'W' and resid 318 through 319 removed outlier: 3.945A pdb=" N VAL W 318 " --> pdb=" O VAL W 325 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'W' and resid 346 through 347 Processing sheet with id=AM7, first strand: chain 'W' and resid 336 through 337 Processing sheet with id=AM8, first strand: chain 'W' and resid 417 through 421 removed outlier: 3.871A pdb=" N ARG W 417 " --> pdb=" O ARG W 428 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'X' and resid 318 through 319 removed outlier: 3.945A pdb=" N VAL X 318 " --> pdb=" O VAL X 325 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'X' and resid 346 through 347 Processing sheet with id=AN2, first strand: chain 'X' and resid 336 through 337 Processing sheet with id=AN3, first strand: chain 'X' and resid 417 through 421 removed outlier: 3.872A pdb=" N ARG X 417 " --> pdb=" O ARG X 428 " (cutoff:3.500A) 2040 hydrogen bonds defined for protein. 5904 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: 10.98 Time building geometry restraints manager: 4.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14327 1.34 - 1.46: 8154 1.46 - 1.58: 20725 1.58 - 1.70: 0 1.70 - 1.81: 600 Bond restraints: 43806 Sorted by residual: bond pdb=" CG1 ILE W 419 " pdb=" CD1 ILE W 419 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.60e+00 bond pdb=" CG1 ILE L 419 " pdb=" CD1 ILE L 419 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.58e+00 bond pdb=" CG1 ILE R 419 " pdb=" CD1 ILE R 419 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.56e+00 bond pdb=" CG1 ILE F 419 " pdb=" CD1 ILE F 419 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.56e+00 bond pdb=" CG1 ILE N 419 " pdb=" CD1 ILE N 419 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.56e+00 ... (remaining 43801 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 55485 1.87 - 3.73: 3071 3.73 - 5.60: 397 5.60 - 7.46: 142 7.46 - 9.33: 72 Bond angle restraints: 59167 Sorted by residual: angle pdb=" CB MET V 247 " pdb=" CG MET V 247 " pdb=" SD MET V 247 " ideal model delta sigma weight residual 112.70 122.03 -9.33 3.00e+00 1.11e-01 9.67e+00 angle pdb=" CB MET W 247 " pdb=" CG MET W 247 " pdb=" SD MET W 247 " ideal model delta sigma weight residual 112.70 122.02 -9.32 3.00e+00 1.11e-01 9.64e+00 angle pdb=" CB MET B 247 " pdb=" CG MET B 247 " pdb=" SD MET B 247 " ideal model delta sigma weight residual 112.70 122.01 -9.31 3.00e+00 1.11e-01 9.63e+00 angle pdb=" CB MET H 247 " pdb=" CG MET H 247 " pdb=" SD MET H 247 " ideal model delta sigma weight residual 112.70 122.01 -9.31 3.00e+00 1.11e-01 9.62e+00 angle pdb=" CB MET F 247 " pdb=" CG MET F 247 " pdb=" SD MET F 247 " ideal model delta sigma weight residual 112.70 122.00 -9.30 3.00e+00 1.11e-01 9.61e+00 ... (remaining 59162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.59: 21553 10.59 - 21.17: 3260 21.17 - 31.76: 1328 31.76 - 42.34: 528 42.34 - 52.93: 120 Dihedral angle restraints: 26789 sinusoidal: 10637 harmonic: 16152 Sorted by residual: dihedral pdb=" CA GLY T 296 " pdb=" C GLY T 296 " pdb=" N PHE T 297 " pdb=" CA PHE T 297 " ideal model delta harmonic sigma weight residual 180.00 154.57 25.43 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA GLY X 296 " pdb=" C GLY X 296 " pdb=" N PHE X 297 " pdb=" CA PHE X 297 " ideal model delta harmonic sigma weight residual 180.00 154.59 25.41 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA GLY E 296 " pdb=" C GLY E 296 " pdb=" N PHE E 297 " pdb=" CA PHE E 297 " ideal model delta harmonic sigma weight residual 180.00 154.59 25.41 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 26786 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 5565 0.074 - 0.149: 1060 0.149 - 0.223: 167 0.223 - 0.298: 24 0.298 - 0.372: 24 Chirality restraints: 6840 Sorted by residual: chirality pdb=" CB ILE H 441 " pdb=" CA ILE H 441 " pdb=" CG1 ILE H 441 " pdb=" CG2 ILE H 441 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CB ILE J 441 " pdb=" CA ILE J 441 " pdb=" CG1 ILE J 441 " pdb=" CG2 ILE J 441 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CB ILE S 441 " pdb=" CA ILE S 441 " pdb=" CG1 ILE S 441 " pdb=" CG2 ILE S 441 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.44e+00 ... (remaining 6837 not shown) Planarity restraints: 7657 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR S 338 " 0.044 5.00e-02 4.00e+02 6.55e-02 6.85e+00 pdb=" N PRO S 339 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO S 339 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO S 339 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR X 338 " -0.043 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO X 339 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO X 339 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO X 339 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR U 338 " -0.043 5.00e-02 4.00e+02 6.53e-02 6.83e+00 pdb=" N PRO U 339 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO U 339 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO U 339 " -0.036 5.00e-02 4.00e+02 ... (remaining 7654 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 14410 2.86 - 3.37: 39589 3.37 - 3.88: 73561 3.88 - 4.39: 76300 4.39 - 4.90: 135607 Nonbonded interactions: 339467 Sorted by model distance: nonbonded pdb=" OD1 ASN B 349 " pdb=" NH2 ARG C 237 " model vdw 2.347 3.120 nonbonded pdb=" OD1 ASN N 349 " pdb=" NH2 ARG O 237 " model vdw 2.349 3.120 nonbonded pdb=" NH2 ARG J 237 " pdb=" OD1 ASN L 349 " model vdw 2.351 3.120 nonbonded pdb=" OD1 ASN H 349 " pdb=" NH2 ARG I 237 " model vdw 2.352 3.120 nonbonded pdb=" OD1 ASN E 349 " pdb=" NH2 ARG F 237 " model vdw 2.354 3.120 ... (remaining 339462 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = (chain 'G' and (resid 235 through 370 or (resid 371 and (name N or name CA or na \ me C or name O or name CB )) or resid 372 through 468)) selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.630 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 44.760 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 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 : 0.005 0.074 43806 Z= 0.218 Angle : 0.983 9.329 59167 Z= 0.511 Chirality : 0.062 0.372 6840 Planarity : 0.008 0.065 7657 Dihedral : 13.180 52.931 16421 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.10), residues: 5568 helix: -1.67 (0.09), residues: 2256 sheet: -1.57 (0.18), residues: 744 loop : -2.13 (0.12), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG U 248 TYR 0.010 0.002 TYR A 355 PHE 0.025 0.003 PHE M 450 HIS 0.005 0.002 HIS G 412 Details of bonding type rmsd covalent geometry : bond 0.00508 (43806) covalent geometry : angle 0.98257 (59167) hydrogen bonds : bond 0.19265 ( 2040) hydrogen bonds : angle 7.90094 ( 5904) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1066 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1066 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ASN cc_start: 0.8912 (p0) cc_final: 0.8657 (p0) REVERT: A 264 MET cc_start: 0.6139 (mmp) cc_final: 0.5706 (mtp) REVERT: A 379 MET cc_start: 0.7528 (mmm) cc_final: 0.7042 (mmm) REVERT: B 245 ASN cc_start: 0.8977 (p0) cc_final: 0.8737 (p0) REVERT: B 264 MET cc_start: 0.6229 (mmp) cc_final: 0.5694 (mtp) REVERT: B 379 MET cc_start: 0.7641 (mmm) cc_final: 0.7049 (mmm) REVERT: C 245 ASN cc_start: 0.9012 (p0) cc_final: 0.8757 (p0) REVERT: C 264 MET cc_start: 0.6117 (mmp) cc_final: 0.5577 (mtp) REVERT: C 379 MET cc_start: 0.7649 (mmm) cc_final: 0.7036 (mmm) REVERT: D 245 ASN cc_start: 0.8897 (p0) cc_final: 0.8624 (p0) REVERT: D 264 MET cc_start: 0.6170 (mmp) cc_final: 0.5750 (mtp) REVERT: D 379 MET cc_start: 0.7664 (mmm) cc_final: 0.7223 (mmm) REVERT: E 245 ASN cc_start: 0.8955 (p0) cc_final: 0.8640 (p0) REVERT: E 264 MET cc_start: 0.6117 (mmp) cc_final: 0.5579 (mtp) REVERT: E 379 MET cc_start: 0.7735 (mmm) cc_final: 0.7096 (mmm) REVERT: F 245 ASN cc_start: 0.8961 (p0) cc_final: 0.8686 (p0) REVERT: F 264 MET cc_start: 0.6104 (mmp) cc_final: 0.5566 (mtp) REVERT: F 379 MET cc_start: 0.7739 (mmm) cc_final: 0.7143 (mmm) REVERT: G 245 ASN cc_start: 0.8950 (p0) cc_final: 0.8686 (p0) REVERT: G 264 MET cc_start: 0.6177 (mmp) cc_final: 0.5753 (mtp) REVERT: G 379 MET cc_start: 0.7665 (mmm) cc_final: 0.7203 (mmm) REVERT: H 245 ASN cc_start: 0.8964 (p0) cc_final: 0.8683 (p0) REVERT: H 264 MET cc_start: 0.6119 (mmp) cc_final: 0.5578 (mtp) REVERT: H 379 MET cc_start: 0.7726 (mmm) cc_final: 0.7093 (mmm) REVERT: I 245 ASN cc_start: 0.8970 (p0) cc_final: 0.8690 (p0) REVERT: I 264 MET cc_start: 0.6156 (mmp) cc_final: 0.5604 (mtp) REVERT: I 379 MET cc_start: 0.7722 (mmm) cc_final: 0.7094 (mmm) REVERT: J 245 ASN cc_start: 0.8940 (p0) cc_final: 0.8710 (p0) REVERT: J 264 MET cc_start: 0.6124 (mmp) cc_final: 0.5746 (mtp) REVERT: J 379 MET cc_start: 0.7635 (mmm) cc_final: 0.7101 (mmm) REVERT: K 245 ASN cc_start: 0.8980 (p0) cc_final: 0.8632 (p0) REVERT: K 264 MET cc_start: 0.6148 (mmp) cc_final: 0.5574 (mtp) REVERT: K 379 MET cc_start: 0.7773 (mmm) cc_final: 0.7187 (mmm) REVERT: L 245 ASN cc_start: 0.8945 (p0) cc_final: 0.8682 (p0) REVERT: L 264 MET cc_start: 0.6156 (mmp) cc_final: 0.5662 (mtp) REVERT: L 379 MET cc_start: 0.7630 (mmm) cc_final: 0.7112 (mmm) REVERT: M 245 ASN cc_start: 0.8941 (p0) cc_final: 0.8675 (p0) REVERT: M 264 MET cc_start: 0.6196 (mmp) cc_final: 0.5745 (mtp) REVERT: M 379 MET cc_start: 0.7568 (mmm) cc_final: 0.7117 (mmm) REVERT: N 245 ASN cc_start: 0.8949 (p0) cc_final: 0.8671 (p0) REVERT: N 264 MET cc_start: 0.6202 (mmp) cc_final: 0.5700 (mtp) REVERT: N 379 MET cc_start: 0.7620 (mmm) cc_final: 0.7018 (mmm) REVERT: O 245 ASN cc_start: 0.9024 (p0) cc_final: 0.8760 (p0) REVERT: O 264 MET cc_start: 0.6068 (mmp) cc_final: 0.5534 (mtp) REVERT: O 379 MET cc_start: 0.7720 (mmm) cc_final: 0.7071 (mmm) REVERT: P 245 ASN cc_start: 0.8936 (p0) cc_final: 0.8661 (p0) REVERT: P 264 MET cc_start: 0.6214 (mmp) cc_final: 0.5758 (mtp) REVERT: P 379 MET cc_start: 0.7665 (mmm) cc_final: 0.7207 (mmm) REVERT: Q 245 ASN cc_start: 0.8954 (p0) cc_final: 0.8623 (p0) REVERT: Q 264 MET cc_start: 0.6136 (mmp) cc_final: 0.5602 (mtp) REVERT: Q 379 MET cc_start: 0.7838 (mmm) cc_final: 0.7296 (mmm) REVERT: R 245 ASN cc_start: 0.8983 (p0) cc_final: 0.8738 (p0) REVERT: R 264 MET cc_start: 0.6124 (mmp) cc_final: 0.5641 (mtp) REVERT: R 379 MET cc_start: 0.7636 (mmm) cc_final: 0.7094 (mmm) REVERT: S 245 ASN cc_start: 0.8910 (p0) cc_final: 0.8666 (p0) REVERT: S 251 ILE cc_start: 0.8603 (mp) cc_final: 0.8400 (mp) REVERT: S 264 MET cc_start: 0.6153 (mmp) cc_final: 0.5670 (mtp) REVERT: S 379 MET cc_start: 0.7544 (mmm) cc_final: 0.7064 (mmm) REVERT: T 245 ASN cc_start: 0.8949 (p0) cc_final: 0.8706 (p0) REVERT: T 264 MET cc_start: 0.6282 (mmp) cc_final: 0.5747 (mtp) REVERT: T 379 MET cc_start: 0.7668 (mmm) cc_final: 0.7212 (mmm) REVERT: U 245 ASN cc_start: 0.9015 (p0) cc_final: 0.8746 (p0) REVERT: U 264 MET cc_start: 0.6069 (mmp) cc_final: 0.5560 (mtp) REVERT: U 379 MET cc_start: 0.7619 (mmm) cc_final: 0.6972 (mmm) REVERT: V 245 ASN cc_start: 0.8928 (p0) cc_final: 0.8668 (p0) REVERT: V 264 MET cc_start: 0.6210 (mmp) cc_final: 0.5750 (mtp) REVERT: V 379 MET cc_start: 0.7548 (mmm) cc_final: 0.7094 (mmm) REVERT: W 245 ASN cc_start: 0.8954 (p0) cc_final: 0.8637 (p0) REVERT: W 264 MET cc_start: 0.6242 (mmp) cc_final: 0.5707 (mtp) REVERT: W 379 MET cc_start: 0.7755 (mmm) cc_final: 0.7301 (mmm) REVERT: X 245 ASN cc_start: 0.8991 (p0) cc_final: 0.8748 (p0) REVERT: X 264 MET cc_start: 0.6172 (mmp) cc_final: 0.5668 (mtp) REVERT: X 379 MET cc_start: 0.7630 (mmm) cc_final: 0.7033 (mmm) outliers start: 0 outliers final: 0 residues processed: 1066 average time/residue: 0.2874 time to fit residues: 491.0001 Evaluate side-chains 750 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 750 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 394 optimal weight: 0.9980 chunk 430 optimal weight: 0.0030 chunk 41 optimal weight: 5.9990 chunk 265 optimal weight: 5.9990 chunk 523 optimal weight: 7.9990 chunk 497 optimal weight: 9.9990 chunk 414 optimal weight: 10.0000 chunk 310 optimal weight: 3.9990 chunk 488 optimal weight: 0.1980 chunk 366 optimal weight: 2.9990 chunk 223 optimal weight: 0.1980 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 405 GLN E 405 GLN ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 405 GLN ** H 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 405 GLN ** I 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 405 GLN ** L 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 405 GLN ** N 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 405 GLN ** P 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 405 GLN ** T 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 405 GLN ** W 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 405 GLN ** X 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.095208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.078183 restraints weight = 142985.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.080775 restraints weight = 74363.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.082691 restraints weight = 48911.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.083867 restraints weight = 36590.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.084721 restraints weight = 29850.337| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 43806 Z= 0.129 Angle : 0.621 5.391 59167 Z= 0.321 Chirality : 0.044 0.120 6840 Planarity : 0.006 0.047 7657 Dihedral : 4.375 22.817 6169 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.60 % Allowed : 11.41 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.51 (0.11), residues: 5568 helix: 0.26 (0.10), residues: 2256 sheet: -2.18 (0.15), residues: 960 loop : -1.65 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 246 TYR 0.010 0.001 TYR U 275 PHE 0.014 0.002 PHE O 450 HIS 0.001 0.000 HIS B 439 Details of bonding type rmsd covalent geometry : bond 0.00301 (43806) covalent geometry : angle 0.62140 (59167) hydrogen bonds : bond 0.03139 ( 2040) hydrogen bonds : angle 5.13109 ( 5904) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 799 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ASN cc_start: 0.9373 (p0) cc_final: 0.9036 (p0) REVERT: A 264 MET cc_start: 0.7297 (mmp) cc_final: 0.5980 (mtp) REVERT: A 379 MET cc_start: 0.8571 (mmm) cc_final: 0.7890 (mmm) REVERT: A 430 MET cc_start: 0.6223 (mmt) cc_final: 0.5834 (mmt) REVERT: B 245 ASN cc_start: 0.9370 (p0) cc_final: 0.9043 (p0) REVERT: B 264 MET cc_start: 0.7340 (mmp) cc_final: 0.5963 (mtp) REVERT: B 379 MET cc_start: 0.8631 (mmm) cc_final: 0.8025 (mmm) REVERT: B 430 MET cc_start: 0.6254 (mmt) cc_final: 0.5797 (mmt) REVERT: C 245 ASN cc_start: 0.9381 (p0) cc_final: 0.9077 (p0) REVERT: C 264 MET cc_start: 0.7295 (mmp) cc_final: 0.5826 (mtp) REVERT: C 379 MET cc_start: 0.8561 (mmm) cc_final: 0.7989 (mmm) REVERT: C 430 MET cc_start: 0.6264 (mmt) cc_final: 0.6058 (mmt) REVERT: D 245 ASN cc_start: 0.9361 (p0) cc_final: 0.9028 (p0) REVERT: D 264 MET cc_start: 0.7285 (mmp) cc_final: 0.5983 (mtp) REVERT: D 379 MET cc_start: 0.8598 (mmm) cc_final: 0.7993 (mmm) REVERT: E 245 ASN cc_start: 0.9388 (p0) cc_final: 0.8952 (p0) REVERT: E 264 MET cc_start: 0.7309 (mmp) cc_final: 0.5846 (mtp) REVERT: E 379 MET cc_start: 0.8624 (mmm) cc_final: 0.8036 (mmm) REVERT: E 416 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8347 (mm-30) REVERT: E 430 MET cc_start: 0.6299 (mmt) cc_final: 0.6098 (mmt) REVERT: F 245 ASN cc_start: 0.9367 (p0) cc_final: 0.8965 (p0) REVERT: F 264 MET cc_start: 0.7305 (mmp) cc_final: 0.5830 (mtp) REVERT: F 379 MET cc_start: 0.8638 (mmm) cc_final: 0.8032 (mmm) REVERT: F 430 MET cc_start: 0.6239 (mmt) cc_final: 0.5828 (mmt) REVERT: G 245 ASN cc_start: 0.9353 (p0) cc_final: 0.9024 (p0) REVERT: G 264 MET cc_start: 0.7305 (mmp) cc_final: 0.6002 (mtp) REVERT: G 379 MET cc_start: 0.8629 (mmm) cc_final: 0.8013 (mmm) REVERT: H 245 ASN cc_start: 0.9385 (p0) cc_final: 0.8946 (p0) REVERT: H 264 MET cc_start: 0.7296 (mmp) cc_final: 0.5839 (mtp) REVERT: H 379 MET cc_start: 0.8588 (mmm) cc_final: 0.8006 (mmm) REVERT: H 430 MET cc_start: 0.6272 (mmt) cc_final: 0.6065 (mmt) REVERT: I 245 ASN cc_start: 0.9413 (p0) cc_final: 0.8988 (p0) REVERT: I 264 MET cc_start: 0.7331 (mmp) cc_final: 0.5860 (mtp) REVERT: I 379 MET cc_start: 0.8672 (mmm) cc_final: 0.8048 (mmm) REVERT: I 430 MET cc_start: 0.6278 (mmt) cc_final: 0.5834 (mmt) REVERT: J 245 ASN cc_start: 0.9367 (p0) cc_final: 0.9035 (p0) REVERT: J 264 MET cc_start: 0.7208 (mmp) cc_final: 0.5927 (mtp) REVERT: J 379 MET cc_start: 0.8567 (mmm) cc_final: 0.7966 (mmm) REVERT: K 245 ASN cc_start: 0.9372 (p0) cc_final: 0.8935 (p0) REVERT: K 264 MET cc_start: 0.7353 (mmp) cc_final: 0.5844 (mtp) REVERT: K 379 MET cc_start: 0.8647 (mmm) cc_final: 0.8072 (mmm) REVERT: K 430 MET cc_start: 0.6261 (mmt) cc_final: 0.6046 (mmt) REVERT: L 245 ASN cc_start: 0.9361 (p0) cc_final: 0.9017 (p0) REVERT: L 264 MET cc_start: 0.7310 (mmp) cc_final: 0.5950 (mtp) REVERT: L 379 MET cc_start: 0.8738 (mmm) cc_final: 0.8119 (mmm) REVERT: L 430 MET cc_start: 0.6277 (mmt) cc_final: 0.6052 (mmt) REVERT: M 245 ASN cc_start: 0.9346 (p0) cc_final: 0.9015 (p0) REVERT: M 264 MET cc_start: 0.7315 (mmp) cc_final: 0.5991 (mtp) REVERT: M 379 MET cc_start: 0.8606 (mmm) cc_final: 0.7935 (mmm) REVERT: M 430 MET cc_start: 0.6255 (mmt) cc_final: 0.5820 (mmt) REVERT: N 245 ASN cc_start: 0.9364 (p0) cc_final: 0.9014 (p0) REVERT: N 264 MET cc_start: 0.7311 (mmp) cc_final: 0.5961 (mtp) REVERT: N 379 MET cc_start: 0.8655 (mmm) cc_final: 0.8051 (mmm) REVERT: N 430 MET cc_start: 0.6299 (mmt) cc_final: 0.6077 (mmt) REVERT: O 245 ASN cc_start: 0.9417 (p0) cc_final: 0.9002 (p0) REVERT: O 264 MET cc_start: 0.7259 (mmp) cc_final: 0.5780 (mtp) REVERT: O 379 MET cc_start: 0.8510 (mmm) cc_final: 0.7942 (mmm) REVERT: O 416 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8364 (mm-30) REVERT: O 430 MET cc_start: 0.6305 (mmt) cc_final: 0.6080 (mmt) REVERT: P 245 ASN cc_start: 0.9343 (p0) cc_final: 0.8997 (p0) REVERT: P 264 MET cc_start: 0.7315 (mmp) cc_final: 0.5991 (mtp) REVERT: P 379 MET cc_start: 0.8613 (mmm) cc_final: 0.8006 (mmm) REVERT: P 430 MET cc_start: 0.6304 (mmt) cc_final: 0.6084 (mmt) REVERT: Q 245 ASN cc_start: 0.9353 (p0) cc_final: 0.8942 (p0) REVERT: Q 264 MET cc_start: 0.7390 (mmp) cc_final: 0.5947 (mtp) REVERT: Q 379 MET cc_start: 0.8634 (mmm) cc_final: 0.8033 (mmm) REVERT: Q 416 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8352 (mm-30) REVERT: R 245 ASN cc_start: 0.9375 (p0) cc_final: 0.9042 (p0) REVERT: R 264 MET cc_start: 0.7275 (mmp) cc_final: 0.5835 (mtp) REVERT: R 379 MET cc_start: 0.8607 (mmm) cc_final: 0.7998 (mmm) REVERT: R 416 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8360 (mm-30) REVERT: R 426 LYS cc_start: 0.9253 (mtpp) cc_final: 0.8896 (mtmm) REVERT: R 430 MET cc_start: 0.6305 (mmt) cc_final: 0.6083 (mmt) REVERT: S 245 ASN cc_start: 0.9336 (p0) cc_final: 0.9023 (p0) REVERT: S 264 MET cc_start: 0.7298 (mmp) cc_final: 0.5961 (mtp) REVERT: S 379 MET cc_start: 0.8537 (mmm) cc_final: 0.7872 (mmm) REVERT: S 430 MET cc_start: 0.6184 (mmt) cc_final: 0.5958 (mmt) REVERT: T 245 ASN cc_start: 0.9363 (p0) cc_final: 0.9028 (p0) REVERT: T 264 MET cc_start: 0.7355 (mmp) cc_final: 0.5972 (mtp) REVERT: T 379 MET cc_start: 0.8639 (mmm) cc_final: 0.8021 (mmm) REVERT: T 430 MET cc_start: 0.6279 (mmt) cc_final: 0.6050 (mmt) REVERT: U 245 ASN cc_start: 0.9384 (p0) cc_final: 0.9065 (p0) REVERT: U 264 MET cc_start: 0.7263 (mmp) cc_final: 0.5815 (mtp) REVERT: U 379 MET cc_start: 0.8550 (mmm) cc_final: 0.7978 (mmm) REVERT: U 416 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8375 (mm-30) REVERT: U 430 MET cc_start: 0.6294 (mmt) cc_final: 0.6076 (mmt) REVERT: V 245 ASN cc_start: 0.9352 (p0) cc_final: 0.9023 (p0) REVERT: V 264 MET cc_start: 0.7311 (mmp) cc_final: 0.6004 (mtp) REVERT: V 379 MET cc_start: 0.8567 (mmm) cc_final: 0.7939 (mmm) REVERT: V 430 MET cc_start: 0.6274 (mmt) cc_final: 0.6069 (mmt) REVERT: W 245 ASN cc_start: 0.9342 (p0) cc_final: 0.8933 (p0) REVERT: W 264 MET cc_start: 0.7362 (mmp) cc_final: 0.5948 (mtp) REVERT: W 379 MET cc_start: 0.8630 (mmm) cc_final: 0.8024 (mmm) REVERT: W 416 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8372 (mm-30) REVERT: W 430 MET cc_start: 0.6288 (mmt) cc_final: 0.6077 (mmt) REVERT: X 245 ASN cc_start: 0.9373 (p0) cc_final: 0.9047 (p0) REVERT: X 264 MET cc_start: 0.7262 (mmp) cc_final: 0.5840 (mtp) REVERT: X 379 MET cc_start: 0.8574 (mmm) cc_final: 0.7974 (mmm) REVERT: X 416 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8330 (mm-30) REVERT: X 430 MET cc_start: 0.6294 (mmt) cc_final: 0.6072 (mmt) outliers start: 72 outliers final: 48 residues processed: 830 average time/residue: 0.2441 time to fit residues: 339.2306 Evaluate side-chains 820 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 772 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 441 ILE Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain H residue 441 ILE Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain I residue 441 ILE Chi-restraints excluded: chain I residue 464 ILE Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain K residue 441 ILE Chi-restraints excluded: chain K residue 464 ILE Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 464 ILE Chi-restraints excluded: chain M residue 441 ILE Chi-restraints excluded: chain M residue 464 ILE Chi-restraints excluded: chain N residue 441 ILE Chi-restraints excluded: chain N residue 464 ILE Chi-restraints excluded: chain O residue 441 ILE Chi-restraints excluded: chain O residue 464 ILE Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 464 ILE Chi-restraints excluded: chain Q residue 441 ILE Chi-restraints excluded: chain Q residue 464 ILE Chi-restraints excluded: chain R residue 441 ILE Chi-restraints excluded: chain R residue 464 ILE Chi-restraints excluded: chain S residue 441 ILE Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain T residue 441 ILE Chi-restraints excluded: chain T residue 464 ILE Chi-restraints excluded: chain U residue 441 ILE Chi-restraints excluded: chain U residue 464 ILE Chi-restraints excluded: chain V residue 441 ILE Chi-restraints excluded: chain V residue 464 ILE Chi-restraints excluded: chain W residue 441 ILE Chi-restraints excluded: chain W residue 464 ILE Chi-restraints excluded: chain X residue 441 ILE Chi-restraints excluded: chain X residue 464 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 219 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 327 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 260 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.089838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.072971 restraints weight = 141464.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.075353 restraints weight = 68194.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.076845 restraints weight = 44769.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.077810 restraints weight = 34336.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.078241 restraints weight = 29108.150| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 43806 Z= 0.297 Angle : 0.705 5.477 59167 Z= 0.375 Chirality : 0.046 0.129 6840 Planarity : 0.006 0.047 7657 Dihedral : 5.030 44.259 6169 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.95 % Allowed : 14.67 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.69 (0.11), residues: 5568 helix: 0.32 (0.10), residues: 2256 sheet: -2.47 (0.14), residues: 1104 loop : -1.81 (0.14), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 452 TYR 0.018 0.002 TYR F 275 PHE 0.025 0.002 PHE S 392 HIS 0.004 0.002 HIS R 439 Details of bonding type rmsd covalent geometry : bond 0.00644 (43806) covalent geometry : angle 0.70483 (59167) hydrogen bonds : bond 0.03694 ( 2040) hydrogen bonds : angle 5.29633 ( 5904) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 745 time to evaluate : 1.802 Fit side-chains REVERT: A 245 ASN cc_start: 0.9325 (p0) cc_final: 0.8975 (p0) REVERT: A 353 MET cc_start: 0.8089 (ttt) cc_final: 0.7802 (ttt) REVERT: A 379 MET cc_start: 0.8927 (mmm) cc_final: 0.7917 (mmm) REVERT: A 416 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8419 (mm-30) REVERT: A 422 LYS cc_start: 0.8860 (mmmm) cc_final: 0.8448 (tppp) REVERT: A 460 ASN cc_start: 0.8751 (t0) cc_final: 0.8476 (t0) REVERT: B 245 ASN cc_start: 0.9367 (p0) cc_final: 0.9071 (p0) REVERT: B 353 MET cc_start: 0.7972 (ttt) cc_final: 0.7639 (ttt) REVERT: B 354 ASN cc_start: 0.8213 (m-40) cc_final: 0.7989 (m110) REVERT: B 379 MET cc_start: 0.8941 (mmm) cc_final: 0.7913 (mmm) REVERT: B 416 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8493 (tp30) REVERT: B 422 LYS cc_start: 0.8888 (mmmm) cc_final: 0.8336 (tppp) REVERT: B 431 MET cc_start: 0.8040 (ptm) cc_final: 0.7571 (ppp) REVERT: B 460 ASN cc_start: 0.8702 (t0) cc_final: 0.8453 (t0) REVERT: C 245 ASN cc_start: 0.9358 (p0) cc_final: 0.9066 (p0) REVERT: C 353 MET cc_start: 0.8055 (ttt) cc_final: 0.7759 (ttt) REVERT: C 379 MET cc_start: 0.8934 (mmm) cc_final: 0.7911 (mmm) REVERT: C 416 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8376 (mm-30) REVERT: C 422 LYS cc_start: 0.8900 (mmmm) cc_final: 0.8338 (tppp) REVERT: C 460 ASN cc_start: 0.8746 (t0) cc_final: 0.8464 (t0) REVERT: D 245 ASN cc_start: 0.9330 (p0) cc_final: 0.9047 (p0) REVERT: D 353 MET cc_start: 0.8019 (ttt) cc_final: 0.7693 (ttt) REVERT: D 379 MET cc_start: 0.8949 (mmm) cc_final: 0.7922 (mmm) REVERT: D 422 LYS cc_start: 0.8858 (mmmm) cc_final: 0.8313 (tppp) REVERT: D 431 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7821 (ttt) REVERT: D 460 ASN cc_start: 0.8665 (t0) cc_final: 0.8417 (t0) REVERT: E 245 ASN cc_start: 0.9324 (p0) cc_final: 0.9003 (p0) REVERT: E 353 MET cc_start: 0.8033 (ttt) cc_final: 0.7684 (ttt) REVERT: E 379 MET cc_start: 0.8959 (mmm) cc_final: 0.7943 (mmm) REVERT: E 422 LYS cc_start: 0.8880 (mmmm) cc_final: 0.8327 (tppp) REVERT: E 431 MET cc_start: 0.8079 (ptm) cc_final: 0.7645 (ppp) REVERT: E 460 ASN cc_start: 0.8759 (t0) cc_final: 0.8487 (t0) REVERT: F 245 ASN cc_start: 0.9348 (p0) cc_final: 0.9106 (p0) REVERT: F 353 MET cc_start: 0.8016 (ttt) cc_final: 0.7662 (ttt) REVERT: F 354 ASN cc_start: 0.8216 (m-40) cc_final: 0.7990 (m110) REVERT: F 379 MET cc_start: 0.8954 (mmm) cc_final: 0.7930 (mmm) REVERT: F 416 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8470 (tp30) REVERT: F 422 LYS cc_start: 0.8908 (mmmm) cc_final: 0.8354 (tppp) REVERT: F 431 MET cc_start: 0.8045 (ptm) cc_final: 0.7578 (ppp) REVERT: F 460 ASN cc_start: 0.8717 (t0) cc_final: 0.8467 (t0) REVERT: G 245 ASN cc_start: 0.9328 (p0) cc_final: 0.9048 (p0) REVERT: G 353 MET cc_start: 0.7977 (ttt) cc_final: 0.7702 (ttt) REVERT: G 379 MET cc_start: 0.8953 (mmm) cc_final: 0.7933 (mmm) REVERT: G 422 LYS cc_start: 0.8867 (mmmm) cc_final: 0.8316 (tppp) REVERT: G 431 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7829 (ttt) REVERT: G 460 ASN cc_start: 0.8725 (t0) cc_final: 0.8454 (t0) REVERT: H 245 ASN cc_start: 0.9343 (p0) cc_final: 0.9101 (p0) REVERT: H 353 MET cc_start: 0.8009 (ttt) cc_final: 0.7670 (ttt) REVERT: H 379 MET cc_start: 0.8873 (mmm) cc_final: 0.7863 (mmm) REVERT: H 416 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8485 (tp30) REVERT: H 422 LYS cc_start: 0.8874 (mmmm) cc_final: 0.8327 (tppp) REVERT: H 431 MET cc_start: 0.8048 (ptm) cc_final: 0.7592 (ppp) REVERT: H 460 ASN cc_start: 0.8713 (t0) cc_final: 0.8444 (t0) REVERT: I 245 ASN cc_start: 0.9361 (p0) cc_final: 0.9120 (p0) REVERT: I 353 MET cc_start: 0.7950 (ttt) cc_final: 0.7603 (ttt) REVERT: I 354 ASN cc_start: 0.8214 (m-40) cc_final: 0.7991 (m110) REVERT: I 379 MET cc_start: 0.8975 (mmm) cc_final: 0.7948 (mmm) REVERT: I 416 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8476 (tp30) REVERT: I 422 LYS cc_start: 0.8891 (mmmm) cc_final: 0.8345 (tppp) REVERT: I 431 MET cc_start: 0.8019 (ptm) cc_final: 0.7587 (ppp) REVERT: I 460 ASN cc_start: 0.8714 (t0) cc_final: 0.8451 (t0) REVERT: J 245 ASN cc_start: 0.9350 (p0) cc_final: 0.9072 (p0) REVERT: J 353 MET cc_start: 0.7951 (ttt) cc_final: 0.7625 (ttt) REVERT: J 379 MET cc_start: 0.8970 (mmm) cc_final: 0.7949 (mmm) REVERT: J 416 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8451 (mm-30) REVERT: J 422 LYS cc_start: 0.8872 (mmmm) cc_final: 0.8322 (tppp) REVERT: J 460 ASN cc_start: 0.8732 (t0) cc_final: 0.8456 (t0) REVERT: K 245 ASN cc_start: 0.9300 (p0) cc_final: 0.8980 (p0) REVERT: K 353 MET cc_start: 0.8058 (ttt) cc_final: 0.7717 (ttt) REVERT: K 379 MET cc_start: 0.8946 (mmm) cc_final: 0.7939 (mmm) REVERT: K 416 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8490 (tp30) REVERT: K 422 LYS cc_start: 0.8894 (mmmm) cc_final: 0.8339 (tppp) REVERT: K 460 ASN cc_start: 0.8730 (t0) cc_final: 0.8479 (t0) REVERT: L 245 ASN cc_start: 0.9342 (p0) cc_final: 0.9057 (p0) REVERT: L 353 MET cc_start: 0.7959 (ttt) cc_final: 0.7613 (ttt) REVERT: L 354 ASN cc_start: 0.8186 (m-40) cc_final: 0.7948 (m110) REVERT: L 379 MET cc_start: 0.8937 (mmm) cc_final: 0.7893 (mmm) REVERT: L 416 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8491 (tp30) REVERT: L 422 LYS cc_start: 0.8897 (mmmm) cc_final: 0.8352 (tppp) REVERT: L 431 MET cc_start: 0.8045 (ptm) cc_final: 0.7588 (ppp) REVERT: L 460 ASN cc_start: 0.8708 (t0) cc_final: 0.8446 (t0) REVERT: M 245 ASN cc_start: 0.9329 (p0) cc_final: 0.9056 (p0) REVERT: M 353 MET cc_start: 0.8063 (ttt) cc_final: 0.7720 (ttt) REVERT: M 354 ASN cc_start: 0.8176 (m-40) cc_final: 0.7952 (m110) REVERT: M 379 MET cc_start: 0.8972 (mmm) cc_final: 0.7962 (mmm) REVERT: M 416 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8391 (mm-30) REVERT: M 422 LYS cc_start: 0.8875 (mmmm) cc_final: 0.8315 (tppp) REVERT: M 460 ASN cc_start: 0.8742 (t0) cc_final: 0.8443 (t0) REVERT: N 245 ASN cc_start: 0.9365 (p0) cc_final: 0.9056 (p0) REVERT: N 353 MET cc_start: 0.7955 (ttt) cc_final: 0.7612 (ttt) REVERT: N 354 ASN cc_start: 0.8183 (m-40) cc_final: 0.7947 (m110) REVERT: N 379 MET cc_start: 0.8968 (mmm) cc_final: 0.7941 (mmm) REVERT: N 416 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8509 (tp30) REVERT: N 422 LYS cc_start: 0.8891 (mmmm) cc_final: 0.8350 (tppp) REVERT: N 431 MET cc_start: 0.8096 (ptm) cc_final: 0.7666 (ppp) REVERT: N 460 ASN cc_start: 0.8718 (t0) cc_final: 0.8466 (t0) REVERT: O 245 ASN cc_start: 0.9355 (p0) cc_final: 0.9123 (p0) REVERT: O 353 MET cc_start: 0.7969 (ttt) cc_final: 0.7689 (ttt) REVERT: O 379 MET cc_start: 0.8931 (mmm) cc_final: 0.7888 (mmm) REVERT: O 422 LYS cc_start: 0.8879 (mmmm) cc_final: 0.8460 (tppp) REVERT: O 431 MET cc_start: 0.8052 (ptm) cc_final: 0.7560 (ppp) REVERT: O 460 ASN cc_start: 0.8697 (t0) cc_final: 0.8423 (t0) REVERT: P 245 ASN cc_start: 0.9338 (p0) cc_final: 0.9059 (p0) REVERT: P 353 MET cc_start: 0.8028 (ttt) cc_final: 0.7706 (ttt) REVERT: P 379 MET cc_start: 0.8946 (mmm) cc_final: 0.7931 (mmm) REVERT: P 416 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8376 (mm-30) REVERT: P 422 LYS cc_start: 0.8899 (mmmm) cc_final: 0.8348 (tppp) REVERT: P 431 MET cc_start: 0.8041 (ptm) cc_final: 0.7564 (ppp) REVERT: P 460 ASN cc_start: 0.8727 (t0) cc_final: 0.8474 (t0) REVERT: Q 245 ASN cc_start: 0.9307 (p0) cc_final: 0.8979 (p0) REVERT: Q 353 MET cc_start: 0.8023 (ttt) cc_final: 0.7698 (ttt) REVERT: Q 379 MET cc_start: 0.8960 (mmm) cc_final: 0.7939 (mmm) REVERT: Q 422 LYS cc_start: 0.8904 (mmmm) cc_final: 0.8351 (tppp) REVERT: Q 431 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7818 (ttt) REVERT: Q 460 ASN cc_start: 0.8715 (t0) cc_final: 0.8470 (t0) REVERT: R 245 ASN cc_start: 0.9367 (p0) cc_final: 0.9068 (p0) REVERT: R 353 MET cc_start: 0.8009 (ttt) cc_final: 0.7681 (ttt) REVERT: R 379 MET cc_start: 0.8943 (mmm) cc_final: 0.7908 (mmm) REVERT: R 422 LYS cc_start: 0.8911 (mmmm) cc_final: 0.8509 (tppp) REVERT: R 431 MET cc_start: 0.8055 (ptm) cc_final: 0.7598 (ppp) REVERT: R 460 ASN cc_start: 0.8685 (t0) cc_final: 0.8436 (t0) REVERT: S 245 ASN cc_start: 0.9312 (p0) cc_final: 0.9038 (p0) REVERT: S 295 PHE cc_start: 0.7626 (OUTLIER) cc_final: 0.7182 (p90) REVERT: S 353 MET cc_start: 0.8111 (ttt) cc_final: 0.7775 (ttt) REVERT: S 354 ASN cc_start: 0.8208 (m-40) cc_final: 0.7988 (m110) REVERT: S 379 MET cc_start: 0.8914 (mmm) cc_final: 0.7899 (mmm) REVERT: S 416 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8405 (mm-30) REVERT: S 422 LYS cc_start: 0.8834 (mmmm) cc_final: 0.8408 (tppp) REVERT: S 460 ASN cc_start: 0.8762 (t0) cc_final: 0.8469 (t0) REVERT: T 245 ASN cc_start: 0.9348 (p0) cc_final: 0.9072 (p0) REVERT: T 353 MET cc_start: 0.7968 (ttt) cc_final: 0.7707 (ttt) REVERT: T 379 MET cc_start: 0.8976 (mmm) cc_final: 0.7956 (mmm) REVERT: T 416 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8378 (mm-30) REVERT: T 422 LYS cc_start: 0.8880 (mmmm) cc_final: 0.8322 (tppp) REVERT: T 431 MET cc_start: 0.8044 (ptm) cc_final: 0.7575 (ppp) REVERT: T 460 ASN cc_start: 0.8722 (t0) cc_final: 0.8451 (t0) REVERT: U 245 ASN cc_start: 0.9364 (p0) cc_final: 0.9069 (p0) REVERT: U 353 MET cc_start: 0.7967 (ttt) cc_final: 0.7684 (ttt) REVERT: U 379 MET cc_start: 0.8916 (mmm) cc_final: 0.7907 (mmm) REVERT: U 422 LYS cc_start: 0.8887 (mmmm) cc_final: 0.8331 (tppp) REVERT: U 431 MET cc_start: 0.8051 (ptm) cc_final: 0.7559 (ppp) REVERT: U 460 ASN cc_start: 0.8701 (t0) cc_final: 0.8465 (t0) REVERT: V 245 ASN cc_start: 0.9337 (p0) cc_final: 0.9068 (p0) REVERT: V 353 MET cc_start: 0.8077 (ttt) cc_final: 0.7731 (ttt) REVERT: V 354 ASN cc_start: 0.8178 (m-40) cc_final: 0.7965 (m110) REVERT: V 379 MET cc_start: 0.8951 (mmm) cc_final: 0.7932 (mmm) REVERT: V 416 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8387 (mm-30) REVERT: V 422 LYS cc_start: 0.8887 (mmmm) cc_final: 0.8332 (tppp) REVERT: V 431 MET cc_start: 0.8046 (ptm) cc_final: 0.7589 (ppp) REVERT: V 460 ASN cc_start: 0.8701 (t0) cc_final: 0.8429 (t0) REVERT: W 245 ASN cc_start: 0.9324 (p0) cc_final: 0.9077 (p0) REVERT: W 353 MET cc_start: 0.7978 (ttt) cc_final: 0.7704 (ttt) REVERT: W 379 MET cc_start: 0.8944 (mmm) cc_final: 0.7917 (mmm) REVERT: W 422 LYS cc_start: 0.8872 (mmmm) cc_final: 0.8320 (tppp) REVERT: W 431 MET cc_start: 0.8035 (ptm) cc_final: 0.7566 (ppp) REVERT: W 460 ASN cc_start: 0.8743 (t0) cc_final: 0.8484 (t0) REVERT: X 245 ASN cc_start: 0.9356 (p0) cc_final: 0.9082 (p0) REVERT: X 353 MET cc_start: 0.7995 (ttt) cc_final: 0.7664 (ttt) REVERT: X 379 MET cc_start: 0.8973 (mmm) cc_final: 0.7949 (mmm) REVERT: X 422 LYS cc_start: 0.8899 (mmmm) cc_final: 0.8483 (tppp) REVERT: X 431 MET cc_start: 0.8045 (ptm) cc_final: 0.7567 (ppp) REVERT: X 460 ASN cc_start: 0.8734 (t0) cc_final: 0.8451 (t0) outliers start: 133 outliers final: 76 residues processed: 875 average time/residue: 0.2402 time to fit residues: 358.0329 Evaluate side-chains 779 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 699 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 441 ILE Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain G residue 431 MET Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain H residue 414 ILE Chi-restraints excluded: chain H residue 441 ILE Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 441 ILE Chi-restraints excluded: chain I residue 464 ILE Chi-restraints excluded: chain J residue 414 ILE Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 441 ILE Chi-restraints excluded: chain K residue 464 ILE Chi-restraints excluded: chain L residue 295 PHE Chi-restraints excluded: chain L residue 414 ILE Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 464 ILE Chi-restraints excluded: chain M residue 414 ILE Chi-restraints excluded: chain M residue 441 ILE Chi-restraints excluded: chain M residue 464 ILE Chi-restraints excluded: chain N residue 295 PHE Chi-restraints excluded: chain N residue 414 ILE Chi-restraints excluded: chain N residue 441 ILE Chi-restraints excluded: chain N residue 464 ILE Chi-restraints excluded: chain O residue 414 ILE Chi-restraints excluded: chain O residue 441 ILE Chi-restraints excluded: chain O residue 464 ILE Chi-restraints excluded: chain P residue 414 ILE Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 464 ILE Chi-restraints excluded: chain Q residue 414 ILE Chi-restraints excluded: chain Q residue 431 MET Chi-restraints excluded: chain Q residue 441 ILE Chi-restraints excluded: chain Q residue 464 ILE Chi-restraints excluded: chain R residue 414 ILE Chi-restraints excluded: chain R residue 441 ILE Chi-restraints excluded: chain R residue 464 ILE Chi-restraints excluded: chain S residue 295 PHE Chi-restraints excluded: chain S residue 414 ILE Chi-restraints excluded: chain S residue 441 ILE Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain T residue 414 ILE Chi-restraints excluded: chain T residue 441 ILE Chi-restraints excluded: chain T residue 464 ILE Chi-restraints excluded: chain U residue 414 ILE Chi-restraints excluded: chain U residue 441 ILE Chi-restraints excluded: chain U residue 464 ILE Chi-restraints excluded: chain V residue 414 ILE Chi-restraints excluded: chain V residue 441 ILE Chi-restraints excluded: chain V residue 464 ILE Chi-restraints excluded: chain W residue 414 ILE Chi-restraints excluded: chain W residue 441 ILE Chi-restraints excluded: chain W residue 464 ILE Chi-restraints excluded: chain X residue 414 ILE Chi-restraints excluded: chain X residue 441 ILE Chi-restraints excluded: chain X residue 464 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 532 optimal weight: 0.9990 chunk 533 optimal weight: 3.9990 chunk 239 optimal weight: 4.9990 chunk 547 optimal weight: 5.9990 chunk 407 optimal weight: 4.9990 chunk 190 optimal weight: 0.9990 chunk 363 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 255 optimal weight: 10.0000 chunk 366 optimal weight: 2.9990 chunk 185 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 GLN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 405 GLN ** K 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 405 GLN ** Q 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 405 GLN ** U 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 405 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.086581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.071347 restraints weight = 138194.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.073957 restraints weight = 69238.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.075543 restraints weight = 44584.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.076605 restraints weight = 33780.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.077242 restraints weight = 28181.678| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 43806 Z= 0.185 Angle : 0.625 5.271 59167 Z= 0.323 Chirality : 0.044 0.121 6840 Planarity : 0.005 0.044 7657 Dihedral : 4.925 46.511 6169 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.53 % Allowed : 17.17 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.11), residues: 5568 helix: 0.77 (0.10), residues: 2256 sheet: -2.80 (0.13), residues: 1152 loop : -1.71 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 452 TYR 0.017 0.002 TYR R 275 PHE 0.017 0.002 PHE S 392 HIS 0.003 0.001 HIS B 439 Details of bonding type rmsd covalent geometry : bond 0.00411 (43806) covalent geometry : angle 0.62494 (59167) hydrogen bonds : bond 0.03028 ( 2040) hydrogen bonds : angle 4.92284 ( 5904) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 747 time to evaluate : 1.413 Fit side-chains revert: symmetry clash REVERT: A 295 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.6654 (p90) REVERT: A 353 MET cc_start: 0.7872 (ttt) cc_final: 0.7599 (ttt) REVERT: A 379 MET cc_start: 0.8830 (mmm) cc_final: 0.7698 (mmm) REVERT: A 422 LYS cc_start: 0.8882 (mmmm) cc_final: 0.8653 (tppp) REVERT: A 460 ASN cc_start: 0.8590 (t0) cc_final: 0.8274 (t0) REVERT: B 245 ASN cc_start: 0.9335 (p0) cc_final: 0.9083 (p0) REVERT: B 295 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.6902 (p90) REVERT: B 353 MET cc_start: 0.7847 (ttt) cc_final: 0.7506 (ttt) REVERT: B 354 ASN cc_start: 0.8160 (m-40) cc_final: 0.7919 (m110) REVERT: B 379 MET cc_start: 0.8883 (mmm) cc_final: 0.7818 (mmm) REVERT: B 416 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8426 (tp30) REVERT: B 422 LYS cc_start: 0.8905 (mmmm) cc_final: 0.8689 (tppp) REVERT: B 460 ASN cc_start: 0.8519 (t0) cc_final: 0.8197 (t0) REVERT: C 239 GLU cc_start: 0.8346 (mp0) cc_final: 0.8073 (mp0) REVERT: C 245 ASN cc_start: 0.9339 (p0) cc_final: 0.9093 (p0) REVERT: C 295 PHE cc_start: 0.7117 (OUTLIER) cc_final: 0.6454 (p90) REVERT: C 353 MET cc_start: 0.7893 (ttt) cc_final: 0.7640 (ttt) REVERT: C 379 MET cc_start: 0.8873 (mmm) cc_final: 0.7809 (mmm) REVERT: C 416 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8485 (tp30) REVERT: C 422 LYS cc_start: 0.8915 (mmmm) cc_final: 0.8694 (tppp) REVERT: C 460 ASN cc_start: 0.8468 (t0) cc_final: 0.8159 (t0) REVERT: D 245 ASN cc_start: 0.9310 (p0) cc_final: 0.9044 (p0) REVERT: D 295 PHE cc_start: 0.7376 (OUTLIER) cc_final: 0.6819 (p90) REVERT: D 353 MET cc_start: 0.7910 (ttt) cc_final: 0.7656 (ttt) REVERT: D 379 MET cc_start: 0.8857 (mmm) cc_final: 0.7765 (mmm) REVERT: D 422 LYS cc_start: 0.8892 (mmmm) cc_final: 0.8527 (tppp) REVERT: D 460 ASN cc_start: 0.8493 (t0) cc_final: 0.8261 (t0) REVERT: E 239 GLU cc_start: 0.8333 (mp0) cc_final: 0.8044 (mp0) REVERT: E 295 PHE cc_start: 0.7214 (OUTLIER) cc_final: 0.6597 (p90) REVERT: E 353 MET cc_start: 0.7878 (ttt) cc_final: 0.7630 (ttt) REVERT: E 379 MET cc_start: 0.8925 (mmm) cc_final: 0.7903 (mmm) REVERT: E 422 LYS cc_start: 0.8893 (mmmm) cc_final: 0.8659 (tppp) REVERT: E 460 ASN cc_start: 0.8644 (t0) cc_final: 0.8296 (t0) REVERT: F 239 GLU cc_start: 0.8361 (mp0) cc_final: 0.8093 (mp0) REVERT: F 245 ASN cc_start: 0.9344 (p0) cc_final: 0.9122 (p0) REVERT: F 295 PHE cc_start: 0.7398 (OUTLIER) cc_final: 0.6870 (p90) REVERT: F 353 MET cc_start: 0.7909 (ttt) cc_final: 0.7553 (ttt) REVERT: F 354 ASN cc_start: 0.8127 (m-40) cc_final: 0.7872 (m110) REVERT: F 379 MET cc_start: 0.8893 (mmm) cc_final: 0.7832 (mmm) REVERT: F 416 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8432 (tp30) REVERT: F 422 LYS cc_start: 0.8915 (mmmm) cc_final: 0.8694 (tppp) REVERT: F 460 ASN cc_start: 0.8536 (t0) cc_final: 0.8199 (t0) REVERT: G 245 ASN cc_start: 0.9300 (p0) cc_final: 0.9035 (p0) REVERT: G 295 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.6630 (p90) REVERT: G 353 MET cc_start: 0.7814 (ttt) cc_final: 0.7541 (ttt) REVERT: G 379 MET cc_start: 0.8853 (mmm) cc_final: 0.7714 (mmm) REVERT: G 422 LYS cc_start: 0.8896 (mmmm) cc_final: 0.8521 (tppp) REVERT: G 460 ASN cc_start: 0.8533 (t0) cc_final: 0.8287 (t0) REVERT: H 239 GLU cc_start: 0.8345 (mp0) cc_final: 0.8071 (mp0) REVERT: H 245 ASN cc_start: 0.9328 (p0) cc_final: 0.9109 (p0) REVERT: H 295 PHE cc_start: 0.7357 (OUTLIER) cc_final: 0.6832 (p90) REVERT: H 353 MET cc_start: 0.7894 (ttt) cc_final: 0.7650 (ttt) REVERT: H 379 MET cc_start: 0.8885 (mmm) cc_final: 0.7872 (mmm) REVERT: H 416 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8453 (tp30) REVERT: H 422 LYS cc_start: 0.8906 (mmmm) cc_final: 0.8684 (tppp) REVERT: H 460 ASN cc_start: 0.8598 (t0) cc_final: 0.8241 (t0) REVERT: I 239 GLU cc_start: 0.8335 (mp0) cc_final: 0.8057 (mp0) REVERT: I 245 ASN cc_start: 0.9346 (p0) cc_final: 0.9130 (p0) REVERT: I 295 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.6939 (p90) REVERT: I 353 MET cc_start: 0.7876 (ttt) cc_final: 0.7529 (ttt) REVERT: I 354 ASN cc_start: 0.8136 (m-40) cc_final: 0.7878 (m110) REVERT: I 379 MET cc_start: 0.8908 (mmm) cc_final: 0.7875 (mmm) REVERT: I 416 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8441 (tp30) REVERT: I 422 LYS cc_start: 0.8898 (mmmm) cc_final: 0.8683 (tppp) REVERT: I 460 ASN cc_start: 0.8534 (t0) cc_final: 0.8213 (t0) REVERT: J 245 ASN cc_start: 0.9351 (p0) cc_final: 0.9090 (p0) REVERT: J 295 PHE cc_start: 0.7235 (OUTLIER) cc_final: 0.6618 (p90) REVERT: J 353 MET cc_start: 0.7878 (ttt) cc_final: 0.7625 (ttt) REVERT: J 379 MET cc_start: 0.8908 (mmm) cc_final: 0.7815 (mmm) REVERT: J 422 LYS cc_start: 0.8896 (mmmm) cc_final: 0.8518 (tppp) REVERT: J 460 ASN cc_start: 0.8606 (t0) cc_final: 0.8290 (t0) REVERT: K 239 GLU cc_start: 0.8352 (mp0) cc_final: 0.8071 (mp0) REVERT: K 295 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6709 (p90) REVERT: K 353 MET cc_start: 0.7872 (ttt) cc_final: 0.7645 (ttt) REVERT: K 379 MET cc_start: 0.8898 (mmm) cc_final: 0.7846 (mmm) REVERT: K 416 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8455 (tp30) REVERT: K 422 LYS cc_start: 0.8905 (mmmm) cc_final: 0.8682 (tppp) REVERT: K 460 ASN cc_start: 0.8566 (t0) cc_final: 0.8217 (t0) REVERT: L 245 ASN cc_start: 0.9323 (p0) cc_final: 0.9061 (p0) REVERT: L 295 PHE cc_start: 0.7430 (OUTLIER) cc_final: 0.6967 (p90) REVERT: L 353 MET cc_start: 0.7893 (ttt) cc_final: 0.7557 (ttt) REVERT: L 354 ASN cc_start: 0.8162 (m-40) cc_final: 0.7908 (m110) REVERT: L 379 MET cc_start: 0.8850 (mmm) cc_final: 0.7706 (mmm) REVERT: L 416 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8453 (tp30) REVERT: L 422 LYS cc_start: 0.8890 (mmmm) cc_final: 0.8675 (tppp) REVERT: L 460 ASN cc_start: 0.8555 (t0) cc_final: 0.8228 (t0) REVERT: M 245 ASN cc_start: 0.9292 (p0) cc_final: 0.9063 (p0) REVERT: M 295 PHE cc_start: 0.7240 (OUTLIER) cc_final: 0.6677 (p90) REVERT: M 353 MET cc_start: 0.7860 (ttt) cc_final: 0.7525 (ttt) REVERT: M 354 ASN cc_start: 0.8132 (m-40) cc_final: 0.7884 (m110) REVERT: M 379 MET cc_start: 0.8894 (mmm) cc_final: 0.7760 (mmm) REVERT: M 422 LYS cc_start: 0.8894 (mmmm) cc_final: 0.8666 (tppp) REVERT: M 460 ASN cc_start: 0.8520 (t0) cc_final: 0.8232 (t0) REVERT: N 245 ASN cc_start: 0.9337 (p0) cc_final: 0.9070 (p0) REVERT: N 295 PHE cc_start: 0.7438 (OUTLIER) cc_final: 0.6929 (p90) REVERT: N 353 MET cc_start: 0.7882 (ttt) cc_final: 0.7549 (ttt) REVERT: N 354 ASN cc_start: 0.8156 (m-40) cc_final: 0.7905 (m110) REVERT: N 379 MET cc_start: 0.8891 (mmm) cc_final: 0.7842 (mmm) REVERT: N 416 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8458 (tp30) REVERT: N 422 LYS cc_start: 0.8911 (mmmm) cc_final: 0.8694 (tppp) REVERT: N 460 ASN cc_start: 0.8606 (t0) cc_final: 0.8262 (t0) REVERT: O 239 GLU cc_start: 0.8315 (mp0) cc_final: 0.8030 (mp0) REVERT: O 245 ASN cc_start: 0.9335 (p0) cc_final: 0.9123 (p0) REVERT: O 295 PHE cc_start: 0.7164 (OUTLIER) cc_final: 0.6535 (p90) REVERT: O 353 MET cc_start: 0.7823 (ttt) cc_final: 0.7539 (ttt) REVERT: O 379 MET cc_start: 0.8868 (mmm) cc_final: 0.7799 (mmm) REVERT: O 416 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8465 (tp30) REVERT: O 422 LYS cc_start: 0.8913 (mmmm) cc_final: 0.8526 (tppp) REVERT: O 460 ASN cc_start: 0.8578 (t0) cc_final: 0.8285 (t0) REVERT: P 245 ASN cc_start: 0.9320 (p0) cc_final: 0.9056 (p0) REVERT: P 295 PHE cc_start: 0.7242 (OUTLIER) cc_final: 0.6623 (p90) REVERT: P 353 MET cc_start: 0.7900 (ttt) cc_final: 0.7655 (ttt) REVERT: P 379 MET cc_start: 0.8856 (mmm) cc_final: 0.7704 (mmm) REVERT: P 405 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7674 (pt0) REVERT: P 416 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8484 (tp30) REVERT: P 422 LYS cc_start: 0.8910 (mmmm) cc_final: 0.8691 (tppp) REVERT: P 460 ASN cc_start: 0.8573 (t0) cc_final: 0.8216 (t0) REVERT: Q 295 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.6729 (p90) REVERT: Q 353 MET cc_start: 0.7901 (ttt) cc_final: 0.7661 (ttt) REVERT: Q 379 MET cc_start: 0.8883 (mmm) cc_final: 0.7801 (mmm) REVERT: Q 422 LYS cc_start: 0.8925 (mmmm) cc_final: 0.8562 (tppp) REVERT: Q 460 ASN cc_start: 0.8570 (t0) cc_final: 0.8222 (t0) REVERT: R 239 GLU cc_start: 0.8320 (mp0) cc_final: 0.8048 (mp0) REVERT: R 245 ASN cc_start: 0.9347 (p0) cc_final: 0.9090 (p0) REVERT: R 295 PHE cc_start: 0.7171 (OUTLIER) cc_final: 0.6541 (p90) REVERT: R 353 MET cc_start: 0.7885 (ttt) cc_final: 0.7635 (ttt) REVERT: R 379 MET cc_start: 0.8883 (mmm) cc_final: 0.7839 (mmm) REVERT: R 416 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8484 (tp30) REVERT: R 422 LYS cc_start: 0.8933 (mmmm) cc_final: 0.8715 (tppp) REVERT: R 460 ASN cc_start: 0.8588 (t0) cc_final: 0.8313 (t0) REVERT: S 245 ASN cc_start: 0.9279 (p0) cc_final: 0.9059 (p0) REVERT: S 295 PHE cc_start: 0.7431 (OUTLIER) cc_final: 0.6635 (p90) REVERT: S 353 MET cc_start: 0.7903 (ttt) cc_final: 0.7590 (ttt) REVERT: S 354 ASN cc_start: 0.8138 (m-40) cc_final: 0.7891 (m110) REVERT: S 379 MET cc_start: 0.8821 (mmm) cc_final: 0.7690 (mmm) REVERT: S 396 MET cc_start: 0.8138 (mmm) cc_final: 0.7755 (mmt) REVERT: S 460 ASN cc_start: 0.8533 (t0) cc_final: 0.8209 (t0) REVERT: T 245 ASN cc_start: 0.9339 (p0) cc_final: 0.9083 (p0) REVERT: T 295 PHE cc_start: 0.7361 (OUTLIER) cc_final: 0.6725 (p90) REVERT: T 353 MET cc_start: 0.7876 (ttt) cc_final: 0.7602 (ttt) REVERT: T 379 MET cc_start: 0.8909 (mmm) cc_final: 0.7801 (mmm) REVERT: T 422 LYS cc_start: 0.8906 (mmmm) cc_final: 0.8684 (tppp) REVERT: T 460 ASN cc_start: 0.8532 (t0) cc_final: 0.8245 (t0) REVERT: U 239 GLU cc_start: 0.8322 (mp0) cc_final: 0.8048 (mp0) REVERT: U 245 ASN cc_start: 0.9343 (p0) cc_final: 0.9091 (p0) REVERT: U 295 PHE cc_start: 0.7159 (OUTLIER) cc_final: 0.6529 (p90) REVERT: U 353 MET cc_start: 0.7817 (ttt) cc_final: 0.7549 (ttt) REVERT: U 379 MET cc_start: 0.8883 (mmm) cc_final: 0.7812 (mmm) REVERT: U 416 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8461 (tp30) REVERT: U 422 LYS cc_start: 0.8915 (mmmm) cc_final: 0.8694 (tppp) REVERT: U 460 ASN cc_start: 0.8430 (t0) cc_final: 0.8149 (t0) REVERT: V 245 ASN cc_start: 0.9308 (p0) cc_final: 0.9048 (p0) REVERT: V 295 PHE cc_start: 0.7228 (OUTLIER) cc_final: 0.6591 (p90) REVERT: V 353 MET cc_start: 0.7883 (ttt) cc_final: 0.7549 (ttt) REVERT: V 354 ASN cc_start: 0.8137 (m-40) cc_final: 0.7900 (m110) REVERT: V 379 MET cc_start: 0.8879 (mmm) cc_final: 0.7774 (mmm) REVERT: V 416 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8472 (tp30) REVERT: V 422 LYS cc_start: 0.8900 (mmmm) cc_final: 0.8676 (tppp) REVERT: V 460 ASN cc_start: 0.8488 (t0) cc_final: 0.8234 (t0) REVERT: W 245 ASN cc_start: 0.9340 (p0) cc_final: 0.9130 (p0) REVERT: W 295 PHE cc_start: 0.7214 (OUTLIER) cc_final: 0.6599 (p90) REVERT: W 353 MET cc_start: 0.7834 (ttt) cc_final: 0.7576 (ttt) REVERT: W 379 MET cc_start: 0.8863 (mmm) cc_final: 0.7777 (mmm) REVERT: W 422 LYS cc_start: 0.8898 (mmmm) cc_final: 0.8663 (tppp) REVERT: W 460 ASN cc_start: 0.8487 (t0) cc_final: 0.8171 (t0) REVERT: X 239 GLU cc_start: 0.8336 (mp0) cc_final: 0.8060 (mp0) REVERT: X 245 ASN cc_start: 0.9344 (p0) cc_final: 0.9091 (p0) REVERT: X 295 PHE cc_start: 0.7182 (OUTLIER) cc_final: 0.6550 (p90) REVERT: X 353 MET cc_start: 0.7882 (ttt) cc_final: 0.7631 (ttt) REVERT: X 379 MET cc_start: 0.8913 (mmm) cc_final: 0.7817 (mmm) REVERT: X 416 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8460 (tp30) REVERT: X 422 LYS cc_start: 0.8920 (mmmm) cc_final: 0.8694 (tppp) REVERT: X 460 ASN cc_start: 0.8571 (t0) cc_final: 0.8239 (t0) outliers start: 114 outliers final: 71 residues processed: 852 average time/residue: 0.2169 time to fit residues: 314.8782 Evaluate side-chains 800 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 704 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 405 GLN Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 295 PHE Chi-restraints excluded: chain C residue 431 MET Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 405 GLN Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 295 PHE Chi-restraints excluded: chain E residue 405 GLN Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 405 GLN Chi-restraints excluded: chain F residue 409 LEU Chi-restraints excluded: chain F residue 441 ILE Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain G residue 295 PHE Chi-restraints excluded: chain G residue 409 LEU Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 405 GLN Chi-restraints excluded: chain H residue 441 ILE Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 405 GLN Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain I residue 441 ILE Chi-restraints excluded: chain I residue 464 ILE Chi-restraints excluded: chain J residue 295 PHE Chi-restraints excluded: chain J residue 405 GLN Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain K residue 295 PHE Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 431 MET Chi-restraints excluded: chain K residue 441 ILE Chi-restraints excluded: chain K residue 464 ILE Chi-restraints excluded: chain L residue 295 PHE Chi-restraints excluded: chain L residue 405 GLN Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 464 ILE Chi-restraints excluded: chain M residue 295 PHE Chi-restraints excluded: chain M residue 431 MET Chi-restraints excluded: chain M residue 441 ILE Chi-restraints excluded: chain M residue 464 ILE Chi-restraints excluded: chain N residue 295 PHE Chi-restraints excluded: chain N residue 441 ILE Chi-restraints excluded: chain N residue 464 ILE Chi-restraints excluded: chain O residue 295 PHE Chi-restraints excluded: chain O residue 405 GLN Chi-restraints excluded: chain O residue 441 ILE Chi-restraints excluded: chain O residue 464 ILE Chi-restraints excluded: chain P residue 295 PHE Chi-restraints excluded: chain P residue 405 GLN Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 464 ILE Chi-restraints excluded: chain Q residue 295 PHE Chi-restraints excluded: chain Q residue 441 ILE Chi-restraints excluded: chain Q residue 464 ILE Chi-restraints excluded: chain R residue 295 PHE Chi-restraints excluded: chain R residue 405 GLN Chi-restraints excluded: chain R residue 441 ILE Chi-restraints excluded: chain R residue 464 ILE Chi-restraints excluded: chain S residue 295 PHE Chi-restraints excluded: chain S residue 441 ILE Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain T residue 295 PHE Chi-restraints excluded: chain T residue 405 GLN Chi-restraints excluded: chain T residue 441 ILE Chi-restraints excluded: chain T residue 464 ILE Chi-restraints excluded: chain U residue 295 PHE Chi-restraints excluded: chain U residue 441 ILE Chi-restraints excluded: chain U residue 464 ILE Chi-restraints excluded: chain V residue 295 PHE Chi-restraints excluded: chain V residue 405 GLN Chi-restraints excluded: chain V residue 441 ILE Chi-restraints excluded: chain V residue 464 ILE Chi-restraints excluded: chain W residue 295 PHE Chi-restraints excluded: chain W residue 405 GLN Chi-restraints excluded: chain W residue 441 ILE Chi-restraints excluded: chain W residue 464 ILE Chi-restraints excluded: chain X residue 295 PHE Chi-restraints excluded: chain X residue 405 GLN Chi-restraints excluded: chain X residue 441 ILE Chi-restraints excluded: chain X residue 464 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 27 optimal weight: 3.9990 chunk 516 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 chunk 199 optimal weight: 0.9980 chunk 173 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 357 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 195 optimal weight: 6.9990 chunk 369 optimal weight: 6.9990 chunk 293 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 GLN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 GLN D 405 GLN ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 405 GLN ** G 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 405 GLN ** K 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 405 GLN ** M 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 405 GLN P 405 GLN R 405 GLN ** S 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 405 GLN U 405 GLN ** V 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 405 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.087737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.073315 restraints weight = 136963.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.075763 restraints weight = 69017.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.077299 restraints weight = 44781.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.078232 restraints weight = 34025.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.078861 restraints weight = 28456.228| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 43806 Z= 0.147 Angle : 0.610 8.291 59167 Z= 0.311 Chirality : 0.044 0.119 6840 Planarity : 0.005 0.045 7657 Dihedral : 4.724 44.554 6169 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.79 % Allowed : 19.12 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.21 (0.11), residues: 5568 helix: 1.01 (0.11), residues: 2256 sheet: -2.65 (0.13), residues: 1152 loop : -1.60 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 452 TYR 0.017 0.002 TYR U 275 PHE 0.016 0.002 PHE S 392 HIS 0.002 0.001 HIS S 439 Details of bonding type rmsd covalent geometry : bond 0.00331 (43806) covalent geometry : angle 0.61001 (59167) hydrogen bonds : bond 0.02907 ( 2040) hydrogen bonds : angle 4.82932 ( 5904) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 749 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 PHE cc_start: 0.7239 (OUTLIER) cc_final: 0.6616 (p90) REVERT: A 353 MET cc_start: 0.7768 (ttt) cc_final: 0.7513 (ttt) REVERT: A 379 MET cc_start: 0.8761 (mmm) cc_final: 0.7712 (mmm) REVERT: A 396 MET cc_start: 0.8110 (mmm) cc_final: 0.7756 (mmt) REVERT: A 422 LYS cc_start: 0.9006 (mmmm) cc_final: 0.8553 (tppp) REVERT: A 460 ASN cc_start: 0.8440 (t0) cc_final: 0.8077 (t0) REVERT: B 241 ARG cc_start: 0.8264 (mmp-170) cc_final: 0.7833 (mmp80) REVERT: B 245 ASN cc_start: 0.9308 (p0) cc_final: 0.9082 (p0) REVERT: B 270 GLU cc_start: 0.7815 (tp30) cc_final: 0.7372 (tp30) REVERT: B 295 PHE cc_start: 0.7384 (OUTLIER) cc_final: 0.6720 (p90) REVERT: B 310 GLN cc_start: 0.8012 (mt0) cc_final: 0.7764 (mt0) REVERT: B 353 MET cc_start: 0.7779 (ttt) cc_final: 0.7452 (ttt) REVERT: B 354 ASN cc_start: 0.8114 (m-40) cc_final: 0.7843 (m110) REVERT: B 379 MET cc_start: 0.8806 (mmm) cc_final: 0.7770 (mmm) REVERT: B 396 MET cc_start: 0.8119 (mmm) cc_final: 0.7786 (mmt) REVERT: B 416 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8349 (tp30) REVERT: B 422 LYS cc_start: 0.8993 (mmmm) cc_final: 0.8553 (tppp) REVERT: B 460 ASN cc_start: 0.8419 (t0) cc_final: 0.8098 (t0) REVERT: C 241 ARG cc_start: 0.8276 (mmp-170) cc_final: 0.7848 (mmp80) REVERT: C 245 ASN cc_start: 0.9340 (p0) cc_final: 0.9122 (p0) REVERT: C 295 PHE cc_start: 0.7165 (OUTLIER) cc_final: 0.6465 (p90) REVERT: C 353 MET cc_start: 0.7805 (ttt) cc_final: 0.7544 (ttt) REVERT: C 379 MET cc_start: 0.8809 (mmm) cc_final: 0.7770 (mmm) REVERT: C 396 MET cc_start: 0.8119 (mmm) cc_final: 0.7787 (mmt) REVERT: C 422 LYS cc_start: 0.8951 (mmmm) cc_final: 0.8514 (tppp) REVERT: C 430 MET cc_start: 0.7418 (mmm) cc_final: 0.7105 (mmm) REVERT: C 460 ASN cc_start: 0.8437 (t0) cc_final: 0.8103 (t0) REVERT: D 245 ASN cc_start: 0.9295 (p0) cc_final: 0.9061 (p0) REVERT: D 295 PHE cc_start: 0.7352 (OUTLIER) cc_final: 0.6648 (p90) REVERT: D 353 MET cc_start: 0.7955 (ttt) cc_final: 0.7729 (ttt) REVERT: D 379 MET cc_start: 0.8800 (mmm) cc_final: 0.7683 (mmm) REVERT: D 396 MET cc_start: 0.8110 (mmm) cc_final: 0.7777 (mmt) REVERT: D 422 LYS cc_start: 0.8924 (mmmm) cc_final: 0.8686 (tppp) REVERT: D 460 ASN cc_start: 0.8444 (t0) cc_final: 0.8137 (t0) REVERT: E 270 GLU cc_start: 0.7838 (tp30) cc_final: 0.7372 (tp30) REVERT: E 295 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.6535 (p90) REVERT: E 353 MET cc_start: 0.7862 (ttt) cc_final: 0.7656 (ttt) REVERT: E 379 MET cc_start: 0.8832 (mmm) cc_final: 0.7838 (mmm) REVERT: E 396 MET cc_start: 0.8130 (mmm) cc_final: 0.7804 (mmt) REVERT: E 422 LYS cc_start: 0.8995 (mmmm) cc_final: 0.8551 (tppp) REVERT: E 460 ASN cc_start: 0.8418 (t0) cc_final: 0.8077 (t0) REVERT: F 241 ARG cc_start: 0.8281 (mmp-170) cc_final: 0.7853 (mmp80) REVERT: F 245 ASN cc_start: 0.9354 (p0) cc_final: 0.9062 (p0) REVERT: F 270 GLU cc_start: 0.7813 (tp30) cc_final: 0.7320 (tp30) REVERT: F 295 PHE cc_start: 0.7269 (OUTLIER) cc_final: 0.6502 (p90) REVERT: F 310 GLN cc_start: 0.8071 (mt0) cc_final: 0.7803 (mt0) REVERT: F 344 VAL cc_start: 0.8891 (OUTLIER) cc_final: 0.8687 (t) REVERT: F 353 MET cc_start: 0.7790 (ttt) cc_final: 0.7459 (ttt) REVERT: F 354 ASN cc_start: 0.8096 (m-40) cc_final: 0.7828 (m110) REVERT: F 379 MET cc_start: 0.8862 (mmm) cc_final: 0.7781 (mmm) REVERT: F 396 MET cc_start: 0.8137 (mmm) cc_final: 0.7804 (mmt) REVERT: F 416 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8346 (tp30) REVERT: F 422 LYS cc_start: 0.8953 (mmmm) cc_final: 0.8528 (tppp) REVERT: F 460 ASN cc_start: 0.8436 (t0) cc_final: 0.8108 (t0) REVERT: G 295 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.6567 (p90) REVERT: G 353 MET cc_start: 0.7758 (ttt) cc_final: 0.7510 (ttt) REVERT: G 379 MET cc_start: 0.8784 (mmm) cc_final: 0.7721 (mmm) REVERT: G 396 MET cc_start: 0.8122 (mmm) cc_final: 0.7812 (mmt) REVERT: G 422 LYS cc_start: 0.8907 (mmmm) cc_final: 0.8689 (tppp) REVERT: G 430 MET cc_start: 0.7535 (mmm) cc_final: 0.7291 (mmm) REVERT: G 460 ASN cc_start: 0.8485 (t0) cc_final: 0.8152 (t0) REVERT: H 245 ASN cc_start: 0.9359 (p0) cc_final: 0.9077 (p0) REVERT: H 270 GLU cc_start: 0.7828 (tp30) cc_final: 0.7351 (tp30) REVERT: H 295 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.6472 (p90) REVERT: H 353 MET cc_start: 0.7946 (ttt) cc_final: 0.7720 (ttt) REVERT: H 379 MET cc_start: 0.8833 (mmm) cc_final: 0.7786 (mmm) REVERT: H 396 MET cc_start: 0.8138 (mmm) cc_final: 0.7806 (mmt) REVERT: H 416 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8367 (tp30) REVERT: H 422 LYS cc_start: 0.8969 (mmmm) cc_final: 0.8535 (tppp) REVERT: H 460 ASN cc_start: 0.8399 (t0) cc_final: 0.8063 (t0) REVERT: I 241 ARG cc_start: 0.8264 (mmp-170) cc_final: 0.7827 (mmp80) REVERT: I 245 ASN cc_start: 0.9380 (p0) cc_final: 0.9096 (p0) REVERT: I 270 GLU cc_start: 0.7815 (tp30) cc_final: 0.7326 (tp30) REVERT: I 295 PHE cc_start: 0.7229 (OUTLIER) cc_final: 0.6576 (p90) REVERT: I 310 GLN cc_start: 0.8067 (mt0) cc_final: 0.7799 (mt0) REVERT: I 353 MET cc_start: 0.7752 (ttt) cc_final: 0.7412 (ttt) REVERT: I 354 ASN cc_start: 0.8115 (m-40) cc_final: 0.7842 (m110) REVERT: I 379 MET cc_start: 0.8892 (mmm) cc_final: 0.7811 (mmm) REVERT: I 396 MET cc_start: 0.8132 (mmm) cc_final: 0.7805 (mmt) REVERT: I 416 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8342 (tp30) REVERT: I 422 LYS cc_start: 0.8969 (mmmm) cc_final: 0.8541 (tppp) REVERT: I 460 ASN cc_start: 0.8426 (t0) cc_final: 0.8116 (t0) REVERT: J 251 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8895 (mp) REVERT: J 295 PHE cc_start: 0.7326 (OUTLIER) cc_final: 0.6692 (p90) REVERT: J 353 MET cc_start: 0.7870 (ttt) cc_final: 0.7644 (ttt) REVERT: J 379 MET cc_start: 0.8835 (mmm) cc_final: 0.7754 (mmm) REVERT: J 396 MET cc_start: 0.8114 (mmm) cc_final: 0.7793 (mmt) REVERT: J 405 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7850 (pt0) REVERT: J 422 LYS cc_start: 0.8897 (mmmm) cc_final: 0.8674 (tppp) REVERT: J 430 MET cc_start: 0.7538 (mmm) cc_final: 0.7294 (mmm) REVERT: J 460 ASN cc_start: 0.8456 (t0) cc_final: 0.8131 (t0) REVERT: K 270 GLU cc_start: 0.7775 (tp30) cc_final: 0.7039 (tp30) REVERT: K 295 PHE cc_start: 0.7251 (OUTLIER) cc_final: 0.6574 (p90) REVERT: K 353 MET cc_start: 0.7903 (ttt) cc_final: 0.7684 (ttt) REVERT: K 379 MET cc_start: 0.8813 (mmm) cc_final: 0.7818 (mmm) REVERT: K 416 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8343 (tp30) REVERT: K 422 LYS cc_start: 0.8979 (mmmm) cc_final: 0.8542 (tppp) REVERT: K 430 MET cc_start: 0.7445 (mmm) cc_final: 0.7156 (mmm) REVERT: K 460 ASN cc_start: 0.8396 (t0) cc_final: 0.8077 (t0) REVERT: L 245 ASN cc_start: 0.9313 (p0) cc_final: 0.9058 (p0) REVERT: L 270 GLU cc_start: 0.7812 (tp30) cc_final: 0.7350 (tp30) REVERT: L 295 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6738 (p90) REVERT: L 353 MET cc_start: 0.7774 (ttt) cc_final: 0.7433 (ttt) REVERT: L 354 ASN cc_start: 0.8134 (m-40) cc_final: 0.7853 (m110) REVERT: L 379 MET cc_start: 0.8821 (mmm) cc_final: 0.7690 (mmm) REVERT: L 396 MET cc_start: 0.8154 (mmm) cc_final: 0.7815 (mmt) REVERT: L 416 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8355 (tp30) REVERT: L 422 LYS cc_start: 0.8965 (mmmm) cc_final: 0.8538 (tppp) REVERT: L 460 ASN cc_start: 0.8423 (t0) cc_final: 0.8093 (t0) REVERT: M 251 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8862 (mp) REVERT: M 270 GLU cc_start: 0.7765 (tp30) cc_final: 0.6967 (tp30) REVERT: M 295 PHE cc_start: 0.7247 (OUTLIER) cc_final: 0.6626 (p90) REVERT: M 353 MET cc_start: 0.7793 (ttt) cc_final: 0.7477 (ttt) REVERT: M 354 ASN cc_start: 0.8109 (m-40) cc_final: 0.7831 (m110) REVERT: M 379 MET cc_start: 0.8805 (mmm) cc_final: 0.7744 (mmm) REVERT: M 422 LYS cc_start: 0.8964 (mmmm) cc_final: 0.8523 (tppp) REVERT: M 430 MET cc_start: 0.7426 (mmm) cc_final: 0.7098 (mmm) REVERT: M 460 ASN cc_start: 0.8446 (t0) cc_final: 0.8109 (t0) REVERT: N 245 ASN cc_start: 0.9325 (p0) cc_final: 0.9096 (p0) REVERT: N 270 GLU cc_start: 0.7820 (tp30) cc_final: 0.7319 (tp30) REVERT: N 295 PHE cc_start: 0.7228 (OUTLIER) cc_final: 0.6643 (p90) REVERT: N 353 MET cc_start: 0.7772 (ttt) cc_final: 0.7442 (ttt) REVERT: N 354 ASN cc_start: 0.8135 (m-40) cc_final: 0.7856 (m110) REVERT: N 379 MET cc_start: 0.8860 (mmm) cc_final: 0.7756 (mmm) REVERT: N 396 MET cc_start: 0.8136 (mmm) cc_final: 0.7806 (mmt) REVERT: N 405 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7781 (pt0) REVERT: N 416 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8355 (tp30) REVERT: N 422 LYS cc_start: 0.8981 (mmmm) cc_final: 0.8550 (tppp) REVERT: N 460 ASN cc_start: 0.8402 (t0) cc_final: 0.8082 (t0) REVERT: O 245 ASN cc_start: 0.9367 (p0) cc_final: 0.9084 (p0) REVERT: O 270 GLU cc_start: 0.7823 (tp30) cc_final: 0.7350 (tp30) REVERT: O 295 PHE cc_start: 0.7176 (OUTLIER) cc_final: 0.6489 (p90) REVERT: O 353 MET cc_start: 0.7767 (ttt) cc_final: 0.7487 (ttt) REVERT: O 379 MET cc_start: 0.8785 (mmm) cc_final: 0.7775 (mmm) REVERT: O 396 MET cc_start: 0.8131 (mmm) cc_final: 0.7801 (mmt) REVERT: O 422 LYS cc_start: 0.8896 (mmmm) cc_final: 0.8660 (tppp) REVERT: O 460 ASN cc_start: 0.8427 (t0) cc_final: 0.8126 (t0) REVERT: P 239 GLU cc_start: 0.8362 (mp0) cc_final: 0.8074 (mp0) REVERT: P 270 GLU cc_start: 0.7824 (tp30) cc_final: 0.7369 (tp30) REVERT: P 295 PHE cc_start: 0.7335 (OUTLIER) cc_final: 0.6693 (p90) REVERT: P 353 MET cc_start: 0.7945 (ttt) cc_final: 0.7720 (ttt) REVERT: P 379 MET cc_start: 0.8771 (mmm) cc_final: 0.7715 (mmm) REVERT: P 396 MET cc_start: 0.8123 (mmm) cc_final: 0.7781 (mmt) REVERT: P 422 LYS cc_start: 0.8985 (mmmm) cc_final: 0.8542 (tppp) REVERT: P 460 ASN cc_start: 0.8406 (t0) cc_final: 0.8071 (t0) REVERT: Q 295 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.6644 (p90) REVERT: Q 353 MET cc_start: 0.7947 (ttt) cc_final: 0.7737 (ttt) REVERT: Q 379 MET cc_start: 0.8807 (mmm) cc_final: 0.7805 (mmm) REVERT: Q 396 MET cc_start: 0.8119 (mmm) cc_final: 0.7805 (mmt) REVERT: Q 422 LYS cc_start: 0.8907 (mmmm) cc_final: 0.8687 (tppp) REVERT: Q 460 ASN cc_start: 0.8395 (t0) cc_final: 0.8079 (t0) REVERT: R 270 GLU cc_start: 0.7822 (tp30) cc_final: 0.7337 (tp30) REVERT: R 295 PHE cc_start: 0.7179 (OUTLIER) cc_final: 0.6486 (p90) REVERT: R 310 GLN cc_start: 0.8009 (mt0) cc_final: 0.7762 (mt0) REVERT: R 344 VAL cc_start: 0.8906 (OUTLIER) cc_final: 0.8701 (t) REVERT: R 353 MET cc_start: 0.7929 (ttt) cc_final: 0.7720 (ttt) REVERT: R 379 MET cc_start: 0.8833 (mmm) cc_final: 0.7742 (mmm) REVERT: R 396 MET cc_start: 0.8168 (mmm) cc_final: 0.7845 (mmt) REVERT: R 416 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8411 (tp30) REVERT: R 422 LYS cc_start: 0.8969 (mmmm) cc_final: 0.8546 (tppp) REVERT: R 460 ASN cc_start: 0.8434 (t0) cc_final: 0.8148 (t0) REVERT: S 295 PHE cc_start: 0.7378 (OUTLIER) cc_final: 0.6551 (p90) REVERT: S 353 MET cc_start: 0.7837 (ttt) cc_final: 0.7518 (ttt) REVERT: S 354 ASN cc_start: 0.8113 (m-40) cc_final: 0.7825 (m110) REVERT: S 379 MET cc_start: 0.8737 (mmm) cc_final: 0.7689 (mmm) REVERT: S 460 ASN cc_start: 0.8430 (t0) cc_final: 0.8091 (t0) REVERT: T 251 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8877 (mp) REVERT: T 270 GLU cc_start: 0.7820 (tp30) cc_final: 0.7333 (tp30) REVERT: T 295 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.6647 (p90) REVERT: T 353 MET cc_start: 0.7742 (ttt) cc_final: 0.7485 (ttt) REVERT: T 379 MET cc_start: 0.8835 (mmm) cc_final: 0.7771 (mmm) REVERT: T 396 MET cc_start: 0.8132 (mmm) cc_final: 0.7799 (mmt) REVERT: T 422 LYS cc_start: 0.8982 (mmmm) cc_final: 0.8544 (tppp) REVERT: T 460 ASN cc_start: 0.8487 (t0) cc_final: 0.8151 (t0) REVERT: U 241 ARG cc_start: 0.8237 (mmp-170) cc_final: 0.7825 (mmp80) REVERT: U 245 ASN cc_start: 0.9335 (p0) cc_final: 0.9114 (p0) REVERT: U 270 GLU cc_start: 0.7858 (tp30) cc_final: 0.7393 (tp30) REVERT: U 295 PHE cc_start: 0.7171 (OUTLIER) cc_final: 0.6485 (p90) REVERT: U 353 MET cc_start: 0.7762 (ttt) cc_final: 0.7477 (ttt) REVERT: U 379 MET cc_start: 0.8790 (mmm) cc_final: 0.7743 (mmm) REVERT: U 396 MET cc_start: 0.8134 (mmm) cc_final: 0.7805 (mmt) REVERT: U 422 LYS cc_start: 0.8945 (mmmm) cc_final: 0.8518 (tppp) REVERT: U 460 ASN cc_start: 0.8403 (t0) cc_final: 0.8091 (t0) REVERT: V 270 GLU cc_start: 0.7802 (tp30) cc_final: 0.7347 (tp30) REVERT: V 295 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6631 (p90) REVERT: V 353 MET cc_start: 0.7796 (ttt) cc_final: 0.7483 (ttt) REVERT: V 354 ASN cc_start: 0.8117 (m-40) cc_final: 0.7825 (m110) REVERT: V 379 MET cc_start: 0.8782 (mmm) cc_final: 0.7722 (mmm) REVERT: V 396 MET cc_start: 0.8115 (mmm) cc_final: 0.7781 (mmt) REVERT: V 422 LYS cc_start: 0.8980 (mmmm) cc_final: 0.8541 (tppp) REVERT: V 460 ASN cc_start: 0.8418 (t0) cc_final: 0.8101 (t0) REVERT: W 245 ASN cc_start: 0.9336 (p0) cc_final: 0.9046 (p0) REVERT: W 270 GLU cc_start: 0.7832 (tp30) cc_final: 0.7373 (tp30) REVERT: W 295 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.6576 (p90) REVERT: W 353 MET cc_start: 0.7749 (ttt) cc_final: 0.7489 (ttt) REVERT: W 379 MET cc_start: 0.8795 (mmm) cc_final: 0.7790 (mmm) REVERT: W 396 MET cc_start: 0.8126 (mmm) cc_final: 0.7804 (mmt) REVERT: W 422 LYS cc_start: 0.8974 (mmmm) cc_final: 0.8527 (tppp) REVERT: W 460 ASN cc_start: 0.8454 (t0) cc_final: 0.8106 (t0) REVERT: X 270 GLU cc_start: 0.7827 (tp30) cc_final: 0.7340 (tp30) REVERT: X 295 PHE cc_start: 0.7185 (OUTLIER) cc_final: 0.6496 (p90) REVERT: X 353 MET cc_start: 0.7920 (ttt) cc_final: 0.7698 (ttt) REVERT: X 379 MET cc_start: 0.8848 (mmm) cc_final: 0.7804 (mmm) REVERT: X 396 MET cc_start: 0.8134 (mmm) cc_final: 0.7818 (mmt) REVERT: X 405 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7820 (pt0) REVERT: X 422 LYS cc_start: 0.8957 (mmmm) cc_final: 0.8526 (tppp) REVERT: X 460 ASN cc_start: 0.8448 (t0) cc_final: 0.8111 (t0) outliers start: 126 outliers final: 63 residues processed: 875 average time/residue: 0.2260 time to fit residues: 333.6852 Evaluate side-chains 800 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 705 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 405 GLN Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 295 PHE Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 405 GLN Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 295 PHE Chi-restraints excluded: chain E residue 405 GLN Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 405 GLN Chi-restraints excluded: chain F residue 441 ILE Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain G residue 295 PHE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 405 GLN Chi-restraints excluded: chain H residue 441 ILE Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 405 GLN Chi-restraints excluded: chain I residue 441 ILE Chi-restraints excluded: chain I residue 464 ILE Chi-restraints excluded: chain J residue 251 ILE Chi-restraints excluded: chain J residue 295 PHE Chi-restraints excluded: chain J residue 405 GLN Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain K residue 295 PHE Chi-restraints excluded: chain K residue 441 ILE Chi-restraints excluded: chain K residue 464 ILE Chi-restraints excluded: chain L residue 295 PHE Chi-restraints excluded: chain L residue 405 GLN Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 464 ILE Chi-restraints excluded: chain M residue 251 ILE Chi-restraints excluded: chain M residue 295 PHE Chi-restraints excluded: chain M residue 441 ILE Chi-restraints excluded: chain M residue 464 ILE Chi-restraints excluded: chain N residue 295 PHE Chi-restraints excluded: chain N residue 405 GLN Chi-restraints excluded: chain N residue 441 ILE Chi-restraints excluded: chain N residue 464 ILE Chi-restraints excluded: chain O residue 295 PHE Chi-restraints excluded: chain O residue 405 GLN Chi-restraints excluded: chain O residue 441 ILE Chi-restraints excluded: chain O residue 464 ILE Chi-restraints excluded: chain P residue 295 PHE Chi-restraints excluded: chain P residue 405 GLN Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 464 ILE Chi-restraints excluded: chain Q residue 295 PHE Chi-restraints excluded: chain Q residue 441 ILE Chi-restraints excluded: chain Q residue 464 ILE Chi-restraints excluded: chain R residue 295 PHE Chi-restraints excluded: chain R residue 344 VAL Chi-restraints excluded: chain R residue 405 GLN Chi-restraints excluded: chain R residue 441 ILE Chi-restraints excluded: chain R residue 464 ILE Chi-restraints excluded: chain S residue 295 PHE Chi-restraints excluded: chain S residue 441 ILE Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain T residue 251 ILE Chi-restraints excluded: chain T residue 295 PHE Chi-restraints excluded: chain T residue 405 GLN Chi-restraints excluded: chain T residue 441 ILE Chi-restraints excluded: chain T residue 464 ILE Chi-restraints excluded: chain U residue 295 PHE Chi-restraints excluded: chain U residue 405 GLN Chi-restraints excluded: chain U residue 441 ILE Chi-restraints excluded: chain U residue 464 ILE Chi-restraints excluded: chain V residue 295 PHE Chi-restraints excluded: chain V residue 405 GLN Chi-restraints excluded: chain V residue 441 ILE Chi-restraints excluded: chain V residue 464 ILE Chi-restraints excluded: chain W residue 295 PHE Chi-restraints excluded: chain W residue 405 GLN Chi-restraints excluded: chain W residue 441 ILE Chi-restraints excluded: chain W residue 464 ILE Chi-restraints excluded: chain X residue 295 PHE Chi-restraints excluded: chain X residue 405 GLN Chi-restraints excluded: chain X residue 441 ILE Chi-restraints excluded: chain X residue 464 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 111 optimal weight: 0.9990 chunk 271 optimal weight: 5.9990 chunk 82 optimal weight: 0.0270 chunk 362 optimal weight: 5.9990 chunk 411 optimal weight: 0.9980 chunk 260 optimal weight: 5.9990 chunk 367 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 293 optimal weight: 1.9990 chunk 523 optimal weight: 8.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN C 405 GLN ** G 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 405 GLN ** N 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 405 GLN ** U 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 405 GLN X 405 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.089852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.073585 restraints weight = 139402.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.076014 restraints weight = 67311.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.077574 restraints weight = 42982.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.078555 restraints weight = 32273.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.079209 restraints weight = 26847.676| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 43806 Z= 0.140 Angle : 0.616 9.627 59167 Z= 0.312 Chirality : 0.044 0.120 6840 Planarity : 0.004 0.046 7657 Dihedral : 4.616 42.959 6169 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.66 % Allowed : 18.90 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.11 (0.11), residues: 5568 helix: 1.07 (0.11), residues: 2256 sheet: -2.52 (0.13), residues: 1152 loop : -1.56 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 452 TYR 0.016 0.002 TYR I 275 PHE 0.014 0.002 PHE A 392 HIS 0.002 0.001 HIS C 439 Details of bonding type rmsd covalent geometry : bond 0.00317 (43806) covalent geometry : angle 0.61645 (59167) hydrogen bonds : bond 0.02840 ( 2040) hydrogen bonds : angle 4.74530 ( 5904) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 887 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 722 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.8989 (ppp) cc_final: 0.8644 (ppp) REVERT: A 273 MET cc_start: 0.7166 (mtp) cc_final: 0.6960 (mtp) REVERT: A 295 PHE cc_start: 0.7185 (OUTLIER) cc_final: 0.6432 (p90) REVERT: A 353 MET cc_start: 0.7791 (ttt) cc_final: 0.7564 (ttt) REVERT: A 379 MET cc_start: 0.8714 (mmm) cc_final: 0.7685 (mmm) REVERT: A 419 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8517 (tp) REVERT: A 422 LYS cc_start: 0.8910 (mmmm) cc_final: 0.8679 (tppp) REVERT: A 460 ASN cc_start: 0.8369 (t0) cc_final: 0.8000 (t0) REVERT: B 245 ASN cc_start: 0.9312 (p0) cc_final: 0.9099 (p0) REVERT: B 270 GLU cc_start: 0.7768 (tp30) cc_final: 0.7027 (tp30) REVERT: B 295 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.6595 (p90) REVERT: B 353 MET cc_start: 0.7876 (ttt) cc_final: 0.7493 (ttt) REVERT: B 354 ASN cc_start: 0.8126 (m-40) cc_final: 0.7865 (m110) REVERT: B 379 MET cc_start: 0.8776 (mmm) cc_final: 0.7711 (mmm) REVERT: B 396 MET cc_start: 0.8105 (mmm) cc_final: 0.7780 (mmt) REVERT: B 416 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8267 (tp30) REVERT: B 422 LYS cc_start: 0.8929 (mmmm) cc_final: 0.8702 (tppp) REVERT: B 460 ASN cc_start: 0.8314 (t0) cc_final: 0.8005 (t0) REVERT: C 245 ASN cc_start: 0.9334 (p0) cc_final: 0.9114 (p0) REVERT: C 270 GLU cc_start: 0.7874 (tp30) cc_final: 0.7461 (tp30) REVERT: C 295 PHE cc_start: 0.7135 (OUTLIER) cc_final: 0.6385 (p90) REVERT: C 379 MET cc_start: 0.8773 (mmm) cc_final: 0.7744 (mmm) REVERT: C 422 LYS cc_start: 0.8941 (mmmm) cc_final: 0.8713 (tppp) REVERT: C 460 ASN cc_start: 0.8361 (t0) cc_final: 0.8014 (t0) REVERT: D 245 ASN cc_start: 0.9303 (p0) cc_final: 0.9081 (p0) REVERT: D 270 GLU cc_start: 0.7517 (tp30) cc_final: 0.6795 (tp30) REVERT: D 295 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.6492 (p90) REVERT: D 353 MET cc_start: 0.7888 (ttt) cc_final: 0.7672 (ttt) REVERT: D 379 MET cc_start: 0.8710 (mmm) cc_final: 0.7648 (mmm) REVERT: D 396 MET cc_start: 0.8088 (mmm) cc_final: 0.7739 (mmt) REVERT: D 422 LYS cc_start: 0.8959 (mmmm) cc_final: 0.8554 (tppp) REVERT: D 430 MET cc_start: 0.8097 (mmm) cc_final: 0.7466 (mmm) REVERT: D 460 ASN cc_start: 0.8353 (t0) cc_final: 0.8024 (t0) REVERT: E 241 ARG cc_start: 0.8308 (mmp-170) cc_final: 0.7893 (mmp80) REVERT: E 270 GLU cc_start: 0.7798 (tp30) cc_final: 0.7359 (tp30) REVERT: E 273 MET cc_start: 0.7228 (mtp) cc_final: 0.7001 (mtp) REVERT: E 295 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.6566 (p90) REVERT: E 353 MET cc_start: 0.7769 (ttt) cc_final: 0.7560 (ttt) REVERT: E 379 MET cc_start: 0.8800 (mmm) cc_final: 0.7817 (mmm) REVERT: E 396 MET cc_start: 0.8104 (mmm) cc_final: 0.7764 (mmt) REVERT: E 422 LYS cc_start: 0.8900 (mmmm) cc_final: 0.8669 (tppp) REVERT: E 460 ASN cc_start: 0.8350 (t0) cc_final: 0.8025 (t0) REVERT: F 270 GLU cc_start: 0.7761 (tp30) cc_final: 0.7002 (tp30) REVERT: F 295 PHE cc_start: 0.7206 (OUTLIER) cc_final: 0.6462 (p90) REVERT: F 310 GLN cc_start: 0.8061 (mt0) cc_final: 0.7797 (mt0) REVERT: F 344 VAL cc_start: 0.8884 (OUTLIER) cc_final: 0.8662 (t) REVERT: F 354 ASN cc_start: 0.8124 (m-40) cc_final: 0.7782 (m110) REVERT: F 379 MET cc_start: 0.8844 (mmm) cc_final: 0.7753 (mmm) REVERT: F 396 MET cc_start: 0.8124 (mmm) cc_final: 0.7807 (mmt) REVERT: F 416 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8264 (tp30) REVERT: F 422 LYS cc_start: 0.8932 (mmmm) cc_final: 0.8693 (tppp) REVERT: F 460 ASN cc_start: 0.8317 (t0) cc_final: 0.7991 (t0) REVERT: G 295 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.6580 (p90) REVERT: G 379 MET cc_start: 0.8738 (mmm) cc_final: 0.7702 (mmm) REVERT: G 396 MET cc_start: 0.8098 (mmm) cc_final: 0.7725 (mmt) REVERT: G 422 LYS cc_start: 0.8959 (mmmm) cc_final: 0.8552 (tppp) REVERT: G 460 ASN cc_start: 0.8387 (t0) cc_final: 0.8037 (t0) REVERT: H 270 GLU cc_start: 0.7792 (tp30) cc_final: 0.7047 (tp30) REVERT: H 295 PHE cc_start: 0.7166 (OUTLIER) cc_final: 0.6435 (p90) REVERT: H 353 MET cc_start: 0.7888 (ttt) cc_final: 0.7667 (ttt) REVERT: H 379 MET cc_start: 0.8757 (mmm) cc_final: 0.7760 (mmm) REVERT: H 396 MET cc_start: 0.8127 (mmm) cc_final: 0.7799 (mmt) REVERT: H 416 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8291 (tp30) REVERT: H 422 LYS cc_start: 0.8914 (mmmm) cc_final: 0.8689 (tppp) REVERT: H 460 ASN cc_start: 0.8325 (t0) cc_final: 0.8013 (t0) REVERT: I 270 GLU cc_start: 0.7763 (tp30) cc_final: 0.7003 (tp30) REVERT: I 295 PHE cc_start: 0.7154 (OUTLIER) cc_final: 0.6493 (p90) REVERT: I 310 GLN cc_start: 0.8061 (mt0) cc_final: 0.7791 (mt0) REVERT: I 353 MET cc_start: 0.7832 (ttt) cc_final: 0.7394 (ttt) REVERT: I 354 ASN cc_start: 0.8094 (m-40) cc_final: 0.7821 (m110) REVERT: I 379 MET cc_start: 0.8812 (mmm) cc_final: 0.7771 (mmm) REVERT: I 396 MET cc_start: 0.8123 (mmm) cc_final: 0.7801 (mmt) REVERT: I 416 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8275 (tp30) REVERT: I 422 LYS cc_start: 0.8923 (mmmm) cc_final: 0.8686 (tppp) REVERT: I 460 ASN cc_start: 0.8343 (t0) cc_final: 0.8002 (t0) REVERT: J 295 PHE cc_start: 0.7282 (OUTLIER) cc_final: 0.6593 (p90) REVERT: J 353 MET cc_start: 0.7812 (ttt) cc_final: 0.7605 (ttt) REVERT: J 379 MET cc_start: 0.8769 (mmm) cc_final: 0.7699 (mmm) REVERT: J 396 MET cc_start: 0.8078 (mmm) cc_final: 0.7713 (mmt) REVERT: J 405 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7764 (pt0) REVERT: J 422 LYS cc_start: 0.8957 (mmmm) cc_final: 0.8552 (tppp) REVERT: J 460 ASN cc_start: 0.8364 (t0) cc_final: 0.8050 (t0) REVERT: K 295 PHE cc_start: 0.7297 (OUTLIER) cc_final: 0.6689 (p90) REVERT: K 353 MET cc_start: 0.7810 (ttt) cc_final: 0.7596 (ttt) REVERT: K 379 MET cc_start: 0.8795 (mmm) cc_final: 0.7816 (mmm) REVERT: K 396 MET cc_start: 0.8125 (mmm) cc_final: 0.7767 (mmt) REVERT: K 416 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8308 (tp30) REVERT: K 422 LYS cc_start: 0.8921 (mmmm) cc_final: 0.8695 (tppp) REVERT: K 430 MET cc_start: 0.7551 (mmm) cc_final: 0.7344 (mmm) REVERT: K 460 ASN cc_start: 0.8288 (t0) cc_final: 0.7981 (t0) REVERT: L 270 GLU cc_start: 0.7763 (tp30) cc_final: 0.7008 (tp30) REVERT: L 295 PHE cc_start: 0.7140 (OUTLIER) cc_final: 0.6417 (p90) REVERT: L 353 MET cc_start: 0.7886 (ttt) cc_final: 0.7492 (ttt) REVERT: L 354 ASN cc_start: 0.8115 (m-40) cc_final: 0.7861 (m110) REVERT: L 379 MET cc_start: 0.8745 (mmm) cc_final: 0.7658 (mmm) REVERT: L 396 MET cc_start: 0.8126 (mmm) cc_final: 0.7802 (mmt) REVERT: L 416 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8283 (tp30) REVERT: L 422 LYS cc_start: 0.8918 (mmmm) cc_final: 0.8682 (tppp) REVERT: L 460 ASN cc_start: 0.8344 (t0) cc_final: 0.7992 (t0) REVERT: M 295 PHE cc_start: 0.7200 (OUTLIER) cc_final: 0.6451 (p90) REVERT: M 353 MET cc_start: 0.7838 (ttt) cc_final: 0.7539 (ttt) REVERT: M 354 ASN cc_start: 0.8101 (m-40) cc_final: 0.7811 (m110) REVERT: M 379 MET cc_start: 0.8763 (mmm) cc_final: 0.7733 (mmm) REVERT: M 422 LYS cc_start: 0.8899 (mmmm) cc_final: 0.8667 (tppp) REVERT: M 430 MET cc_start: 0.7529 (mmm) cc_final: 0.7318 (mmm) REVERT: M 460 ASN cc_start: 0.8337 (t0) cc_final: 0.7974 (t0) REVERT: N 241 ARG cc_start: 0.8260 (mmp-170) cc_final: 0.7841 (mmp80) REVERT: N 245 ASN cc_start: 0.9326 (p0) cc_final: 0.9103 (p0) REVERT: N 270 GLU cc_start: 0.7807 (tp30) cc_final: 0.7061 (tp30) REVERT: N 295 PHE cc_start: 0.7134 (OUTLIER) cc_final: 0.6486 (p90) REVERT: N 354 ASN cc_start: 0.8118 (m-40) cc_final: 0.7792 (m110) REVERT: N 379 MET cc_start: 0.8771 (mmm) cc_final: 0.7714 (mmm) REVERT: N 396 MET cc_start: 0.8103 (mmm) cc_final: 0.7787 (mmt) REVERT: N 416 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8293 (tp30) REVERT: N 422 LYS cc_start: 0.8911 (mmmm) cc_final: 0.8686 (tppp) REVERT: N 460 ASN cc_start: 0.8342 (t0) cc_final: 0.8052 (t0) REVERT: O 239 GLU cc_start: 0.8453 (mp0) cc_final: 0.8082 (mp0) REVERT: O 245 ASN cc_start: 0.9326 (p0) cc_final: 0.9122 (p0) REVERT: O 270 GLU cc_start: 0.7817 (tp30) cc_final: 0.7382 (tp30) REVERT: O 295 PHE cc_start: 0.7134 (OUTLIER) cc_final: 0.6403 (p90) REVERT: O 353 MET cc_start: 0.7778 (ttt) cc_final: 0.7405 (ttt) REVERT: O 379 MET cc_start: 0.8747 (mmm) cc_final: 0.7719 (mmm) REVERT: O 396 MET cc_start: 0.8125 (mmm) cc_final: 0.7786 (mmt) REVERT: O 422 LYS cc_start: 0.8966 (mmmm) cc_final: 0.8571 (tppp) REVERT: O 460 ASN cc_start: 0.8314 (t0) cc_final: 0.7980 (t0) REVERT: P 270 GLU cc_start: 0.7775 (tp30) cc_final: 0.7345 (tp30) REVERT: P 295 PHE cc_start: 0.7279 (OUTLIER) cc_final: 0.6594 (p90) REVERT: P 353 MET cc_start: 0.7889 (ttt) cc_final: 0.7678 (ttt) REVERT: P 379 MET cc_start: 0.8736 (mmm) cc_final: 0.7690 (mmm) REVERT: P 396 MET cc_start: 0.8116 (mmm) cc_final: 0.7783 (mmt) REVERT: P 422 LYS cc_start: 0.8937 (mmmm) cc_final: 0.8708 (tppp) REVERT: P 460 ASN cc_start: 0.8329 (t0) cc_final: 0.8024 (t0) REVERT: Q 241 ARG cc_start: 0.8250 (mmp-170) cc_final: 0.7836 (mmp80) REVERT: Q 295 PHE cc_start: 0.7291 (OUTLIER) cc_final: 0.6543 (p90) REVERT: Q 353 MET cc_start: 0.7894 (ttt) cc_final: 0.7689 (ttt) REVERT: Q 379 MET cc_start: 0.8739 (mmm) cc_final: 0.7698 (mmm) REVERT: Q 396 MET cc_start: 0.8141 (mmm) cc_final: 0.7803 (mmt) REVERT: Q 422 LYS cc_start: 0.8988 (mmmm) cc_final: 0.8602 (tppp) REVERT: Q 430 MET cc_start: 0.8065 (mmm) cc_final: 0.7282 (mmp) REVERT: Q 460 ASN cc_start: 0.8333 (t0) cc_final: 0.8040 (t0) REVERT: R 241 ARG cc_start: 0.8271 (mmp-170) cc_final: 0.7852 (mmp80) REVERT: R 270 GLU cc_start: 0.7822 (tp30) cc_final: 0.7400 (tp30) REVERT: R 295 PHE cc_start: 0.7139 (OUTLIER) cc_final: 0.6418 (p90) REVERT: R 344 VAL cc_start: 0.8884 (OUTLIER) cc_final: 0.8669 (t) REVERT: R 353 MET cc_start: 0.7872 (ttt) cc_final: 0.7655 (ttt) REVERT: R 379 MET cc_start: 0.8780 (mmm) cc_final: 0.7700 (mmm) REVERT: R 396 MET cc_start: 0.8122 (mmm) cc_final: 0.7794 (mmt) REVERT: R 416 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8338 (tp30) REVERT: R 422 LYS cc_start: 0.8947 (mmmm) cc_final: 0.8724 (tppp) REVERT: R 460 ASN cc_start: 0.8320 (t0) cc_final: 0.7996 (t0) REVERT: S 241 ARG cc_start: 0.8268 (mmp-170) cc_final: 0.7845 (mmp80) REVERT: S 295 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.6402 (p90) REVERT: S 353 MET cc_start: 0.7876 (ttt) cc_final: 0.7595 (ttt) REVERT: S 354 ASN cc_start: 0.8106 (m-40) cc_final: 0.7818 (m110) REVERT: S 379 MET cc_start: 0.8668 (mmm) cc_final: 0.7647 (mmm) REVERT: S 396 MET cc_start: 0.8187 (mmm) cc_final: 0.7937 (mmm) REVERT: S 419 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8534 (tp) REVERT: S 460 ASN cc_start: 0.8361 (t0) cc_final: 0.8016 (t0) REVERT: T 241 ARG cc_start: 0.8269 (mmp-170) cc_final: 0.7855 (mmp80) REVERT: T 270 GLU cc_start: 0.7762 (tp30) cc_final: 0.6992 (tp30) REVERT: T 295 PHE cc_start: 0.7301 (OUTLIER) cc_final: 0.6548 (p90) REVERT: T 379 MET cc_start: 0.8784 (mmm) cc_final: 0.7730 (mmm) REVERT: T 396 MET cc_start: 0.8128 (mmm) cc_final: 0.7799 (mmt) REVERT: T 422 LYS cc_start: 0.8925 (mmmm) cc_final: 0.8692 (tppp) REVERT: T 460 ASN cc_start: 0.8380 (t0) cc_final: 0.8031 (t0) REVERT: U 245 ASN cc_start: 0.9322 (p0) cc_final: 0.9101 (p0) REVERT: U 270 GLU cc_start: 0.7780 (tp30) cc_final: 0.7342 (tp30) REVERT: U 295 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.6403 (p90) REVERT: U 379 MET cc_start: 0.8761 (mmm) cc_final: 0.7728 (mmm) REVERT: U 396 MET cc_start: 0.8125 (mmm) cc_final: 0.7787 (mmt) REVERT: U 422 LYS cc_start: 0.8919 (mmmm) cc_final: 0.8687 (tppp) REVERT: U 460 ASN cc_start: 0.8300 (t0) cc_final: 0.8010 (t0) REVERT: V 270 GLU cc_start: 0.7765 (tp30) cc_final: 0.7323 (tp30) REVERT: V 295 PHE cc_start: 0.7195 (OUTLIER) cc_final: 0.6456 (p90) REVERT: V 353 MET cc_start: 0.7839 (ttt) cc_final: 0.7550 (ttt) REVERT: V 354 ASN cc_start: 0.8102 (m-40) cc_final: 0.7817 (m110) REVERT: V 379 MET cc_start: 0.8751 (mmm) cc_final: 0.7703 (mmm) REVERT: V 396 MET cc_start: 0.8122 (mmm) cc_final: 0.7791 (mmt) REVERT: V 419 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8502 (tp) REVERT: V 422 LYS cc_start: 0.8918 (mmmm) cc_final: 0.8685 (tppp) REVERT: V 460 ASN cc_start: 0.8314 (t0) cc_final: 0.7985 (t0) REVERT: W 241 ARG cc_start: 0.8276 (mmp-170) cc_final: 0.7857 (mmp80) REVERT: W 270 GLU cc_start: 0.7785 (tp30) cc_final: 0.7354 (tp30) REVERT: W 273 MET cc_start: 0.7198 (mtp) cc_final: 0.6972 (mtp) REVERT: W 295 PHE cc_start: 0.7256 (OUTLIER) cc_final: 0.6558 (p90) REVERT: W 379 MET cc_start: 0.8742 (mmm) cc_final: 0.7722 (mmm) REVERT: W 396 MET cc_start: 0.8123 (mmm) cc_final: 0.7794 (mmt) REVERT: W 422 LYS cc_start: 0.8906 (mmmm) cc_final: 0.8670 (tppp) REVERT: W 460 ASN cc_start: 0.8354 (t0) cc_final: 0.8008 (t0) REVERT: X 270 GLU cc_start: 0.7824 (tp30) cc_final: 0.7389 (tp30) REVERT: X 295 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6420 (p90) REVERT: X 353 MET cc_start: 0.7861 (ttt) cc_final: 0.7644 (ttt) REVERT: X 379 MET cc_start: 0.8805 (mmm) cc_final: 0.7734 (mmm) REVERT: X 396 MET cc_start: 0.8127 (mmm) cc_final: 0.7793 (mmt) REVERT: X 405 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7782 (pt0) REVERT: X 422 LYS cc_start: 0.8922 (mmmm) cc_final: 0.8684 (tppp) REVERT: X 460 ASN cc_start: 0.8371 (t0) cc_final: 0.8038 (t0) outliers start: 165 outliers final: 86 residues processed: 887 average time/residue: 0.2218 time to fit residues: 332.6854 Evaluate side-chains 819 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 702 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 405 GLN Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 295 PHE Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 405 GLN Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 295 PHE Chi-restraints excluded: chain E residue 405 GLN Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 405 GLN Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 441 ILE Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain G residue 295 PHE Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 405 GLN Chi-restraints excluded: chain H residue 414 ILE Chi-restraints excluded: chain H residue 441 ILE Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 405 GLN Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 441 ILE Chi-restraints excluded: chain I residue 464 ILE Chi-restraints excluded: chain J residue 295 PHE Chi-restraints excluded: chain J residue 405 GLN Chi-restraints excluded: chain J residue 414 ILE Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain K residue 295 PHE Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 441 ILE Chi-restraints excluded: chain K residue 464 ILE Chi-restraints excluded: chain L residue 295 PHE Chi-restraints excluded: chain L residue 405 GLN Chi-restraints excluded: chain L residue 414 ILE Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 464 ILE Chi-restraints excluded: chain M residue 295 PHE Chi-restraints excluded: chain M residue 414 ILE Chi-restraints excluded: chain M residue 441 ILE Chi-restraints excluded: chain M residue 464 ILE Chi-restraints excluded: chain N residue 295 PHE Chi-restraints excluded: chain N residue 414 ILE Chi-restraints excluded: chain N residue 441 ILE Chi-restraints excluded: chain N residue 464 ILE Chi-restraints excluded: chain O residue 295 PHE Chi-restraints excluded: chain O residue 405 GLN Chi-restraints excluded: chain O residue 414 ILE Chi-restraints excluded: chain O residue 441 ILE Chi-restraints excluded: chain O residue 464 ILE Chi-restraints excluded: chain P residue 295 PHE Chi-restraints excluded: chain P residue 414 ILE Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 464 ILE Chi-restraints excluded: chain Q residue 295 PHE Chi-restraints excluded: chain Q residue 414 ILE Chi-restraints excluded: chain Q residue 441 ILE Chi-restraints excluded: chain Q residue 464 ILE Chi-restraints excluded: chain R residue 295 PHE Chi-restraints excluded: chain R residue 344 VAL Chi-restraints excluded: chain R residue 405 GLN Chi-restraints excluded: chain R residue 414 ILE Chi-restraints excluded: chain R residue 441 ILE Chi-restraints excluded: chain R residue 464 ILE Chi-restraints excluded: chain S residue 295 PHE Chi-restraints excluded: chain S residue 405 GLN Chi-restraints excluded: chain S residue 414 ILE Chi-restraints excluded: chain S residue 419 ILE Chi-restraints excluded: chain S residue 441 ILE Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain T residue 295 PHE Chi-restraints excluded: chain T residue 414 ILE Chi-restraints excluded: chain T residue 441 ILE Chi-restraints excluded: chain T residue 464 ILE Chi-restraints excluded: chain U residue 295 PHE Chi-restraints excluded: chain U residue 405 GLN Chi-restraints excluded: chain U residue 414 ILE Chi-restraints excluded: chain U residue 441 ILE Chi-restraints excluded: chain U residue 464 ILE Chi-restraints excluded: chain V residue 295 PHE Chi-restraints excluded: chain V residue 405 GLN Chi-restraints excluded: chain V residue 414 ILE Chi-restraints excluded: chain V residue 419 ILE Chi-restraints excluded: chain V residue 441 ILE Chi-restraints excluded: chain V residue 464 ILE Chi-restraints excluded: chain W residue 295 PHE Chi-restraints excluded: chain W residue 405 GLN Chi-restraints excluded: chain W residue 414 ILE Chi-restraints excluded: chain W residue 441 ILE Chi-restraints excluded: chain W residue 464 ILE Chi-restraints excluded: chain X residue 295 PHE Chi-restraints excluded: chain X residue 405 GLN Chi-restraints excluded: chain X residue 414 ILE Chi-restraints excluded: chain X residue 441 ILE Chi-restraints excluded: chain X residue 464 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 307 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 446 optimal weight: 9.9990 chunk 260 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 184 optimal weight: 8.9990 chunk 337 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 252 optimal weight: 0.0970 chunk 360 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN B 405 GLN C 405 GLN ** G 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 405 GLN T 405 GLN ** U 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 405 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.086363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.071461 restraints weight = 129309.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.073411 restraints weight = 69504.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.074710 restraints weight = 48398.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.075553 restraints weight = 38985.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.076018 restraints weight = 33972.104| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 43806 Z= 0.139 Angle : 0.640 11.803 59167 Z= 0.321 Chirality : 0.044 0.129 6840 Planarity : 0.004 0.044 7657 Dihedral : 4.571 42.455 6169 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.35 % Allowed : 20.03 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.11), residues: 5568 helix: 1.07 (0.11), residues: 2256 sheet: -2.44 (0.13), residues: 1152 loop : -1.50 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 248 TYR 0.015 0.001 TYR A 275 PHE 0.014 0.002 PHE W 392 HIS 0.003 0.001 HIS S 439 Details of bonding type rmsd covalent geometry : bond 0.00314 (43806) covalent geometry : angle 0.64046 (59167) hydrogen bonds : bond 0.02798 ( 2040) hydrogen bonds : angle 4.70763 ( 5904) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 721 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 PHE cc_start: 0.7155 (OUTLIER) cc_final: 0.6338 (p90) REVERT: A 379 MET cc_start: 0.8671 (mmm) cc_final: 0.7640 (mmm) REVERT: A 396 MET cc_start: 0.8175 (mmm) cc_final: 0.7649 (mmt) REVERT: A 422 LYS cc_start: 0.9104 (mmmm) cc_final: 0.8740 (tppp) REVERT: A 430 MET cc_start: 0.7491 (mmm) cc_final: 0.7214 (mmm) REVERT: A 460 ASN cc_start: 0.8296 (t0) cc_final: 0.7966 (t0) REVERT: B 245 ASN cc_start: 0.9348 (p0) cc_final: 0.9139 (p0) REVERT: B 270 GLU cc_start: 0.7256 (tp30) cc_final: 0.6971 (tp30) REVERT: B 295 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.6537 (p90) REVERT: B 354 ASN cc_start: 0.8166 (m-40) cc_final: 0.7821 (m110) REVERT: B 379 MET cc_start: 0.8712 (mmm) cc_final: 0.7648 (mmm) REVERT: B 396 MET cc_start: 0.8081 (mmm) cc_final: 0.7702 (mmt) REVERT: B 416 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8194 (tp30) REVERT: B 422 LYS cc_start: 0.9144 (mmmm) cc_final: 0.8788 (tppp) REVERT: B 430 MET cc_start: 0.8033 (mmm) cc_final: 0.7722 (mmm) REVERT: B 460 ASN cc_start: 0.8397 (t0) cc_final: 0.8008 (t0) REVERT: C 239 GLU cc_start: 0.8533 (mp0) cc_final: 0.8173 (mp0) REVERT: C 270 GLU cc_start: 0.7731 (tp30) cc_final: 0.7100 (tp30) REVERT: C 273 MET cc_start: 0.7091 (mtp) cc_final: 0.6833 (mtp) REVERT: C 295 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.6313 (p90) REVERT: C 353 MET cc_start: 0.7423 (tpp) cc_final: 0.7038 (ttt) REVERT: C 379 MET cc_start: 0.8734 (mmm) cc_final: 0.7668 (mmm) REVERT: C 422 LYS cc_start: 0.9142 (mmmm) cc_final: 0.8783 (tppp) REVERT: C 460 ASN cc_start: 0.8325 (t0) cc_final: 0.8002 (t0) REVERT: D 270 GLU cc_start: 0.7418 (tp30) cc_final: 0.6851 (tp30) REVERT: D 273 MET cc_start: 0.7063 (mtp) cc_final: 0.6810 (mtp) REVERT: D 295 PHE cc_start: 0.7153 (OUTLIER) cc_final: 0.6336 (p90) REVERT: D 353 MET cc_start: 0.7807 (ttt) cc_final: 0.7588 (ttt) REVERT: D 379 MET cc_start: 0.8662 (mmm) cc_final: 0.7599 (mmm) REVERT: D 430 MET cc_start: 0.8155 (mmm) cc_final: 0.7807 (mmm) REVERT: D 460 ASN cc_start: 0.8305 (t0) cc_final: 0.7987 (t0) REVERT: E 239 GLU cc_start: 0.8544 (mp0) cc_final: 0.8169 (mp0) REVERT: E 270 GLU cc_start: 0.7624 (tp30) cc_final: 0.7268 (tp30) REVERT: E 295 PHE cc_start: 0.7263 (OUTLIER) cc_final: 0.6547 (p90) REVERT: E 353 MET cc_start: 0.7608 (ttt) cc_final: 0.7352 (ttt) REVERT: E 379 MET cc_start: 0.8753 (mmm) cc_final: 0.7763 (mmm) REVERT: E 422 LYS cc_start: 0.9099 (mmmm) cc_final: 0.8737 (tppp) REVERT: E 460 ASN cc_start: 0.8442 (t0) cc_final: 0.8040 (t0) REVERT: F 239 GLU cc_start: 0.8544 (mp0) cc_final: 0.8171 (mp0) REVERT: F 270 GLU cc_start: 0.7193 (tp30) cc_final: 0.6895 (tp30) REVERT: F 295 PHE cc_start: 0.7183 (OUTLIER) cc_final: 0.6432 (p90) REVERT: F 344 VAL cc_start: 0.8938 (OUTLIER) cc_final: 0.8723 (t) REVERT: F 354 ASN cc_start: 0.8115 (m-40) cc_final: 0.7808 (m110) REVERT: F 379 MET cc_start: 0.8823 (mmm) cc_final: 0.7712 (mmm) REVERT: F 396 MET cc_start: 0.8155 (mmm) cc_final: 0.7793 (mmt) REVERT: F 416 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8185 (tp30) REVERT: F 422 LYS cc_start: 0.9136 (mmmm) cc_final: 0.8764 (tppp) REVERT: F 430 MET cc_start: 0.8095 (mmm) cc_final: 0.7735 (mmm) REVERT: F 460 ASN cc_start: 0.8323 (t0) cc_final: 0.7995 (t0) REVERT: G 270 GLU cc_start: 0.7650 (tp30) cc_final: 0.7138 (tp30) REVERT: G 273 MET cc_start: 0.7099 (mtp) cc_final: 0.6855 (mtp) REVERT: G 295 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.6445 (p90) REVERT: G 353 MET cc_start: 0.7619 (tpp) cc_final: 0.6965 (ttt) REVERT: G 379 MET cc_start: 0.8703 (mmm) cc_final: 0.7656 (mmm) REVERT: G 460 ASN cc_start: 0.8367 (t0) cc_final: 0.8012 (t0) REVERT: H 239 GLU cc_start: 0.8523 (mp0) cc_final: 0.8140 (mp0) REVERT: H 270 GLU cc_start: 0.7219 (tp30) cc_final: 0.6933 (tp30) REVERT: H 295 PHE cc_start: 0.7173 (OUTLIER) cc_final: 0.6507 (p90) REVERT: H 353 MET cc_start: 0.7848 (ttt) cc_final: 0.7619 (ttt) REVERT: H 379 MET cc_start: 0.8667 (mmm) cc_final: 0.7681 (mmm) REVERT: H 396 MET cc_start: 0.8159 (mmm) cc_final: 0.7804 (mmt) REVERT: H 416 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8193 (tp30) REVERT: H 422 LYS cc_start: 0.9108 (mmmm) cc_final: 0.8749 (tppp) REVERT: H 430 MET cc_start: 0.8079 (mmm) cc_final: 0.7725 (mmm) REVERT: H 460 ASN cc_start: 0.8410 (t0) cc_final: 0.8023 (t0) REVERT: I 239 GLU cc_start: 0.8531 (mp0) cc_final: 0.8156 (mp0) REVERT: I 270 GLU cc_start: 0.7201 (tp30) cc_final: 0.6907 (tp30) REVERT: I 295 PHE cc_start: 0.7171 (OUTLIER) cc_final: 0.6444 (p90) REVERT: I 354 ASN cc_start: 0.8168 (m-40) cc_final: 0.7796 (m110) REVERT: I 379 MET cc_start: 0.8774 (mmm) cc_final: 0.7732 (mmm) REVERT: I 396 MET cc_start: 0.8144 (mmm) cc_final: 0.7770 (mmt) REVERT: I 416 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8202 (tp30) REVERT: I 422 LYS cc_start: 0.9100 (mmmm) cc_final: 0.8716 (tppp) REVERT: I 430 MET cc_start: 0.8109 (mmm) cc_final: 0.7711 (mmm) REVERT: I 460 ASN cc_start: 0.8362 (t0) cc_final: 0.8005 (t0) REVERT: J 247 MET cc_start: 0.9004 (ppp) cc_final: 0.8400 (ppp) REVERT: J 270 GLU cc_start: 0.7656 (tp30) cc_final: 0.7136 (tp30) REVERT: J 273 MET cc_start: 0.7080 (mtp) cc_final: 0.6829 (mtp) REVERT: J 295 PHE cc_start: 0.7298 (OUTLIER) cc_final: 0.6570 (p90) REVERT: J 353 MET cc_start: 0.7626 (ttt) cc_final: 0.7408 (ttt) REVERT: J 379 MET cc_start: 0.8753 (mmm) cc_final: 0.7685 (mmm) REVERT: J 460 ASN cc_start: 0.8409 (t0) cc_final: 0.8012 (t0) REVERT: K 239 GLU cc_start: 0.8503 (mp0) cc_final: 0.8121 (mp0) REVERT: K 270 GLU cc_start: 0.7823 (tp30) cc_final: 0.7550 (tp30) REVERT: K 295 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.6567 (p90) REVERT: K 353 MET cc_start: 0.7726 (ttt) cc_final: 0.7464 (ttt) REVERT: K 379 MET cc_start: 0.8734 (mmm) cc_final: 0.7745 (mmm) REVERT: K 416 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8246 (tp30) REVERT: K 422 LYS cc_start: 0.9102 (mmmm) cc_final: 0.8726 (tppp) REVERT: K 430 MET cc_start: 0.7567 (mmm) cc_final: 0.7294 (mmm) REVERT: K 460 ASN cc_start: 0.8301 (t0) cc_final: 0.7943 (t0) REVERT: L 270 GLU cc_start: 0.7200 (tp30) cc_final: 0.6901 (tp30) REVERT: L 295 PHE cc_start: 0.7144 (OUTLIER) cc_final: 0.6412 (p90) REVERT: L 354 ASN cc_start: 0.8150 (m-40) cc_final: 0.7808 (m110) REVERT: L 379 MET cc_start: 0.8663 (mmm) cc_final: 0.7586 (mmm) REVERT: L 396 MET cc_start: 0.8143 (mmm) cc_final: 0.7768 (mmt) REVERT: L 416 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8223 (tp30) REVERT: L 422 LYS cc_start: 0.9104 (mmmm) cc_final: 0.8716 (tppp) REVERT: L 430 MET cc_start: 0.8113 (mmm) cc_final: 0.7728 (mmm) REVERT: L 460 ASN cc_start: 0.8434 (t0) cc_final: 0.8050 (t0) REVERT: M 270 GLU cc_start: 0.7812 (tp30) cc_final: 0.7531 (tp30) REVERT: M 295 PHE cc_start: 0.7207 (OUTLIER) cc_final: 0.6417 (p90) REVERT: M 354 ASN cc_start: 0.8148 (m-40) cc_final: 0.7771 (m110) REVERT: M 379 MET cc_start: 0.8738 (mmm) cc_final: 0.7697 (mmm) REVERT: M 396 MET cc_start: 0.8196 (mmm) cc_final: 0.7659 (mmt) REVERT: M 422 LYS cc_start: 0.9085 (mmmm) cc_final: 0.8712 (tppp) REVERT: M 430 MET cc_start: 0.7559 (mmm) cc_final: 0.7271 (mmm) REVERT: M 460 ASN cc_start: 0.8342 (t0) cc_final: 0.8001 (t0) REVERT: N 270 GLU cc_start: 0.7223 (tp30) cc_final: 0.6934 (tp30) REVERT: N 295 PHE cc_start: 0.7147 (OUTLIER) cc_final: 0.6484 (p90) REVERT: N 354 ASN cc_start: 0.8104 (m-40) cc_final: 0.7818 (m110) REVERT: N 379 MET cc_start: 0.8724 (mmm) cc_final: 0.7641 (mmm) REVERT: N 396 MET cc_start: 0.8138 (mmm) cc_final: 0.7767 (mmt) REVERT: N 416 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8224 (tp30) REVERT: N 422 LYS cc_start: 0.9113 (mmmm) cc_final: 0.8733 (tppp) REVERT: N 430 MET cc_start: 0.8083 (mmm) cc_final: 0.7725 (mmm) REVERT: N 460 ASN cc_start: 0.8441 (t0) cc_final: 0.8045 (t0) REVERT: O 239 GLU cc_start: 0.8523 (mp0) cc_final: 0.8153 (mp0) REVERT: O 245 ASN cc_start: 0.9356 (p0) cc_final: 0.8945 (p0) REVERT: O 295 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6282 (p90) REVERT: O 379 MET cc_start: 0.8677 (mmm) cc_final: 0.7648 (mmm) REVERT: O 422 LYS cc_start: 0.9042 (mmmm) cc_final: 0.8823 (tppp) REVERT: O 460 ASN cc_start: 0.8379 (t0) cc_final: 0.8004 (t0) REVERT: P 241 ARG cc_start: 0.8417 (mmp-170) cc_final: 0.7952 (mmp80) REVERT: P 247 MET cc_start: 0.9053 (ppp) cc_final: 0.8662 (ppp) REVERT: P 295 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.6490 (p90) REVERT: P 353 MET cc_start: 0.7822 (ttt) cc_final: 0.7608 (ttt) REVERT: P 379 MET cc_start: 0.8689 (mmm) cc_final: 0.7637 (mmm) REVERT: P 422 LYS cc_start: 0.9139 (mmmm) cc_final: 0.8786 (tppp) REVERT: P 460 ASN cc_start: 0.8428 (t0) cc_final: 0.8037 (t0) REVERT: Q 273 MET cc_start: 0.6942 (mtp) cc_final: 0.6708 (mtp) REVERT: Q 295 PHE cc_start: 0.7292 (OUTLIER) cc_final: 0.6500 (p90) REVERT: Q 379 MET cc_start: 0.8712 (mmm) cc_final: 0.7661 (mmm) REVERT: Q 396 MET cc_start: 0.8168 (mmm) cc_final: 0.7796 (mmt) REVERT: Q 460 ASN cc_start: 0.8439 (t0) cc_final: 0.8050 (t0) REVERT: R 239 GLU cc_start: 0.8526 (mp0) cc_final: 0.8143 (mp0) REVERT: R 247 MET cc_start: 0.9030 (ppp) cc_final: 0.8645 (ppp) REVERT: R 295 PHE cc_start: 0.7141 (OUTLIER) cc_final: 0.6339 (p90) REVERT: R 344 VAL cc_start: 0.8965 (OUTLIER) cc_final: 0.8750 (t) REVERT: R 379 MET cc_start: 0.8690 (mmm) cc_final: 0.7563 (mmm) REVERT: R 416 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8259 (tp30) REVERT: R 422 LYS cc_start: 0.9141 (mmmm) cc_final: 0.8787 (tppp) REVERT: R 460 ASN cc_start: 0.8318 (t0) cc_final: 0.7984 (t0) REVERT: S 247 MET cc_start: 0.9015 (ppp) cc_final: 0.8619 (ppp) REVERT: S 273 MET cc_start: 0.7088 (mtp) cc_final: 0.6806 (mtp) REVERT: S 295 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.6373 (p90) REVERT: S 354 ASN cc_start: 0.8145 (m-40) cc_final: 0.7779 (m110) REVERT: S 379 MET cc_start: 0.8602 (mmm) cc_final: 0.7578 (mmm) REVERT: S 396 MET cc_start: 0.8187 (mmm) cc_final: 0.7937 (mmm) REVERT: S 430 MET cc_start: 0.7516 (mmm) cc_final: 0.7212 (mmm) REVERT: S 460 ASN cc_start: 0.8336 (t0) cc_final: 0.8002 (t0) REVERT: T 247 MET cc_start: 0.9014 (ppp) cc_final: 0.8381 (ppp) REVERT: T 270 GLU cc_start: 0.7205 (tp30) cc_final: 0.6906 (tp30) REVERT: T 295 PHE cc_start: 0.7303 (OUTLIER) cc_final: 0.6513 (p90) REVERT: T 353 MET cc_start: 0.7483 (tpp) cc_final: 0.7097 (ttt) REVERT: T 379 MET cc_start: 0.8757 (mmm) cc_final: 0.7697 (mmm) REVERT: T 396 MET cc_start: 0.8133 (mmm) cc_final: 0.7754 (mmt) REVERT: T 422 LYS cc_start: 0.9106 (mmmm) cc_final: 0.8722 (tppp) REVERT: T 430 MET cc_start: 0.8082 (mmm) cc_final: 0.7695 (mmm) REVERT: T 460 ASN cc_start: 0.8356 (t0) cc_final: 0.7982 (t0) REVERT: U 239 GLU cc_start: 0.8535 (mp0) cc_final: 0.8190 (mp0) REVERT: U 245 ASN cc_start: 0.9351 (p0) cc_final: 0.9134 (p0) REVERT: U 295 PHE cc_start: 0.7139 (OUTLIER) cc_final: 0.6264 (p90) REVERT: U 379 MET cc_start: 0.8726 (mmm) cc_final: 0.7682 (mmm) REVERT: U 422 LYS cc_start: 0.9112 (mmmm) cc_final: 0.8746 (tppp) REVERT: U 460 ASN cc_start: 0.8335 (t0) cc_final: 0.8006 (t0) REVERT: V 247 MET cc_start: 0.9040 (ppp) cc_final: 0.8645 (ppp) REVERT: V 295 PHE cc_start: 0.7188 (OUTLIER) cc_final: 0.6311 (p90) REVERT: V 354 ASN cc_start: 0.8143 (m-40) cc_final: 0.7782 (m110) REVERT: V 379 MET cc_start: 0.8685 (mmm) cc_final: 0.7637 (mmm) REVERT: V 422 LYS cc_start: 0.9089 (mmmm) cc_final: 0.8706 (tppp) REVERT: V 460 ASN cc_start: 0.8303 (t0) cc_final: 0.7978 (t0) REVERT: W 270 GLU cc_start: 0.7597 (tp30) cc_final: 0.7228 (tp30) REVERT: W 295 PHE cc_start: 0.7253 (OUTLIER) cc_final: 0.6448 (p90) REVERT: W 353 MET cc_start: 0.7515 (tpp) cc_final: 0.7139 (ttt) REVERT: W 379 MET cc_start: 0.8660 (mmm) cc_final: 0.7619 (mmm) REVERT: W 422 LYS cc_start: 0.9106 (mmmm) cc_final: 0.8726 (tppp) REVERT: W 460 ASN cc_start: 0.8444 (t0) cc_final: 0.8060 (t0) REVERT: X 239 GLU cc_start: 0.8540 (mp0) cc_final: 0.8186 (mp0) REVERT: X 247 MET cc_start: 0.9028 (ppp) cc_final: 0.8643 (ppp) REVERT: X 295 PHE cc_start: 0.7167 (OUTLIER) cc_final: 0.6367 (p90) REVERT: X 353 MET cc_start: 0.7764 (ttt) cc_final: 0.7551 (ttt) REVERT: X 379 MET cc_start: 0.8767 (mmm) cc_final: 0.7691 (mmm) REVERT: X 422 LYS cc_start: 0.9108 (mmmm) cc_final: 0.8712 (tppp) REVERT: X 460 ASN cc_start: 0.8333 (t0) cc_final: 0.8011 (t0) outliers start: 151 outliers final: 89 residues processed: 870 average time/residue: 0.2378 time to fit residues: 351.8553 Evaluate side-chains 821 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 706 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 405 GLN Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 405 GLN Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 295 PHE Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 405 GLN Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 295 PHE Chi-restraints excluded: chain E residue 405 GLN Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 405 GLN Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 441 ILE Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain G residue 295 PHE Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 405 GLN Chi-restraints excluded: chain H residue 414 ILE Chi-restraints excluded: chain H residue 441 ILE Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 405 GLN Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 441 ILE Chi-restraints excluded: chain I residue 464 ILE Chi-restraints excluded: chain J residue 295 PHE Chi-restraints excluded: chain J residue 414 ILE Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain K residue 295 PHE Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 441 ILE Chi-restraints excluded: chain K residue 464 ILE Chi-restraints excluded: chain L residue 295 PHE Chi-restraints excluded: chain L residue 405 GLN Chi-restraints excluded: chain L residue 414 ILE Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 464 ILE Chi-restraints excluded: chain M residue 295 PHE Chi-restraints excluded: chain M residue 414 ILE Chi-restraints excluded: chain M residue 441 ILE Chi-restraints excluded: chain M residue 464 ILE Chi-restraints excluded: chain N residue 295 PHE Chi-restraints excluded: chain N residue 414 ILE Chi-restraints excluded: chain N residue 441 ILE Chi-restraints excluded: chain N residue 464 ILE Chi-restraints excluded: chain O residue 295 PHE Chi-restraints excluded: chain O residue 405 GLN Chi-restraints excluded: chain O residue 414 ILE Chi-restraints excluded: chain O residue 441 ILE Chi-restraints excluded: chain O residue 464 ILE Chi-restraints excluded: chain P residue 295 PHE Chi-restraints excluded: chain P residue 414 ILE Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 464 ILE Chi-restraints excluded: chain Q residue 295 PHE Chi-restraints excluded: chain Q residue 414 ILE Chi-restraints excluded: chain Q residue 441 ILE Chi-restraints excluded: chain Q residue 464 ILE Chi-restraints excluded: chain R residue 295 PHE Chi-restraints excluded: chain R residue 344 VAL Chi-restraints excluded: chain R residue 405 GLN Chi-restraints excluded: chain R residue 414 ILE Chi-restraints excluded: chain R residue 441 ILE Chi-restraints excluded: chain R residue 464 ILE Chi-restraints excluded: chain S residue 295 PHE Chi-restraints excluded: chain S residue 405 GLN Chi-restraints excluded: chain S residue 414 ILE Chi-restraints excluded: chain S residue 441 ILE Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain T residue 295 PHE Chi-restraints excluded: chain T residue 405 GLN Chi-restraints excluded: chain T residue 414 ILE Chi-restraints excluded: chain T residue 441 ILE Chi-restraints excluded: chain T residue 464 ILE Chi-restraints excluded: chain U residue 295 PHE Chi-restraints excluded: chain U residue 405 GLN Chi-restraints excluded: chain U residue 414 ILE Chi-restraints excluded: chain U residue 441 ILE Chi-restraints excluded: chain U residue 464 ILE Chi-restraints excluded: chain V residue 295 PHE Chi-restraints excluded: chain V residue 405 GLN Chi-restraints excluded: chain V residue 414 ILE Chi-restraints excluded: chain V residue 441 ILE Chi-restraints excluded: chain V residue 464 ILE Chi-restraints excluded: chain W residue 295 PHE Chi-restraints excluded: chain W residue 405 GLN Chi-restraints excluded: chain W residue 414 ILE Chi-restraints excluded: chain W residue 441 ILE Chi-restraints excluded: chain W residue 464 ILE Chi-restraints excluded: chain X residue 295 PHE Chi-restraints excluded: chain X residue 414 ILE Chi-restraints excluded: chain X residue 441 ILE Chi-restraints excluded: chain X residue 464 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 106 optimal weight: 4.9990 chunk 236 optimal weight: 1.9990 chunk 426 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 435 optimal weight: 0.5980 chunk 453 optimal weight: 1.9990 chunk 326 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 458 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 344 optimal weight: 0.0770 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN B 405 GLN C 405 GLN ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 405 GLN P 405 GLN S 405 GLN T 405 GLN ** U 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 405 GLN X 405 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.086052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.071531 restraints weight = 127380.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.073474 restraints weight = 67765.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.074815 restraints weight = 46932.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.075613 restraints weight = 37349.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.076053 restraints weight = 32382.784| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 43806 Z= 0.139 Angle : 0.665 15.624 59167 Z= 0.329 Chirality : 0.044 0.159 6840 Planarity : 0.004 0.044 7657 Dihedral : 4.583 42.222 6169 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.28 % Allowed : 21.16 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.06 (0.11), residues: 5568 helix: 1.01 (0.11), residues: 2256 sheet: -2.40 (0.14), residues: 1152 loop : -1.47 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 417 TYR 0.015 0.001 TYR P 275 PHE 0.014 0.002 PHE A 392 HIS 0.003 0.001 HIS B 439 Details of bonding type rmsd covalent geometry : bond 0.00314 (43806) covalent geometry : angle 0.66473 (59167) hydrogen bonds : bond 0.02801 ( 2040) hydrogen bonds : angle 4.66957 ( 5904) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 741 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 PHE cc_start: 0.7162 (OUTLIER) cc_final: 0.6311 (p90) REVERT: A 379 MET cc_start: 0.8675 (mmm) cc_final: 0.7647 (mmm) REVERT: A 396 MET cc_start: 0.8182 (mmm) cc_final: 0.7617 (mmt) REVERT: A 460 ASN cc_start: 0.8377 (t0) cc_final: 0.7965 (t0) REVERT: B 295 PHE cc_start: 0.7149 (OUTLIER) cc_final: 0.6353 (p90) REVERT: B 379 MET cc_start: 0.8699 (mmm) cc_final: 0.7638 (mmm) REVERT: B 416 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8176 (tp30) REVERT: B 460 ASN cc_start: 0.8392 (t0) cc_final: 0.8005 (t0) REVERT: C 239 GLU cc_start: 0.8561 (mp0) cc_final: 0.8140 (mp0) REVERT: C 270 GLU cc_start: 0.7273 (tp30) cc_final: 0.6944 (tp30) REVERT: C 273 MET cc_start: 0.6982 (mtp) cc_final: 0.6739 (mtp) REVERT: C 295 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.6255 (p90) REVERT: C 353 MET cc_start: 0.7479 (tpp) cc_final: 0.7076 (ttt) REVERT: C 379 MET cc_start: 0.8707 (mmm) cc_final: 0.7660 (mmm) REVERT: C 396 MET cc_start: 0.8203 (mmm) cc_final: 0.7657 (mmt) REVERT: C 430 MET cc_start: 0.8250 (mmm) cc_final: 0.7884 (mmm) REVERT: C 460 ASN cc_start: 0.8365 (t0) cc_final: 0.7955 (t0) REVERT: D 270 GLU cc_start: 0.7407 (tp30) cc_final: 0.6980 (tp30) REVERT: D 273 MET cc_start: 0.7073 (mtp) cc_final: 0.6813 (mtp) REVERT: D 295 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.6330 (p90) REVERT: D 353 MET cc_start: 0.7727 (ttt) cc_final: 0.7495 (ttt) REVERT: D 379 MET cc_start: 0.8648 (mmm) cc_final: 0.7600 (mmm) REVERT: D 396 MET cc_start: 0.8171 (mmm) cc_final: 0.7658 (mmt) REVERT: D 430 MET cc_start: 0.8216 (mmm) cc_final: 0.7957 (mmm) REVERT: D 460 ASN cc_start: 0.8350 (t0) cc_final: 0.7964 (t0) REVERT: E 239 GLU cc_start: 0.8515 (mp0) cc_final: 0.8272 (mp0) REVERT: E 295 PHE cc_start: 0.7087 (OUTLIER) cc_final: 0.6303 (p90) REVERT: E 353 MET cc_start: 0.7575 (ttt) cc_final: 0.7328 (ttt) REVERT: E 379 MET cc_start: 0.8762 (mmm) cc_final: 0.7795 (mmm) REVERT: E 396 MET cc_start: 0.8183 (mmm) cc_final: 0.7649 (mmt) REVERT: E 422 LYS cc_start: 0.9056 (mmmm) cc_final: 0.8843 (tppp) REVERT: E 430 MET cc_start: 0.8344 (mmm) cc_final: 0.8093 (mmm) REVERT: E 460 ASN cc_start: 0.8348 (t0) cc_final: 0.7923 (t0) REVERT: F 239 GLU cc_start: 0.8537 (mp0) cc_final: 0.8114 (mp0) REVERT: F 247 MET cc_start: 0.9010 (ppp) cc_final: 0.8562 (ppp) REVERT: F 295 PHE cc_start: 0.7198 (OUTLIER) cc_final: 0.6388 (p90) REVERT: F 344 VAL cc_start: 0.8925 (OUTLIER) cc_final: 0.8695 (t) REVERT: F 354 ASN cc_start: 0.8078 (m-40) cc_final: 0.7774 (m110) REVERT: F 379 MET cc_start: 0.8777 (mmm) cc_final: 0.7614 (mmm) REVERT: F 416 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8187 (tp30) REVERT: F 422 LYS cc_start: 0.9086 (mmmm) cc_final: 0.8884 (tppp) REVERT: F 460 ASN cc_start: 0.8277 (t0) cc_final: 0.7906 (t0) REVERT: G 273 MET cc_start: 0.6892 (mtp) cc_final: 0.6643 (mtp) REVERT: G 295 PHE cc_start: 0.7104 (OUTLIER) cc_final: 0.6269 (p90) REVERT: G 379 MET cc_start: 0.8699 (mmm) cc_final: 0.7661 (mmm) REVERT: G 396 MET cc_start: 0.8178 (mmm) cc_final: 0.7652 (mmt) REVERT: G 460 ASN cc_start: 0.8390 (t0) cc_final: 0.7999 (t0) REVERT: H 239 GLU cc_start: 0.8502 (mp0) cc_final: 0.8273 (mp0) REVERT: H 247 MET cc_start: 0.9003 (ppp) cc_final: 0.8549 (ppp) REVERT: H 273 MET cc_start: 0.6997 (mtp) cc_final: 0.6785 (mtp) REVERT: H 295 PHE cc_start: 0.7183 (OUTLIER) cc_final: 0.6531 (p90) REVERT: H 353 MET cc_start: 0.7763 (ttt) cc_final: 0.7520 (ttt) REVERT: H 379 MET cc_start: 0.8639 (mmm) cc_final: 0.7649 (mmm) REVERT: H 416 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8168 (tp30) REVERT: H 422 LYS cc_start: 0.9064 (mmmm) cc_final: 0.8858 (tppp) REVERT: H 460 ASN cc_start: 0.8327 (t0) cc_final: 0.7903 (t0) REVERT: I 239 GLU cc_start: 0.8566 (mp0) cc_final: 0.8144 (mp0) REVERT: I 247 MET cc_start: 0.9008 (ppp) cc_final: 0.8547 (ppp) REVERT: I 295 PHE cc_start: 0.7164 (OUTLIER) cc_final: 0.6441 (p90) REVERT: I 379 MET cc_start: 0.8759 (mmm) cc_final: 0.7719 (mmm) REVERT: I 416 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8200 (tp30) REVERT: I 422 LYS cc_start: 0.9058 (mmmm) cc_final: 0.8845 (tppp) REVERT: I 460 ASN cc_start: 0.8387 (t0) cc_final: 0.8013 (t0) REVERT: J 247 MET cc_start: 0.9048 (ppp) cc_final: 0.8582 (ppp) REVERT: J 273 MET cc_start: 0.6864 (mtp) cc_final: 0.6625 (mtp) REVERT: J 295 PHE cc_start: 0.7161 (OUTLIER) cc_final: 0.6362 (p90) REVERT: J 379 MET cc_start: 0.8744 (mmm) cc_final: 0.7680 (mmm) REVERT: J 396 MET cc_start: 0.8184 (mmm) cc_final: 0.7649 (mmt) REVERT: J 460 ASN cc_start: 0.8362 (t0) cc_final: 0.7974 (t0) REVERT: K 239 GLU cc_start: 0.8483 (mp0) cc_final: 0.8243 (mp0) REVERT: K 295 PHE cc_start: 0.7169 (OUTLIER) cc_final: 0.6450 (p90) REVERT: K 353 MET cc_start: 0.7680 (ttt) cc_final: 0.7435 (ttt) REVERT: K 379 MET cc_start: 0.8737 (mmm) cc_final: 0.7772 (mmm) REVERT: K 396 MET cc_start: 0.8194 (mmm) cc_final: 0.7667 (mmt) REVERT: K 416 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8217 (tp30) REVERT: K 422 LYS cc_start: 0.9069 (mmmm) cc_final: 0.8865 (tppp) REVERT: K 430 MET cc_start: 0.7580 (mmm) cc_final: 0.7367 (mmm) REVERT: K 460 ASN cc_start: 0.8310 (t0) cc_final: 0.7910 (t0) REVERT: L 247 MET cc_start: 0.9013 (ppp) cc_final: 0.8604 (ppp) REVERT: L 295 PHE cc_start: 0.7107 (OUTLIER) cc_final: 0.6317 (p90) REVERT: L 354 ASN cc_start: 0.8096 (m-40) cc_final: 0.7807 (m110) REVERT: L 379 MET cc_start: 0.8614 (mmm) cc_final: 0.7557 (mmm) REVERT: L 416 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8197 (tp30) REVERT: L 422 LYS cc_start: 0.9056 (mmmm) cc_final: 0.8841 (tppp) REVERT: L 460 ASN cc_start: 0.8388 (t0) cc_final: 0.8013 (t0) REVERT: M 247 MET cc_start: 0.9140 (ppp) cc_final: 0.8395 (ppp) REVERT: M 295 PHE cc_start: 0.7193 (OUTLIER) cc_final: 0.6281 (p90) REVERT: M 353 MET cc_start: 0.7408 (tpp) cc_final: 0.6942 (ttt) REVERT: M 354 ASN cc_start: 0.8103 (m-40) cc_final: 0.7852 (m110) REVERT: M 379 MET cc_start: 0.8711 (mmm) cc_final: 0.7676 (mmm) REVERT: M 396 MET cc_start: 0.8205 (mmm) cc_final: 0.7601 (mmt) REVERT: M 422 LYS cc_start: 0.9052 (mmmm) cc_final: 0.8840 (tppp) REVERT: M 430 MET cc_start: 0.7574 (mmm) cc_final: 0.7356 (mmm) REVERT: M 460 ASN cc_start: 0.8406 (t0) cc_final: 0.7986 (t0) REVERT: N 295 PHE cc_start: 0.7135 (OUTLIER) cc_final: 0.6406 (p90) REVERT: N 354 ASN cc_start: 0.8072 (m-40) cc_final: 0.7767 (m110) REVERT: N 379 MET cc_start: 0.8693 (mmm) cc_final: 0.7624 (mmm) REVERT: N 416 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8222 (tp30) REVERT: N 422 LYS cc_start: 0.9068 (mmmm) cc_final: 0.8863 (tppp) REVERT: N 460 ASN cc_start: 0.8330 (t0) cc_final: 0.7933 (t0) REVERT: O 239 GLU cc_start: 0.8613 (mp0) cc_final: 0.8187 (mp0) REVERT: O 295 PHE cc_start: 0.7103 (OUTLIER) cc_final: 0.6204 (p90) REVERT: O 379 MET cc_start: 0.8660 (mmm) cc_final: 0.7632 (mmm) REVERT: O 396 MET cc_start: 0.8217 (mmm) cc_final: 0.7689 (mmt) REVERT: O 422 LYS cc_start: 0.9108 (mmmm) cc_final: 0.8819 (tppp) REVERT: O 430 MET cc_start: 0.8328 (mmm) cc_final: 0.7969 (mmm) REVERT: O 460 ASN cc_start: 0.8342 (t0) cc_final: 0.7971 (t0) REVERT: P 270 GLU cc_start: 0.7701 (tp30) cc_final: 0.7159 (tp30) REVERT: P 295 PHE cc_start: 0.7169 (OUTLIER) cc_final: 0.6375 (p90) REVERT: P 353 MET cc_start: 0.7749 (ttt) cc_final: 0.7525 (ttt) REVERT: P 379 MET cc_start: 0.8659 (mmm) cc_final: 0.7625 (mmm) REVERT: P 396 MET cc_start: 0.8206 (mmm) cc_final: 0.7654 (mmt) REVERT: P 460 ASN cc_start: 0.8298 (t0) cc_final: 0.7899 (t0) REVERT: Q 273 MET cc_start: 0.6991 (mtp) cc_final: 0.6748 (mtp) REVERT: Q 295 PHE cc_start: 0.7126 (OUTLIER) cc_final: 0.6343 (p90) REVERT: Q 379 MET cc_start: 0.8692 (mmm) cc_final: 0.7655 (mmm) REVERT: Q 460 ASN cc_start: 0.8296 (t0) cc_final: 0.7910 (t0) REVERT: R 239 GLU cc_start: 0.8555 (mp0) cc_final: 0.8134 (mp0) REVERT: R 273 MET cc_start: 0.6905 (mtp) cc_final: 0.6697 (mtp) REVERT: R 295 PHE cc_start: 0.7145 (OUTLIER) cc_final: 0.6303 (p90) REVERT: R 344 VAL cc_start: 0.8991 (OUTLIER) cc_final: 0.8771 (t) REVERT: R 379 MET cc_start: 0.8750 (mmm) cc_final: 0.7612 (mmm) REVERT: R 396 MET cc_start: 0.8199 (mmm) cc_final: 0.7699 (mmt) REVERT: R 416 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8217 (tp30) REVERT: R 430 MET cc_start: 0.8311 (mmm) cc_final: 0.7968 (mmm) REVERT: R 460 ASN cc_start: 0.8337 (t0) cc_final: 0.7997 (t0) REVERT: S 295 PHE cc_start: 0.7111 (OUTLIER) cc_final: 0.6258 (p90) REVERT: S 353 MET cc_start: 0.7480 (tpp) cc_final: 0.7016 (ttt) REVERT: S 354 ASN cc_start: 0.8101 (m-40) cc_final: 0.7863 (m110) REVERT: S 379 MET cc_start: 0.8597 (mmm) cc_final: 0.7555 (mmm) REVERT: S 460 ASN cc_start: 0.8361 (t0) cc_final: 0.7948 (t0) REVERT: T 295 PHE cc_start: 0.7175 (OUTLIER) cc_final: 0.6358 (p90) REVERT: T 379 MET cc_start: 0.8751 (mmm) cc_final: 0.7696 (mmm) REVERT: T 422 LYS cc_start: 0.9063 (mmmm) cc_final: 0.8844 (tppp) REVERT: T 460 ASN cc_start: 0.8391 (t0) cc_final: 0.7977 (t0) REVERT: U 239 GLU cc_start: 0.8574 (mp0) cc_final: 0.8217 (mp0) REVERT: U 270 GLU cc_start: 0.7765 (tp30) cc_final: 0.7187 (tp30) REVERT: U 295 PHE cc_start: 0.7125 (OUTLIER) cc_final: 0.6218 (p90) REVERT: U 379 MET cc_start: 0.8690 (mmm) cc_final: 0.7634 (mmm) REVERT: U 396 MET cc_start: 0.8219 (mmm) cc_final: 0.7673 (mmt) REVERT: U 422 LYS cc_start: 0.9056 (mmmm) cc_final: 0.8841 (tppp) REVERT: U 460 ASN cc_start: 0.8358 (t0) cc_final: 0.7973 (t0) REVERT: V 295 PHE cc_start: 0.7181 (OUTLIER) cc_final: 0.6359 (p90) REVERT: V 353 MET cc_start: 0.7461 (tpp) cc_final: 0.6981 (ttt) REVERT: V 354 ASN cc_start: 0.8108 (m-40) cc_final: 0.7863 (m110) REVERT: V 379 MET cc_start: 0.8658 (mmm) cc_final: 0.7621 (mmm) REVERT: V 396 MET cc_start: 0.8206 (mmm) cc_final: 0.7695 (mmt) REVERT: V 422 LYS cc_start: 0.9036 (mmmm) cc_final: 0.8822 (tppp) REVERT: V 460 ASN cc_start: 0.8354 (t0) cc_final: 0.7969 (t0) REVERT: W 247 MET cc_start: 0.8981 (ppp) cc_final: 0.8504 (ppp) REVERT: W 295 PHE cc_start: 0.7083 (OUTLIER) cc_final: 0.6209 (p90) REVERT: W 379 MET cc_start: 0.8644 (mmm) cc_final: 0.7602 (mmm) REVERT: W 396 MET cc_start: 0.8185 (mmm) cc_final: 0.7660 (mmt) REVERT: W 422 LYS cc_start: 0.9045 (mmmm) cc_final: 0.8820 (tppp) REVERT: W 430 MET cc_start: 0.8365 (mmm) cc_final: 0.8109 (mmm) REVERT: W 460 ASN cc_start: 0.8356 (t0) cc_final: 0.7926 (t0) REVERT: X 239 GLU cc_start: 0.8570 (mp0) cc_final: 0.8161 (mp0) REVERT: X 295 PHE cc_start: 0.7170 (OUTLIER) cc_final: 0.6329 (p90) REVERT: X 353 MET cc_start: 0.7695 (ttt) cc_final: 0.7446 (ttt) REVERT: X 379 MET cc_start: 0.8766 (mmm) cc_final: 0.7700 (mmm) REVERT: X 396 MET cc_start: 0.8203 (mmm) cc_final: 0.7690 (mmt) REVERT: X 422 LYS cc_start: 0.9043 (mmmm) cc_final: 0.8816 (tppp) REVERT: X 430 MET cc_start: 0.8290 (mmm) cc_final: 0.7987 (mmm) REVERT: X 460 ASN cc_start: 0.8368 (t0) cc_final: 0.7967 (t0) outliers start: 148 outliers final: 96 residues processed: 884 average time/residue: 0.2263 time to fit residues: 340.6647 Evaluate side-chains 814 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 692 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 405 GLN Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 405 GLN Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 295 PHE Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 405 GLN Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 295 PHE Chi-restraints excluded: chain E residue 405 GLN Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 405 GLN Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 441 ILE Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain G residue 295 PHE Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 405 GLN Chi-restraints excluded: chain H residue 414 ILE Chi-restraints excluded: chain H residue 441 ILE Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 405 GLN Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 441 ILE Chi-restraints excluded: chain I residue 464 ILE Chi-restraints excluded: chain J residue 295 PHE Chi-restraints excluded: chain J residue 405 GLN Chi-restraints excluded: chain J residue 414 ILE Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain K residue 295 PHE Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 441 ILE Chi-restraints excluded: chain K residue 464 ILE Chi-restraints excluded: chain L residue 295 PHE Chi-restraints excluded: chain L residue 405 GLN Chi-restraints excluded: chain L residue 414 ILE Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 464 ILE Chi-restraints excluded: chain M residue 295 PHE Chi-restraints excluded: chain M residue 414 ILE Chi-restraints excluded: chain M residue 441 ILE Chi-restraints excluded: chain M residue 464 ILE Chi-restraints excluded: chain N residue 295 PHE Chi-restraints excluded: chain N residue 414 ILE Chi-restraints excluded: chain N residue 441 ILE Chi-restraints excluded: chain N residue 464 ILE Chi-restraints excluded: chain O residue 295 PHE Chi-restraints excluded: chain O residue 405 GLN Chi-restraints excluded: chain O residue 414 ILE Chi-restraints excluded: chain O residue 441 ILE Chi-restraints excluded: chain O residue 464 ILE Chi-restraints excluded: chain P residue 295 PHE Chi-restraints excluded: chain P residue 405 GLN Chi-restraints excluded: chain P residue 414 ILE Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 464 ILE Chi-restraints excluded: chain Q residue 242 VAL Chi-restraints excluded: chain Q residue 295 PHE Chi-restraints excluded: chain Q residue 414 ILE Chi-restraints excluded: chain Q residue 441 ILE Chi-restraints excluded: chain Q residue 464 ILE Chi-restraints excluded: chain R residue 295 PHE Chi-restraints excluded: chain R residue 344 VAL Chi-restraints excluded: chain R residue 405 GLN Chi-restraints excluded: chain R residue 414 ILE Chi-restraints excluded: chain R residue 441 ILE Chi-restraints excluded: chain R residue 464 ILE Chi-restraints excluded: chain S residue 295 PHE Chi-restraints excluded: chain S residue 405 GLN Chi-restraints excluded: chain S residue 414 ILE Chi-restraints excluded: chain S residue 431 MET Chi-restraints excluded: chain S residue 441 ILE Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain T residue 242 VAL Chi-restraints excluded: chain T residue 295 PHE Chi-restraints excluded: chain T residue 405 GLN Chi-restraints excluded: chain T residue 414 ILE Chi-restraints excluded: chain T residue 441 ILE Chi-restraints excluded: chain T residue 464 ILE Chi-restraints excluded: chain U residue 295 PHE Chi-restraints excluded: chain U residue 405 GLN Chi-restraints excluded: chain U residue 414 ILE Chi-restraints excluded: chain U residue 441 ILE Chi-restraints excluded: chain U residue 464 ILE Chi-restraints excluded: chain V residue 295 PHE Chi-restraints excluded: chain V residue 405 GLN Chi-restraints excluded: chain V residue 414 ILE Chi-restraints excluded: chain V residue 441 ILE Chi-restraints excluded: chain V residue 464 ILE Chi-restraints excluded: chain W residue 242 VAL Chi-restraints excluded: chain W residue 295 PHE Chi-restraints excluded: chain W residue 405 GLN Chi-restraints excluded: chain W residue 414 ILE Chi-restraints excluded: chain W residue 441 ILE Chi-restraints excluded: chain W residue 464 ILE Chi-restraints excluded: chain X residue 295 PHE Chi-restraints excluded: chain X residue 405 GLN Chi-restraints excluded: chain X residue 414 ILE Chi-restraints excluded: chain X residue 441 ILE Chi-restraints excluded: chain X residue 464 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 175 optimal weight: 0.0370 chunk 284 optimal weight: 1.9990 chunk 486 optimal weight: 2.9990 chunk 524 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 241 optimal weight: 7.9990 chunk 504 optimal weight: 2.9990 chunk 520 optimal weight: 10.0000 chunk 490 optimal weight: 0.8980 chunk 491 optimal weight: 0.9990 chunk 163 optimal weight: 10.0000 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 405 GLN ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 405 GLN ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 405 GLN T 405 GLN ** U 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 405 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.086498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.071620 restraints weight = 128304.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.073630 restraints weight = 69403.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.074904 restraints weight = 48611.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.075639 restraints weight = 39161.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.076194 restraints weight = 34689.329| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 43806 Z= 0.132 Angle : 0.682 13.988 59167 Z= 0.336 Chirality : 0.045 0.139 6840 Planarity : 0.004 0.042 7657 Dihedral : 4.579 42.004 6169 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.01 % Allowed : 21.25 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.00 (0.11), residues: 5568 helix: 1.02 (0.11), residues: 2256 sheet: -2.35 (0.14), residues: 1152 loop : -1.41 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 417 TYR 0.015 0.001 TYR O 275 PHE 0.013 0.002 PHE S 392 HIS 0.002 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00300 (43806) covalent geometry : angle 0.68219 (59167) hydrogen bonds : bond 0.02789 ( 2040) hydrogen bonds : angle 4.68050 ( 5904) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 733 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 MET cc_start: 0.7060 (mtp) cc_final: 0.6832 (mtp) REVERT: A 295 PHE cc_start: 0.7135 (OUTLIER) cc_final: 0.6335 (p90) REVERT: A 353 MET cc_start: 0.7549 (ttt) cc_final: 0.6986 (ttm) REVERT: A 379 MET cc_start: 0.8700 (mmm) cc_final: 0.7648 (mmm) REVERT: A 396 MET cc_start: 0.8200 (mmm) cc_final: 0.7628 (mmt) REVERT: A 460 ASN cc_start: 0.8269 (t0) cc_final: 0.7829 (t0) REVERT: B 270 GLU cc_start: 0.7219 (tp30) cc_final: 0.6455 (tm-30) REVERT: B 295 PHE cc_start: 0.7135 (OUTLIER) cc_final: 0.6333 (p90) REVERT: B 379 MET cc_start: 0.8755 (mmm) cc_final: 0.7695 (mmm) REVERT: B 396 MET cc_start: 0.8166 (mmm) cc_final: 0.7664 (mmt) REVERT: B 416 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8147 (tp30) REVERT: B 430 MET cc_start: 0.8126 (mmp) cc_final: 0.7090 (mmt) REVERT: B 460 ASN cc_start: 0.8268 (t0) cc_final: 0.7833 (t0) REVERT: C 239 GLU cc_start: 0.8605 (mp0) cc_final: 0.8174 (mp0) REVERT: C 247 MET cc_start: 0.9102 (ppp) cc_final: 0.8524 (ppp) REVERT: C 295 PHE cc_start: 0.6965 (OUTLIER) cc_final: 0.6032 (p90) REVERT: C 353 MET cc_start: 0.7380 (tpp) cc_final: 0.6980 (ttt) REVERT: C 379 MET cc_start: 0.8761 (mmm) cc_final: 0.7703 (mmm) REVERT: C 396 MET cc_start: 0.8212 (mmm) cc_final: 0.7613 (mmt) REVERT: C 405 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7927 (pt0) REVERT: C 460 ASN cc_start: 0.8296 (t0) cc_final: 0.7849 (t0) REVERT: D 247 MET cc_start: 0.9007 (ppp) cc_final: 0.8604 (ppp) REVERT: D 270 GLU cc_start: 0.7351 (tp30) cc_final: 0.6890 (tp30) REVERT: D 295 PHE cc_start: 0.7077 (OUTLIER) cc_final: 0.6283 (p90) REVERT: D 379 MET cc_start: 0.8713 (mmm) cc_final: 0.7654 (mmm) REVERT: D 396 MET cc_start: 0.8197 (mmm) cc_final: 0.7614 (mmt) REVERT: D 430 MET cc_start: 0.8240 (mmm) cc_final: 0.7910 (mmm) REVERT: D 460 ASN cc_start: 0.8237 (t0) cc_final: 0.7815 (t0) REVERT: E 270 GLU cc_start: 0.7654 (tp30) cc_final: 0.7149 (tp30) REVERT: E 273 MET cc_start: 0.7048 (mtp) cc_final: 0.6829 (mtp) REVERT: E 295 PHE cc_start: 0.7126 (OUTLIER) cc_final: 0.6350 (p90) REVERT: E 379 MET cc_start: 0.8799 (mmm) cc_final: 0.7836 (mmm) REVERT: E 396 MET cc_start: 0.8181 (mmm) cc_final: 0.7599 (mmt) REVERT: E 422 LYS cc_start: 0.9133 (mmmm) cc_final: 0.8761 (tppp) REVERT: E 460 ASN cc_start: 0.8284 (t0) cc_final: 0.7804 (t0) REVERT: F 247 MET cc_start: 0.9033 (ppp) cc_final: 0.8663 (ppp) REVERT: F 295 PHE cc_start: 0.7239 (OUTLIER) cc_final: 0.6505 (p90) REVERT: F 344 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8724 (t) REVERT: F 379 MET cc_start: 0.8832 (mmm) cc_final: 0.7692 (mmm) REVERT: F 396 MET cc_start: 0.8194 (mmm) cc_final: 0.7682 (mmt) REVERT: F 416 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8141 (tp30) REVERT: F 422 LYS cc_start: 0.9169 (mmmm) cc_final: 0.8803 (tppp) REVERT: F 460 ASN cc_start: 0.8204 (t0) cc_final: 0.7805 (t0) REVERT: G 295 PHE cc_start: 0.7095 (OUTLIER) cc_final: 0.6291 (p90) REVERT: G 379 MET cc_start: 0.8737 (mmm) cc_final: 0.7699 (mmm) REVERT: G 396 MET cc_start: 0.8203 (mmm) cc_final: 0.7964 (mmm) REVERT: G 430 MET cc_start: 0.7857 (mmm) cc_final: 0.7508 (mmm) REVERT: G 460 ASN cc_start: 0.8263 (t0) cc_final: 0.7828 (t0) REVERT: H 247 MET cc_start: 0.9026 (ppp) cc_final: 0.8654 (ppp) REVERT: H 295 PHE cc_start: 0.7203 (OUTLIER) cc_final: 0.6490 (p90) REVERT: H 353 MET cc_start: 0.7575 (ttt) cc_final: 0.7330 (ttt) REVERT: H 379 MET cc_start: 0.8709 (mmm) cc_final: 0.7715 (mmm) REVERT: H 396 MET cc_start: 0.8205 (mmm) cc_final: 0.7700 (mmt) REVERT: H 416 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8107 (tp30) REVERT: H 422 LYS cc_start: 0.9159 (mmmm) cc_final: 0.8804 (tppp) REVERT: H 460 ASN cc_start: 0.8256 (t0) cc_final: 0.7806 (t0) REVERT: I 295 PHE cc_start: 0.7181 (OUTLIER) cc_final: 0.6445 (p90) REVERT: I 379 MET cc_start: 0.8779 (mmm) cc_final: 0.7717 (mmm) REVERT: I 396 MET cc_start: 0.8206 (mmm) cc_final: 0.7696 (mmt) REVERT: I 416 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8121 (tp30) REVERT: I 422 LYS cc_start: 0.9155 (mmmm) cc_final: 0.8796 (tppp) REVERT: I 460 ASN cc_start: 0.8223 (t0) cc_final: 0.7802 (t0) REVERT: J 295 PHE cc_start: 0.7116 (OUTLIER) cc_final: 0.6340 (p90) REVERT: J 379 MET cc_start: 0.8796 (mmm) cc_final: 0.7742 (mmm) REVERT: J 396 MET cc_start: 0.8159 (mmm) cc_final: 0.7916 (mmm) REVERT: J 430 MET cc_start: 0.7849 (mmm) cc_final: 0.7501 (mmm) REVERT: J 460 ASN cc_start: 0.8269 (t0) cc_final: 0.7817 (t0) REVERT: K 239 GLU cc_start: 0.8566 (mp0) cc_final: 0.8343 (mp0) REVERT: K 270 GLU cc_start: 0.7609 (tp30) cc_final: 0.7017 (tp30) REVERT: K 295 PHE cc_start: 0.7173 (OUTLIER) cc_final: 0.6442 (p90) REVERT: K 310 GLN cc_start: 0.8076 (mt0) cc_final: 0.7797 (mp10) REVERT: K 379 MET cc_start: 0.8785 (mmm) cc_final: 0.7818 (mmm) REVERT: K 396 MET cc_start: 0.8173 (mmm) cc_final: 0.7629 (mmt) REVERT: K 416 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8156 (tp30) REVERT: K 422 LYS cc_start: 0.9159 (mmmm) cc_final: 0.8799 (tppp) REVERT: K 460 ASN cc_start: 0.8258 (t0) cc_final: 0.7817 (t0) REVERT: L 295 PHE cc_start: 0.7088 (OUTLIER) cc_final: 0.6291 (p90) REVERT: L 354 ASN cc_start: 0.8056 (m-40) cc_final: 0.7748 (m110) REVERT: L 379 MET cc_start: 0.8657 (mmm) cc_final: 0.7576 (mmm) REVERT: L 396 MET cc_start: 0.8187 (mmm) cc_final: 0.7667 (mmt) REVERT: L 416 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8117 (tp30) REVERT: L 422 LYS cc_start: 0.9152 (mmmm) cc_final: 0.8793 (tppp) REVERT: L 460 ASN cc_start: 0.8360 (t0) cc_final: 0.7914 (t0) REVERT: M 270 GLU cc_start: 0.7646 (tp30) cc_final: 0.7059 (tp30) REVERT: M 295 PHE cc_start: 0.7161 (OUTLIER) cc_final: 0.6255 (p90) REVERT: M 353 MET cc_start: 0.7283 (tpp) cc_final: 0.6815 (ttt) REVERT: M 354 ASN cc_start: 0.8118 (m-40) cc_final: 0.7877 (m110) REVERT: M 379 MET cc_start: 0.8729 (mmm) cc_final: 0.7681 (mmm) REVERT: M 396 MET cc_start: 0.8218 (mmm) cc_final: 0.7967 (mmm) REVERT: M 422 LYS cc_start: 0.9147 (mmmm) cc_final: 0.8776 (tppp) REVERT: M 460 ASN cc_start: 0.8252 (t0) cc_final: 0.7804 (t0) REVERT: N 247 MET cc_start: 0.9045 (ppp) cc_final: 0.8587 (ppp) REVERT: N 295 PHE cc_start: 0.7210 (OUTLIER) cc_final: 0.6478 (p90) REVERT: N 354 ASN cc_start: 0.8070 (m-40) cc_final: 0.7763 (m110) REVERT: N 379 MET cc_start: 0.8734 (mmm) cc_final: 0.7687 (mmm) REVERT: N 396 MET cc_start: 0.8186 (mmm) cc_final: 0.7680 (mmt) REVERT: N 416 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8138 (tp30) REVERT: N 422 LYS cc_start: 0.9153 (mmmm) cc_final: 0.8805 (tppp) REVERT: N 460 ASN cc_start: 0.8263 (t0) cc_final: 0.7845 (t0) REVERT: O 295 PHE cc_start: 0.7072 (OUTLIER) cc_final: 0.6176 (p90) REVERT: O 353 MET cc_start: 0.7361 (tpp) cc_final: 0.6838 (ttt) REVERT: O 379 MET cc_start: 0.8734 (mmm) cc_final: 0.7728 (mmm) REVERT: O 396 MET cc_start: 0.8233 (mmm) cc_final: 0.7647 (mmt) REVERT: O 422 LYS cc_start: 0.9121 (mmmm) cc_final: 0.8841 (tppp) REVERT: O 430 MET cc_start: 0.8330 (mmm) cc_final: 0.7970 (mmm) REVERT: O 460 ASN cc_start: 0.8200 (t0) cc_final: 0.7808 (t0) REVERT: P 270 GLU cc_start: 0.7675 (tp30) cc_final: 0.7058 (tp30) REVERT: P 295 PHE cc_start: 0.7189 (OUTLIER) cc_final: 0.6464 (p90) REVERT: P 379 MET cc_start: 0.8719 (mmm) cc_final: 0.7678 (mmm) REVERT: P 396 MET cc_start: 0.8210 (mmm) cc_final: 0.7622 (mmt) REVERT: P 460 ASN cc_start: 0.8290 (t0) cc_final: 0.7834 (t0) REVERT: Q 295 PHE cc_start: 0.7080 (OUTLIER) cc_final: 0.6308 (p90) REVERT: Q 379 MET cc_start: 0.8770 (mmm) cc_final: 0.7729 (mmm) REVERT: Q 396 MET cc_start: 0.8194 (mmm) cc_final: 0.7700 (mmt) REVERT: Q 460 ASN cc_start: 0.8274 (t0) cc_final: 0.7832 (t0) REVERT: R 239 GLU cc_start: 0.8585 (mp0) cc_final: 0.8156 (mp0) REVERT: R 295 PHE cc_start: 0.7090 (OUTLIER) cc_final: 0.6211 (p90) REVERT: R 344 VAL cc_start: 0.8948 (OUTLIER) cc_final: 0.8715 (t) REVERT: R 379 MET cc_start: 0.8758 (mmm) cc_final: 0.7594 (mmm) REVERT: R 396 MET cc_start: 0.8226 (mmm) cc_final: 0.7661 (mmt) REVERT: R 416 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8178 (tp30) REVERT: R 430 MET cc_start: 0.8298 (mmm) cc_final: 0.7949 (mmm) REVERT: R 460 ASN cc_start: 0.8285 (t0) cc_final: 0.7892 (t0) REVERT: S 295 PHE cc_start: 0.7116 (OUTLIER) cc_final: 0.6320 (p90) REVERT: S 353 MET cc_start: 0.7379 (tpp) cc_final: 0.6926 (ttt) REVERT: S 354 ASN cc_start: 0.8118 (m-40) cc_final: 0.7879 (m110) REVERT: S 379 MET cc_start: 0.8646 (mmm) cc_final: 0.7604 (mmm) REVERT: S 396 MET cc_start: 0.8181 (mmm) cc_final: 0.7909 (mmm) REVERT: S 460 ASN cc_start: 0.8283 (t0) cc_final: 0.7839 (t0) REVERT: T 295 PHE cc_start: 0.7143 (OUTLIER) cc_final: 0.6328 (p90) REVERT: T 353 MET cc_start: 0.7368 (tpp) cc_final: 0.6904 (ttt) REVERT: T 379 MET cc_start: 0.8808 (mmm) cc_final: 0.7749 (mmm) REVERT: T 396 MET cc_start: 0.8181 (mmm) cc_final: 0.7669 (mmt) REVERT: T 422 LYS cc_start: 0.9170 (mmmm) cc_final: 0.8800 (tppp) REVERT: T 460 ASN cc_start: 0.8274 (t0) cc_final: 0.7829 (t0) REVERT: U 239 GLU cc_start: 0.8607 (mp0) cc_final: 0.8261 (mp0) REVERT: U 295 PHE cc_start: 0.7100 (OUTLIER) cc_final: 0.6189 (p90) REVERT: U 379 MET cc_start: 0.8711 (mmm) cc_final: 0.7650 (mmm) REVERT: U 396 MET cc_start: 0.8205 (mmm) cc_final: 0.7626 (mmt) REVERT: U 422 LYS cc_start: 0.9147 (mmmm) cc_final: 0.8768 (tppp) REVERT: U 460 ASN cc_start: 0.8283 (t0) cc_final: 0.7864 (t0) REVERT: V 270 GLU cc_start: 0.8073 (tp30) cc_final: 0.7774 (tp30) REVERT: V 295 PHE cc_start: 0.7156 (OUTLIER) cc_final: 0.6255 (p90) REVERT: V 353 MET cc_start: 0.7361 (tpp) cc_final: 0.6875 (ttt) REVERT: V 354 ASN cc_start: 0.8127 (m-40) cc_final: 0.7891 (m110) REVERT: V 379 MET cc_start: 0.8735 (mmm) cc_final: 0.7691 (mmm) REVERT: V 396 MET cc_start: 0.8189 (mmm) cc_final: 0.7666 (mmt) REVERT: V 422 LYS cc_start: 0.9137 (mmmm) cc_final: 0.8753 (tppp) REVERT: V 460 ASN cc_start: 0.8256 (t0) cc_final: 0.7826 (t0) REVERT: W 270 GLU cc_start: 0.7660 (tp30) cc_final: 0.7156 (tp30) REVERT: W 295 PHE cc_start: 0.7080 (OUTLIER) cc_final: 0.6262 (p90) REVERT: W 353 MET cc_start: 0.7398 (tpp) cc_final: 0.6964 (ttt) REVERT: W 379 MET cc_start: 0.8697 (mmm) cc_final: 0.7658 (mmm) REVERT: W 396 MET cc_start: 0.8205 (mmm) cc_final: 0.7625 (mmt) REVERT: W 422 LYS cc_start: 0.9138 (mmmm) cc_final: 0.8759 (tppp) REVERT: W 460 ASN cc_start: 0.8296 (t0) cc_final: 0.7855 (t0) REVERT: X 239 GLU cc_start: 0.8603 (mp0) cc_final: 0.8197 (mp0) REVERT: X 295 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.6325 (p90) REVERT: X 353 MET cc_start: 0.7497 (ttt) cc_final: 0.7259 (ttt) REVERT: X 379 MET cc_start: 0.8790 (mmm) cc_final: 0.7731 (mmm) REVERT: X 396 MET cc_start: 0.8239 (mmm) cc_final: 0.7659 (mmt) REVERT: X 422 LYS cc_start: 0.9131 (mmmm) cc_final: 0.8722 (tppp) REVERT: X 430 MET cc_start: 0.8321 (mmm) cc_final: 0.7998 (mmm) REVERT: X 460 ASN cc_start: 0.8297 (t0) cc_final: 0.7864 (t0) outliers start: 136 outliers final: 97 residues processed: 846 average time/residue: 0.2408 time to fit residues: 347.0066 Evaluate side-chains 836 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 712 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 405 GLN Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 295 PHE Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 405 GLN Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 295 PHE Chi-restraints excluded: chain E residue 405 GLN Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 405 GLN Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 441 ILE Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain G residue 295 PHE Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 405 GLN Chi-restraints excluded: chain H residue 414 ILE Chi-restraints excluded: chain H residue 419 ILE Chi-restraints excluded: chain H residue 441 ILE Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 405 GLN Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 441 ILE Chi-restraints excluded: chain I residue 464 ILE Chi-restraints excluded: chain J residue 295 PHE Chi-restraints excluded: chain J residue 405 GLN Chi-restraints excluded: chain J residue 414 ILE Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain K residue 242 VAL Chi-restraints excluded: chain K residue 295 PHE Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 441 ILE Chi-restraints excluded: chain K residue 464 ILE Chi-restraints excluded: chain L residue 295 PHE Chi-restraints excluded: chain L residue 405 GLN Chi-restraints excluded: chain L residue 414 ILE Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 464 ILE Chi-restraints excluded: chain M residue 295 PHE Chi-restraints excluded: chain M residue 414 ILE Chi-restraints excluded: chain M residue 441 ILE Chi-restraints excluded: chain M residue 464 ILE Chi-restraints excluded: chain N residue 295 PHE Chi-restraints excluded: chain N residue 414 ILE Chi-restraints excluded: chain N residue 419 ILE Chi-restraints excluded: chain N residue 441 ILE Chi-restraints excluded: chain N residue 464 ILE Chi-restraints excluded: chain O residue 295 PHE Chi-restraints excluded: chain O residue 405 GLN Chi-restraints excluded: chain O residue 414 ILE Chi-restraints excluded: chain O residue 441 ILE Chi-restraints excluded: chain O residue 464 ILE Chi-restraints excluded: chain P residue 295 PHE Chi-restraints excluded: chain P residue 405 GLN Chi-restraints excluded: chain P residue 414 ILE Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 464 ILE Chi-restraints excluded: chain Q residue 242 VAL Chi-restraints excluded: chain Q residue 295 PHE Chi-restraints excluded: chain Q residue 414 ILE Chi-restraints excluded: chain Q residue 441 ILE Chi-restraints excluded: chain Q residue 464 ILE Chi-restraints excluded: chain R residue 295 PHE Chi-restraints excluded: chain R residue 344 VAL Chi-restraints excluded: chain R residue 405 GLN Chi-restraints excluded: chain R residue 414 ILE Chi-restraints excluded: chain R residue 441 ILE Chi-restraints excluded: chain R residue 464 ILE Chi-restraints excluded: chain S residue 295 PHE Chi-restraints excluded: chain S residue 414 ILE Chi-restraints excluded: chain S residue 441 ILE Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain T residue 242 VAL Chi-restraints excluded: chain T residue 295 PHE Chi-restraints excluded: chain T residue 405 GLN Chi-restraints excluded: chain T residue 414 ILE Chi-restraints excluded: chain T residue 419 ILE Chi-restraints excluded: chain T residue 441 ILE Chi-restraints excluded: chain T residue 464 ILE Chi-restraints excluded: chain U residue 295 PHE Chi-restraints excluded: chain U residue 414 ILE Chi-restraints excluded: chain U residue 441 ILE Chi-restraints excluded: chain U residue 464 ILE Chi-restraints excluded: chain V residue 295 PHE Chi-restraints excluded: chain V residue 405 GLN Chi-restraints excluded: chain V residue 414 ILE Chi-restraints excluded: chain V residue 441 ILE Chi-restraints excluded: chain V residue 464 ILE Chi-restraints excluded: chain W residue 242 VAL Chi-restraints excluded: chain W residue 295 PHE Chi-restraints excluded: chain W residue 405 GLN Chi-restraints excluded: chain W residue 414 ILE Chi-restraints excluded: chain W residue 441 ILE Chi-restraints excluded: chain W residue 464 ILE Chi-restraints excluded: chain X residue 295 PHE Chi-restraints excluded: chain X residue 405 GLN Chi-restraints excluded: chain X residue 414 ILE Chi-restraints excluded: chain X residue 441 ILE Chi-restraints excluded: chain X residue 464 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 497 optimal weight: 4.9990 chunk 520 optimal weight: 9.9990 chunk 286 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 392 optimal weight: 8.9990 chunk 296 optimal weight: 1.9990 chunk 406 optimal weight: 0.3980 chunk 42 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 405 GLN ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 405 GLN ** U 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 405 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.089479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.072520 restraints weight = 146622.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.075016 restraints weight = 73432.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.076508 restraints weight = 48087.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.077468 restraints weight = 36931.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.078128 restraints weight = 31301.630| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 43806 Z= 0.178 Angle : 0.706 16.059 59167 Z= 0.351 Chirality : 0.045 0.136 6840 Planarity : 0.005 0.049 7657 Dihedral : 4.680 44.133 6169 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.95 % Allowed : 22.05 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.08 (0.11), residues: 5568 helix: 0.96 (0.11), residues: 2256 sheet: -2.44 (0.14), residues: 1152 loop : -1.42 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG X 417 TYR 0.015 0.002 TYR R 275 PHE 0.016 0.002 PHE S 392 HIS 0.003 0.001 HIS B 439 Details of bonding type rmsd covalent geometry : bond 0.00395 (43806) covalent geometry : angle 0.70564 (59167) hydrogen bonds : bond 0.02895 ( 2040) hydrogen bonds : angle 4.74391 ( 5904) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 700 time to evaluate : 1.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.6404 (p90) REVERT: A 379 MET cc_start: 0.8761 (mmm) cc_final: 0.7718 (mmm) REVERT: A 396 MET cc_start: 0.8147 (mmm) cc_final: 0.7904 (mmm) REVERT: A 430 MET cc_start: 0.7307 (mtp) cc_final: 0.7017 (mtt) REVERT: A 460 ASN cc_start: 0.8416 (t0) cc_final: 0.7998 (t0) REVERT: B 247 MET cc_start: 0.9013 (ppp) cc_final: 0.8546 (ppp) REVERT: B 295 PHE cc_start: 0.7331 (OUTLIER) cc_final: 0.6425 (p90) REVERT: B 354 ASN cc_start: 0.8053 (m-40) cc_final: 0.7734 (m110) REVERT: B 379 MET cc_start: 0.8783 (mmm) cc_final: 0.7706 (mmm) REVERT: B 396 MET cc_start: 0.8078 (mmm) cc_final: 0.7598 (mmt) REVERT: B 416 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8270 (tp30) REVERT: B 460 ASN cc_start: 0.8428 (t0) cc_final: 0.8031 (t0) REVERT: C 239 GLU cc_start: 0.8509 (mp0) cc_final: 0.8130 (mp0) REVERT: C 247 MET cc_start: 0.9052 (ppp) cc_final: 0.8561 (ppp) REVERT: C 295 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.6361 (p90) REVERT: C 353 MET cc_start: 0.7558 (tpp) cc_final: 0.7192 (ttt) REVERT: C 379 MET cc_start: 0.8754 (mmm) cc_final: 0.7676 (mmm) REVERT: C 396 MET cc_start: 0.8082 (mmm) cc_final: 0.7798 (mmm) REVERT: C 430 MET cc_start: 0.7960 (mmm) cc_final: 0.6741 (mmp) REVERT: C 460 ASN cc_start: 0.8416 (t0) cc_final: 0.8024 (t0) REVERT: D 247 MET cc_start: 0.8985 (ppp) cc_final: 0.8562 (ppp) REVERT: D 270 GLU cc_start: 0.7602 (tp30) cc_final: 0.7155 (tp30) REVERT: D 295 PHE cc_start: 0.7334 (OUTLIER) cc_final: 0.6486 (p90) REVERT: D 379 MET cc_start: 0.8784 (mmm) cc_final: 0.7729 (mmm) REVERT: D 396 MET cc_start: 0.8163 (mmm) cc_final: 0.7608 (mmt) REVERT: D 430 MET cc_start: 0.8148 (mmm) cc_final: 0.7692 (mmm) REVERT: D 460 ASN cc_start: 0.8393 (t0) cc_final: 0.8003 (t0) REVERT: E 270 GLU cc_start: 0.7886 (tp30) cc_final: 0.7591 (tp30) REVERT: E 295 PHE cc_start: 0.7277 (OUTLIER) cc_final: 0.6460 (p90) REVERT: E 379 MET cc_start: 0.8857 (mmm) cc_final: 0.7879 (mmm) REVERT: E 396 MET cc_start: 0.8149 (mmm) cc_final: 0.7614 (mmt) REVERT: E 422 LYS cc_start: 0.8968 (mmmm) cc_final: 0.8707 (tppp) REVERT: E 460 ASN cc_start: 0.8350 (t0) cc_final: 0.7916 (t0) REVERT: F 295 PHE cc_start: 0.7402 (OUTLIER) cc_final: 0.6680 (p90) REVERT: F 344 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8681 (t) REVERT: F 354 ASN cc_start: 0.8059 (m-40) cc_final: 0.7746 (m110) REVERT: F 379 MET cc_start: 0.8882 (mmm) cc_final: 0.7721 (mmm) REVERT: F 396 MET cc_start: 0.8161 (mmm) cc_final: 0.7679 (mmt) REVERT: F 416 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8220 (tp30) REVERT: F 422 LYS cc_start: 0.9017 (mmmm) cc_final: 0.8756 (tppp) REVERT: F 460 ASN cc_start: 0.8366 (t0) cc_final: 0.8008 (t0) REVERT: G 295 PHE cc_start: 0.7337 (OUTLIER) cc_final: 0.6398 (p90) REVERT: G 379 MET cc_start: 0.8768 (mmm) cc_final: 0.7728 (mmm) REVERT: G 396 MET cc_start: 0.8180 (mmm) cc_final: 0.7937 (mmm) REVERT: G 430 MET cc_start: 0.7862 (mmm) cc_final: 0.7471 (mmm) REVERT: G 460 ASN cc_start: 0.8437 (t0) cc_final: 0.8027 (t0) REVERT: H 295 PHE cc_start: 0.7404 (OUTLIER) cc_final: 0.6686 (p90) REVERT: H 353 MET cc_start: 0.7885 (ttt) cc_final: 0.7669 (ttt) REVERT: H 379 MET cc_start: 0.8795 (mmm) cc_final: 0.7769 (mmm) REVERT: H 396 MET cc_start: 0.8083 (mmm) cc_final: 0.7612 (mmt) REVERT: H 416 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8210 (tp30) REVERT: H 422 LYS cc_start: 0.8977 (mmmm) cc_final: 0.8728 (tppp) REVERT: H 430 MET cc_start: 0.7836 (mmp) cc_final: 0.7152 (mmt) REVERT: H 460 ASN cc_start: 0.8440 (t0) cc_final: 0.8017 (t0) REVERT: I 295 PHE cc_start: 0.7396 (OUTLIER) cc_final: 0.6681 (p90) REVERT: I 354 ASN cc_start: 0.8065 (m-40) cc_final: 0.7743 (m110) REVERT: I 379 MET cc_start: 0.8849 (mmm) cc_final: 0.7797 (mmm) REVERT: I 396 MET cc_start: 0.8188 (mmm) cc_final: 0.7689 (mmt) REVERT: I 416 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8230 (tp30) REVERT: I 422 LYS cc_start: 0.9001 (mmmm) cc_final: 0.8747 (tppp) REVERT: I 460 ASN cc_start: 0.8433 (t0) cc_final: 0.8015 (t0) REVERT: J 295 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.6532 (p90) REVERT: J 379 MET cc_start: 0.8812 (mmm) cc_final: 0.7752 (mmm) REVERT: J 396 MET cc_start: 0.8083 (mmm) cc_final: 0.7828 (mmm) REVERT: J 430 MET cc_start: 0.7896 (mmm) cc_final: 0.7433 (mmm) REVERT: J 460 ASN cc_start: 0.8430 (t0) cc_final: 0.8016 (t0) REVERT: K 239 GLU cc_start: 0.8488 (mp0) cc_final: 0.8090 (mp0) REVERT: K 295 PHE cc_start: 0.7341 (OUTLIER) cc_final: 0.6580 (p90) REVERT: K 379 MET cc_start: 0.8825 (mmm) cc_final: 0.7844 (mmm) REVERT: K 396 MET cc_start: 0.8187 (mmm) cc_final: 0.7912 (mmm) REVERT: K 416 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8249 (tp30) REVERT: K 422 LYS cc_start: 0.8992 (mmmm) cc_final: 0.8750 (tppp) REVERT: K 460 ASN cc_start: 0.8395 (t0) cc_final: 0.8005 (t0) REVERT: L 295 PHE cc_start: 0.7321 (OUTLIER) cc_final: 0.6481 (p90) REVERT: L 354 ASN cc_start: 0.8077 (m-40) cc_final: 0.7775 (m110) REVERT: L 379 MET cc_start: 0.8741 (mmm) cc_final: 0.7657 (mmm) REVERT: L 396 MET cc_start: 0.8177 (mmm) cc_final: 0.7679 (mmt) REVERT: L 416 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8214 (tp30) REVERT: L 422 LYS cc_start: 0.8995 (mmmm) cc_final: 0.8739 (tppp) REVERT: L 430 MET cc_start: 0.7878 (mmp) cc_final: 0.7198 (mmt) REVERT: L 460 ASN cc_start: 0.8423 (t0) cc_final: 0.8003 (t0) REVERT: M 295 PHE cc_start: 0.7322 (OUTLIER) cc_final: 0.6455 (p90) REVERT: M 353 MET cc_start: 0.7529 (tpp) cc_final: 0.7140 (ttt) REVERT: M 354 ASN cc_start: 0.8136 (m-40) cc_final: 0.7898 (m110) REVERT: M 379 MET cc_start: 0.8808 (mmm) cc_final: 0.7767 (mmm) REVERT: M 422 LYS cc_start: 0.8996 (mmmm) cc_final: 0.8744 (tppp) REVERT: M 460 ASN cc_start: 0.8411 (t0) cc_final: 0.7992 (t0) REVERT: N 295 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.6584 (p90) REVERT: N 353 MET cc_start: 0.7719 (tpp) cc_final: 0.7111 (ttt) REVERT: N 354 ASN cc_start: 0.8079 (m-40) cc_final: 0.7845 (m110) REVERT: N 379 MET cc_start: 0.8786 (mmm) cc_final: 0.7728 (mmm) REVERT: N 396 MET cc_start: 0.8167 (mmm) cc_final: 0.7690 (mmt) REVERT: N 416 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8215 (tp30) REVERT: N 422 LYS cc_start: 0.8991 (mmmm) cc_final: 0.8746 (tppp) REVERT: N 460 ASN cc_start: 0.8451 (t0) cc_final: 0.8060 (t0) REVERT: O 247 MET cc_start: 0.8967 (ppp) cc_final: 0.8499 (ppp) REVERT: O 295 PHE cc_start: 0.7275 (OUTLIER) cc_final: 0.6338 (p90) REVERT: O 379 MET cc_start: 0.8815 (mmm) cc_final: 0.7747 (mmm) REVERT: O 396 MET cc_start: 0.8175 (mmm) cc_final: 0.7620 (mmt) REVERT: O 422 LYS cc_start: 0.9004 (mmmm) cc_final: 0.8682 (tppp) REVERT: O 460 ASN cc_start: 0.8380 (t0) cc_final: 0.7990 (t0) REVERT: P 270 GLU cc_start: 0.7747 (tp30) cc_final: 0.7244 (tp30) REVERT: P 295 PHE cc_start: 0.7356 (OUTLIER) cc_final: 0.6580 (p90) REVERT: P 379 MET cc_start: 0.8769 (mmm) cc_final: 0.7707 (mmm) REVERT: P 396 MET cc_start: 0.8201 (mmm) cc_final: 0.7616 (mmt) REVERT: P 460 ASN cc_start: 0.8402 (t0) cc_final: 0.8005 (t0) REVERT: Q 295 PHE cc_start: 0.7345 (OUTLIER) cc_final: 0.6517 (p90) REVERT: Q 379 MET cc_start: 0.8798 (mmm) cc_final: 0.7767 (mmm) REVERT: Q 396 MET cc_start: 0.8124 (mmm) cc_final: 0.7633 (mmt) REVERT: Q 460 ASN cc_start: 0.8446 (t0) cc_final: 0.8035 (t0) REVERT: R 239 GLU cc_start: 0.8495 (mp0) cc_final: 0.8090 (mp0) REVERT: R 295 PHE cc_start: 0.7290 (OUTLIER) cc_final: 0.6451 (p90) REVERT: R 344 VAL cc_start: 0.8910 (OUTLIER) cc_final: 0.8667 (t) REVERT: R 379 MET cc_start: 0.8846 (mmm) cc_final: 0.7678 (mmm) REVERT: R 396 MET cc_start: 0.8199 (mmm) cc_final: 0.7656 (mmt) REVERT: R 416 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8281 (tp30) REVERT: R 460 ASN cc_start: 0.8328 (t0) cc_final: 0.7997 (t0) REVERT: S 295 PHE cc_start: 0.7317 (OUTLIER) cc_final: 0.6323 (p90) REVERT: S 353 MET cc_start: 0.7542 (tpp) cc_final: 0.7243 (ttt) REVERT: S 354 ASN cc_start: 0.8137 (m-40) cc_final: 0.7897 (m110) REVERT: S 379 MET cc_start: 0.8722 (mmm) cc_final: 0.7680 (mmm) REVERT: S 396 MET cc_start: 0.8157 (mmm) cc_final: 0.7889 (mmm) REVERT: S 430 MET cc_start: 0.7279 (mtp) cc_final: 0.6997 (mtt) REVERT: S 460 ASN cc_start: 0.8402 (t0) cc_final: 0.7994 (t0) REVERT: T 295 PHE cc_start: 0.7334 (OUTLIER) cc_final: 0.6414 (p90) REVERT: T 353 MET cc_start: 0.7702 (tpp) cc_final: 0.7090 (ttt) REVERT: T 354 ASN cc_start: 0.8162 (m-40) cc_final: 0.7944 (m110) REVERT: T 379 MET cc_start: 0.8825 (mmm) cc_final: 0.7755 (mmm) REVERT: T 396 MET cc_start: 0.8114 (mmm) cc_final: 0.7639 (mmt) REVERT: T 422 LYS cc_start: 0.9000 (mmmm) cc_final: 0.8741 (tppp) REVERT: T 430 MET cc_start: 0.7826 (mmp) cc_final: 0.7200 (mmt) REVERT: T 460 ASN cc_start: 0.8435 (t0) cc_final: 0.8021 (t0) REVERT: U 239 GLU cc_start: 0.8492 (mp0) cc_final: 0.8107 (mp0) REVERT: U 247 MET cc_start: 0.9032 (ppp) cc_final: 0.8442 (ppp) REVERT: U 295 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.6430 (p90) REVERT: U 379 MET cc_start: 0.8776 (mmm) cc_final: 0.7691 (mmm) REVERT: U 396 MET cc_start: 0.8178 (mmm) cc_final: 0.7628 (mmt) REVERT: U 422 LYS cc_start: 0.8991 (mmmm) cc_final: 0.8720 (tppp) REVERT: U 460 ASN cc_start: 0.8410 (t0) cc_final: 0.8043 (t0) REVERT: V 295 PHE cc_start: 0.7310 (OUTLIER) cc_final: 0.6450 (p90) REVERT: V 353 MET cc_start: 0.7579 (tpp) cc_final: 0.7171 (ttt) REVERT: V 354 ASN cc_start: 0.8135 (m-40) cc_final: 0.7895 (m110) REVERT: V 379 MET cc_start: 0.8800 (mmm) cc_final: 0.7761 (mmm) REVERT: V 396 MET cc_start: 0.8168 (mmm) cc_final: 0.7649 (mmt) REVERT: V 422 LYS cc_start: 0.8982 (mmmm) cc_final: 0.8713 (tppp) REVERT: V 460 ASN cc_start: 0.8371 (t0) cc_final: 0.7994 (t0) REVERT: W 270 GLU cc_start: 0.7884 (tp30) cc_final: 0.7596 (tp30) REVERT: W 295 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.6381 (p90) REVERT: W 353 MET cc_start: 0.7683 (tpp) cc_final: 0.7131 (ttt) REVERT: W 379 MET cc_start: 0.8761 (mmm) cc_final: 0.7721 (mmm) REVERT: W 396 MET cc_start: 0.8090 (mmm) cc_final: 0.7587 (mmt) REVERT: W 422 LYS cc_start: 0.8984 (mmmm) cc_final: 0.8720 (tppp) REVERT: W 460 ASN cc_start: 0.8430 (t0) cc_final: 0.8034 (t0) REVERT: X 239 GLU cc_start: 0.8512 (mp0) cc_final: 0.8113 (mp0) REVERT: X 295 PHE cc_start: 0.7300 (OUTLIER) cc_final: 0.6456 (p90) REVERT: X 379 MET cc_start: 0.8812 (mmm) cc_final: 0.7740 (mmm) REVERT: X 396 MET cc_start: 0.8184 (mmm) cc_final: 0.7643 (mmt) REVERT: X 422 LYS cc_start: 0.8936 (mmmm) cc_final: 0.8688 (tppp) REVERT: X 460 ASN cc_start: 0.8471 (t0) cc_final: 0.8069 (t0) outliers start: 133 outliers final: 84 residues processed: 828 average time/residue: 0.2444 time to fit residues: 343.6389 Evaluate side-chains 803 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 693 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 405 GLN Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 295 PHE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 405 GLN Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 295 PHE Chi-restraints excluded: chain E residue 405 GLN Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 405 GLN Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 441 ILE Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain G residue 295 PHE Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 405 GLN Chi-restraints excluded: chain H residue 414 ILE Chi-restraints excluded: chain H residue 441 ILE Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 405 GLN Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 441 ILE Chi-restraints excluded: chain I residue 464 ILE Chi-restraints excluded: chain J residue 295 PHE Chi-restraints excluded: chain J residue 414 ILE Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain K residue 295 PHE Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 441 ILE Chi-restraints excluded: chain K residue 464 ILE Chi-restraints excluded: chain L residue 295 PHE Chi-restraints excluded: chain L residue 405 GLN Chi-restraints excluded: chain L residue 414 ILE Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 464 ILE Chi-restraints excluded: chain M residue 295 PHE Chi-restraints excluded: chain M residue 414 ILE Chi-restraints excluded: chain M residue 441 ILE Chi-restraints excluded: chain M residue 464 ILE Chi-restraints excluded: chain N residue 295 PHE Chi-restraints excluded: chain N residue 414 ILE Chi-restraints excluded: chain N residue 441 ILE Chi-restraints excluded: chain N residue 464 ILE Chi-restraints excluded: chain O residue 295 PHE Chi-restraints excluded: chain O residue 405 GLN Chi-restraints excluded: chain O residue 414 ILE Chi-restraints excluded: chain O residue 441 ILE Chi-restraints excluded: chain O residue 464 ILE Chi-restraints excluded: chain P residue 295 PHE Chi-restraints excluded: chain P residue 414 ILE Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 464 ILE Chi-restraints excluded: chain Q residue 295 PHE Chi-restraints excluded: chain Q residue 414 ILE Chi-restraints excluded: chain Q residue 441 ILE Chi-restraints excluded: chain Q residue 464 ILE Chi-restraints excluded: chain R residue 295 PHE Chi-restraints excluded: chain R residue 344 VAL Chi-restraints excluded: chain R residue 405 GLN Chi-restraints excluded: chain R residue 414 ILE Chi-restraints excluded: chain R residue 441 ILE Chi-restraints excluded: chain R residue 464 ILE Chi-restraints excluded: chain S residue 295 PHE Chi-restraints excluded: chain S residue 414 ILE Chi-restraints excluded: chain S residue 441 ILE Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain T residue 295 PHE Chi-restraints excluded: chain T residue 405 GLN Chi-restraints excluded: chain T residue 414 ILE Chi-restraints excluded: chain T residue 441 ILE Chi-restraints excluded: chain T residue 464 ILE Chi-restraints excluded: chain U residue 295 PHE Chi-restraints excluded: chain U residue 414 ILE Chi-restraints excluded: chain U residue 441 ILE Chi-restraints excluded: chain U residue 464 ILE Chi-restraints excluded: chain V residue 295 PHE Chi-restraints excluded: chain V residue 405 GLN Chi-restraints excluded: chain V residue 414 ILE Chi-restraints excluded: chain V residue 441 ILE Chi-restraints excluded: chain V residue 464 ILE Chi-restraints excluded: chain W residue 295 PHE Chi-restraints excluded: chain W residue 405 GLN Chi-restraints excluded: chain W residue 414 ILE Chi-restraints excluded: chain W residue 441 ILE Chi-restraints excluded: chain W residue 464 ILE Chi-restraints excluded: chain X residue 295 PHE Chi-restraints excluded: chain X residue 414 ILE Chi-restraints excluded: chain X residue 441 ILE Chi-restraints excluded: chain X residue 464 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 401 optimal weight: 3.9990 chunk 367 optimal weight: 0.6980 chunk 420 optimal weight: 0.9980 chunk 418 optimal weight: 4.9990 chunk 322 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 483 optimal weight: 10.0000 chunk 337 optimal weight: 2.9990 chunk 458 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 236 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN B 405 GLN F 405 GLN ** G 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 405 GLN ** J 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 405 GLN ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 405 GLN P 405 GLN R 405 GLN S 405 GLN T 405 GLN ** U 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 405 GLN X 405 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.086665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.072160 restraints weight = 127641.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.074164 restraints weight = 68818.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.075447 restraints weight = 47781.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.076181 restraints weight = 38251.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.076700 restraints weight = 33724.247| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 43806 Z= 0.132 Angle : 0.702 14.732 59167 Z= 0.345 Chirality : 0.045 0.158 6840 Planarity : 0.004 0.044 7657 Dihedral : 4.686 43.846 6169 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.73 % Allowed : 21.89 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.00 (0.11), residues: 5568 helix: 1.00 (0.11), residues: 2256 sheet: -2.36 (0.14), residues: 1152 loop : -1.36 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG V 417 TYR 0.015 0.001 TYR I 275 PHE 0.014 0.002 PHE A 392 HIS 0.003 0.002 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00301 (43806) covalent geometry : angle 0.70182 (59167) hydrogen bonds : bond 0.02806 ( 2040) hydrogen bonds : angle 4.68391 ( 5904) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7608.01 seconds wall clock time: 132 minutes 13.74 seconds (7933.74 seconds total)