Starting phenix.real_space_refine on Tue Aug 26 23:02:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mu6_48621/08_2025/9mu6_48621.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mu6_48621/08_2025/9mu6_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_48621/08_2025/9mu6_48621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mu6_48621/08_2025/9mu6_48621.map" model { file = "/net/cci-nas-00/data/ceres_data/9mu6_48621/08_2025/9mu6_48621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mu6_48621/08_2025/9mu6_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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: 10.10, per 1000 atoms: 0.23 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: 3.20 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.85 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: 10.92 Time building geometry restraints manager: 4.01 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: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 39.920 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.120 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.960 ------------------------------------------------------------------------------- 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 aren 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 : 1.734 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: 0.8656 (p0) REVERT: A 264 MET cc_start: 0.6139 (mmp) cc_final: 0.5707 (mtp) REVERT: A 379 MET cc_start: 0.7528 (mmm) cc_final: 0.7042 (mmm) REVERT: B 245 ASN cc_start: 0.8978 (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: 0.6116 (mmp) cc_final: 0.5576 (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: 0.6171 (mmp) cc_final: 0.5750 (mtp) REVERT: D 379 MET cc_start: 0.7664 (mmm) cc_final: 0.7222 (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: 0.8962 (p0) cc_final: 0.8686 (p0) REVERT: F 264 MET cc_start: 0.6102 (mmp) cc_final: 0.5565 (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: 0.7202 (mmm) REVERT: H 245 ASN cc_start: 0.8964 (p0) cc_final: 0.8684 (p0) REVERT: H 264 MET cc_start: 0.6119 (mmp) cc_final: 0.5577 (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: 0.6157 (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: 0.8939 (p0) cc_final: 0.8711 (p0) REVERT: J 264 MET cc_start: 0.6125 (mmp) cc_final: 0.5746 (mtp) REVERT: J 379 MET cc_start: 0.7634 (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: 0.6149 (mmp) cc_final: 0.5574 (mtp) REVERT: K 379 MET cc_start: 0.7772 (mmm) cc_final: 0.7187 (mmm) REVERT: L 245 ASN cc_start: 0.8944 (p0) cc_final: 0.8682 (p0) REVERT: L 264 MET cc_start: 0.6154 (mmp) cc_final: 0.5661 (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: 0.8676 (p0) REVERT: M 264 MET cc_start: 0.6196 (mmp) cc_final: 0.5745 (mtp) REVERT: M 379 MET cc_start: 0.7569 (mmm) cc_final: 0.7116 (mmm) REVERT: N 245 ASN cc_start: 0.8949 (p0) cc_final: 0.8671 (p0) REVERT: N 264 MET cc_start: 0.6203 (mmp) cc_final: 0.5700 (mtp) REVERT: N 379 MET cc_start: 0.7622 (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: 0.7721 (mmm) cc_final: 0.7072 (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: 0.5603 (mtp) REVERT: Q 379 MET cc_start: 0.7838 (mmm) cc_final: 0.7295 (mmm) REVERT: R 245 ASN cc_start: 0.8983 (p0) cc_final: 0.8738 (p0) REVERT: R 264 MET cc_start: 0.6123 (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: 0.8911 (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: 0.5672 (mtp) REVERT: S 379 MET cc_start: 0.7544 (mmm) cc_final: 0.7064 (mmm) REVERT: T 245 ASN cc_start: 0.8950 (p0) cc_final: 0.8706 (p0) REVERT: T 264 MET cc_start: 0.6281 (mmp) cc_final: 0.5746 (mtp) REVERT: T 379 MET cc_start: 0.7669 (mmm) cc_final: 0.7212 (mmm) REVERT: U 245 ASN cc_start: 0.9014 (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: 0.5751 (mtp) REVERT: V 379 MET cc_start: 0.7548 (mmm) cc_final: 0.7094 (mmm) REVERT: W 245 ASN cc_start: 0.8955 (p0) cc_final: 0.8637 (p0) REVERT: W 264 MET cc_start: 0.6242 (mmp) cc_final: 0.5706 (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: 0.6171 (mmp) cc_final: 0.5668 (mtp) REVERT: X 379 MET cc_start: 0.7629 (mmm) cc_final: 0.7033 (mmm) outliers start: 0 outliers final: 0 residues processed: 1066 average time/residue: 0.2796 time to fit residues: 477.7276 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 : 1.030 ------------------------------------------------------------------------------- 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 aren 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 : 1.495 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: 0.9374 (p0) cc_final: 0.9037 (p0) REVERT: A 264 MET cc_start: 0.7296 (mmp) cc_final: 0.5980 (mtp) REVERT: A 379 MET cc_start: 0.8572 (mmm) cc_final: 0.7890 (mmm) REVERT: A 430 MET cc_start: 0.6222 (mmt) cc_final: 0.5833 (mmt) REVERT: B 245 ASN cc_start: 0.9370 (p0) cc_final: 0.9043 (p0) REVERT: B 264 MET cc_start: 0.7338 (mmp) cc_final: 0.5962 (mtp) REVERT: B 379 MET cc_start: 0.8631 (mmm) cc_final: 0.8025 (mmm) REVERT: B 430 MET cc_start: 0.6253 (mmt) cc_final: 0.5799 (mmt) REVERT: C 245 ASN cc_start: 0.9381 (p0) cc_final: 0.9077 (p0) REVERT: C 264 MET cc_start: 0.7296 (mmp) cc_final: 0.5827 (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: 0.6061 (mmt) REVERT: D 245 ASN cc_start: 0.9362 (p0) cc_final: 0.9028 (p0) REVERT: D 264 MET cc_start: 0.7286 (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: 0.8348 (mm-30) REVERT: E 430 MET cc_start: 0.6300 (mmt) cc_final: 0.6099 (mmt) REVERT: F 245 ASN cc_start: 0.9366 (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: 0.8639 (mmm) cc_final: 0.8032 (mmm) REVERT: F 430 MET cc_start: 0.6238 (mmt) cc_final: 0.5827 (mmt) REVERT: G 245 ASN cc_start: 0.9353 (p0) cc_final: 0.9024 (p0) REVERT: G 264 MET cc_start: 0.7307 (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: 0.5840 (mtp) REVERT: H 379 MET cc_start: 0.8587 (mmm) cc_final: 0.8005 (mmm) REVERT: H 430 MET cc_start: 0.6272 (mmt) cc_final: 0.6064 (mmt) REVERT: I 245 ASN cc_start: 0.9413 (p0) cc_final: 0.8987 (p0) REVERT: I 264 MET cc_start: 0.7330 (mmp) cc_final: 0.5860 (mtp) REVERT: I 379 MET cc_start: 0.8672 (mmm) cc_final: 0.8047 (mmm) REVERT: I 430 MET cc_start: 0.6280 (mmt) cc_final: 0.5833 (mmt) REVERT: J 245 ASN cc_start: 0.9367 (p0) cc_final: 0.9035 (p0) REVERT: J 264 MET cc_start: 0.7209 (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: 0.7354 (mmp) cc_final: 0.5845 (mtp) REVERT: K 379 MET cc_start: 0.8646 (mmm) cc_final: 0.8072 (mmm) REVERT: K 430 MET cc_start: 0.6259 (mmt) cc_final: 0.6044 (mmt) REVERT: L 245 ASN cc_start: 0.9362 (p0) cc_final: 0.9018 (p0) REVERT: L 264 MET cc_start: 0.7311 (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: 0.6275 (mmt) cc_final: 0.6051 (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: 0.5993 (mtp) REVERT: M 379 MET cc_start: 0.8607 (mmm) cc_final: 0.7935 (mmm) REVERT: M 430 MET cc_start: 0.6255 (mmt) cc_final: 0.5819 (mmt) REVERT: N 245 ASN cc_start: 0.9364 (p0) cc_final: 0.9013 (p0) REVERT: N 264 MET cc_start: 0.7311 (mmp) cc_final: 0.5960 (mtp) REVERT: N 379 MET cc_start: 0.8656 (mmm) cc_final: 0.8052 (mmm) REVERT: N 430 MET cc_start: 0.6301 (mmt) cc_final: 0.6077 (mmt) REVERT: O 245 ASN cc_start: 0.9416 (p0) cc_final: 0.9002 (p0) REVERT: O 264 MET cc_start: 0.7259 (mmp) cc_final: 0.5779 (mtp) REVERT: O 379 MET cc_start: 0.8510 (mmm) cc_final: 0.7942 (mmm) REVERT: O 416 GLU cc_start: 0.8679 (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: 0.9342 (p0) cc_final: 0.8997 (p0) REVERT: P 264 MET cc_start: 0.7316 (mmp) cc_final: 0.5992 (mtp) REVERT: P 379 MET cc_start: 0.8614 (mmm) cc_final: 0.8006 (mmm) REVERT: P 430 MET cc_start: 0.6304 (mmt) cc_final: 0.6086 (mmt) REVERT: Q 245 ASN cc_start: 0.9352 (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: 0.8632 (mm-30) cc_final: 0.8352 (mm-30) REVERT: Q 430 MET cc_start: 0.6278 (mmt) cc_final: 0.6077 (mmt) REVERT: R 245 ASN cc_start: 0.9375 (p0) cc_final: 0.9042 (p0) REVERT: R 264 MET cc_start: 0.7276 (mmp) cc_final: 0.5835 (mtp) REVERT: R 379 MET cc_start: 0.8607 (mmm) cc_final: 0.7997 (mmm) REVERT: R 416 GLU cc_start: 0.8679 (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: 0.7297 (mmp) cc_final: 0.5960 (mtp) REVERT: S 379 MET cc_start: 0.8537 (mmm) cc_final: 0.7872 (mmm) REVERT: S 430 MET cc_start: 0.6185 (mmt) cc_final: 0.5959 (mmt) REVERT: T 245 ASN cc_start: 0.9363 (p0) cc_final: 0.9028 (p0) REVERT: T 264 MET cc_start: 0.7356 (mmp) cc_final: 0.5973 (mtp) REVERT: T 379 MET cc_start: 0.8639 (mmm) cc_final: 0.8021 (mmm) REVERT: T 430 MET cc_start: 0.6280 (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: 0.5814 (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: 0.6293 (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: 0.6273 (mmt) cc_final: 0.6070 (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: 0.6289 (mmt) cc_final: 0.6077 (mmt) REVERT: X 245 ASN cc_start: 0.9374 (p0) cc_final: 0.9047 (p0) REVERT: X 264 MET cc_start: 0.7262 (mmp) cc_final: 0.5841 (mtp) REVERT: X 379 MET cc_start: 0.8574 (mmm) cc_final: 0.7975 (mmm) REVERT: X 416 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8330 (mm-30) REVERT: X 430 MET cc_start: 0.6296 (mmt) cc_final: 0.6073 (mmt) outliers start: 72 outliers final: 48 residues processed: 830 average time/residue: 0.2351 time to fit residues: 326.4395 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 : 1.568 ------------------------------------------------------------------------------- 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** ** Q 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 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 = 0.3730 r_free = 0.3730 target = 0.090010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.072999 restraints weight = 141439.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.075510 restraints weight = 69848.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.076980 restraints weight = 45229.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.077716 restraints weight = 34564.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.078437 restraints weight = 30424.288| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 43806 Z= 0.297 Angle : 0.703 5.688 59167 Z= 0.373 Chirality : 0.045 0.127 6840 Planarity : 0.006 0.047 7657 Dihedral : 4.997 43.604 6169 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.88 % Allowed : 14.67 % Favored : 82.45 % 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 aren not related in a simple way. whole: -1.68 (0.11), residues: 5568 helix: 0.32 (0.10), residues: 2256 sheet: -2.44 (0.14), residues: 1104 loop : -1.81 (0.14), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 428 TYR 0.021 0.002 TYR S 307 PHE 0.024 0.002 PHE A 392 HIS 0.003 0.001 HIS R 439 Details of bonding type rmsd covalent geometry : bond 0.00649 (43806) covalent geometry : angle 0.70279 (59167) hydrogen bonds : bond 0.03628 ( 2040) hydrogen bonds : angle 5.28710 ( 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 874 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 744 time to evaluate : 1.530 Fit side-chains REVERT: A 245 ASN cc_start: 0.9325 (p0) cc_final: 0.8974 (p0) REVERT: A 353 MET cc_start: 0.8069 (ttt) cc_final: 0.7785 (ttt) REVERT: A 379 MET cc_start: 0.8925 (mmm) cc_final: 0.7916 (mmm) REVERT: A 416 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8432 (mm-30) REVERT: A 422 LYS cc_start: 0.8892 (mmmm) cc_final: 0.8456 (tppp) REVERT: A 431 MET cc_start: 0.7813 (ptm) cc_final: 0.7577 (ppp) REVERT: A 460 ASN cc_start: 0.8740 (t0) cc_final: 0.8463 (t0) REVERT: B 245 ASN cc_start: 0.9364 (p0) cc_final: 0.9067 (p0) REVERT: B 353 MET cc_start: 0.7949 (ttt) cc_final: 0.7673 (ttt) REVERT: B 379 MET cc_start: 0.8941 (mmm) cc_final: 0.7912 (mmm) REVERT: B 416 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8497 (tp30) REVERT: B 422 LYS cc_start: 0.8877 (mmmm) cc_final: 0.8463 (tppp) REVERT: B 431 MET cc_start: 0.8161 (ptm) cc_final: 0.7639 (ppp) REVERT: B 460 ASN cc_start: 0.8676 (t0) cc_final: 0.8383 (t0) REVERT: C 245 ASN cc_start: 0.9358 (p0) cc_final: 0.9067 (p0) REVERT: C 353 MET cc_start: 0.8039 (ttt) cc_final: 0.7745 (ttt) REVERT: C 379 MET cc_start: 0.8882 (mmm) cc_final: 0.7878 (mmm) REVERT: C 416 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8377 (mm-30) REVERT: C 422 LYS cc_start: 0.8890 (mmmm) cc_final: 0.8466 (tppp) REVERT: C 431 MET cc_start: 0.7826 (ptm) cc_final: 0.7567 (ppp) REVERT: C 460 ASN cc_start: 0.8737 (t0) cc_final: 0.8453 (t0) REVERT: D 245 ASN cc_start: 0.9326 (p0) cc_final: 0.9043 (p0) REVERT: D 353 MET cc_start: 0.7999 (ttt) cc_final: 0.7664 (ttt) REVERT: D 379 MET cc_start: 0.8938 (mmm) cc_final: 0.7909 (mmm) REVERT: D 422 LYS cc_start: 0.8853 (mmmm) cc_final: 0.8442 (tppp) REVERT: D 431 MET cc_start: 0.8092 (ptm) cc_final: 0.7673 (ppp) REVERT: D 460 ASN cc_start: 0.8660 (t0) cc_final: 0.8390 (t0) REVERT: E 245 ASN cc_start: 0.9316 (p0) cc_final: 0.8994 (p0) REVERT: E 353 MET cc_start: 0.8012 (ttt) cc_final: 0.7712 (ttt) REVERT: E 379 MET cc_start: 0.8908 (mmm) cc_final: 0.7908 (mmm) REVERT: E 422 LYS cc_start: 0.8876 (mmmm) cc_final: 0.8456 (tppp) REVERT: E 431 MET cc_start: 0.8160 (ptm) cc_final: 0.7649 (ppp) REVERT: E 460 ASN cc_start: 0.8740 (t0) cc_final: 0.8469 (t0) REVERT: F 245 ASN cc_start: 0.9345 (p0) cc_final: 0.9102 (p0) REVERT: F 353 MET cc_start: 0.7950 (ttt) cc_final: 0.7601 (ttt) REVERT: F 354 ASN cc_start: 0.8216 (m-40) cc_final: 0.7992 (m110) REVERT: F 379 MET cc_start: 0.8938 (mmm) cc_final: 0.7905 (mmm) REVERT: F 416 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8477 (tp30) REVERT: F 422 LYS cc_start: 0.8901 (mmmm) cc_final: 0.8489 (tppp) REVERT: F 431 MET cc_start: 0.8173 (ptm) cc_final: 0.7620 (ppp) REVERT: F 460 ASN cc_start: 0.8686 (t0) cc_final: 0.8401 (t0) REVERT: G 245 ASN cc_start: 0.9329 (p0) cc_final: 0.9047 (p0) REVERT: G 353 MET cc_start: 0.7964 (ttt) cc_final: 0.7688 (ttt) REVERT: G 379 MET cc_start: 0.8941 (mmm) cc_final: 0.7924 (mmm) REVERT: G 416 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8481 (mm-30) REVERT: G 422 LYS cc_start: 0.8858 (mmmm) cc_final: 0.8443 (tppp) REVERT: G 431 MET cc_start: 0.8087 (ptm) cc_final: 0.7656 (ppp) REVERT: G 460 ASN cc_start: 0.8720 (t0) cc_final: 0.8423 (t0) REVERT: H 245 ASN cc_start: 0.9338 (p0) cc_final: 0.9096 (p0) REVERT: H 353 MET cc_start: 0.7988 (ttt) cc_final: 0.7651 (ttt) REVERT: H 379 MET cc_start: 0.8861 (mmm) cc_final: 0.7852 (mmm) REVERT: H 416 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8489 (tp30) REVERT: H 422 LYS cc_start: 0.8881 (mmmm) cc_final: 0.8462 (tppp) REVERT: H 431 MET cc_start: 0.8173 (ptm) cc_final: 0.7627 (ppp) REVERT: H 460 ASN cc_start: 0.8709 (t0) cc_final: 0.8415 (t0) REVERT: I 245 ASN cc_start: 0.9353 (p0) cc_final: 0.9113 (p0) REVERT: I 353 MET cc_start: 0.7921 (ttt) cc_final: 0.7581 (ttt) REVERT: I 354 ASN cc_start: 0.8212 (m-40) cc_final: 0.7985 (m110) REVERT: I 379 MET cc_start: 0.8969 (mmm) cc_final: 0.7940 (mmm) REVERT: I 416 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8486 (tp30) REVERT: I 422 LYS cc_start: 0.8883 (mmmm) cc_final: 0.8476 (tppp) REVERT: I 431 MET cc_start: 0.8144 (ptm) cc_final: 0.7629 (ppp) REVERT: I 460 ASN cc_start: 0.8681 (t0) cc_final: 0.8395 (t0) REVERT: J 245 ASN cc_start: 0.9348 (p0) cc_final: 0.9068 (p0) REVERT: J 353 MET cc_start: 0.7933 (ttt) cc_final: 0.7601 (ttt) REVERT: J 379 MET cc_start: 0.8962 (mmm) cc_final: 0.7940 (mmm) REVERT: J 416 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8454 (mm-30) REVERT: J 422 LYS cc_start: 0.8855 (mmmm) cc_final: 0.8434 (tppp) REVERT: J 460 ASN cc_start: 0.8725 (t0) cc_final: 0.8439 (t0) REVERT: K 245 ASN cc_start: 0.9295 (p0) cc_final: 0.8975 (p0) REVERT: K 353 MET cc_start: 0.8042 (ttt) cc_final: 0.7707 (ttt) REVERT: K 379 MET cc_start: 0.8939 (mmm) cc_final: 0.7932 (mmm) REVERT: K 416 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8488 (tp30) REVERT: K 422 LYS cc_start: 0.8883 (mmmm) cc_final: 0.8464 (tppp) REVERT: K 431 MET cc_start: 0.7799 (ptm) cc_final: 0.7547 (ppp) REVERT: K 460 ASN cc_start: 0.8721 (t0) cc_final: 0.8445 (t0) REVERT: L 245 ASN cc_start: 0.9339 (p0) cc_final: 0.9053 (p0) REVERT: L 353 MET cc_start: 0.7943 (ttt) cc_final: 0.7662 (ttt) REVERT: L 379 MET cc_start: 0.8927 (mmm) cc_final: 0.7880 (mmm) REVERT: L 416 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8494 (tp30) REVERT: L 422 LYS cc_start: 0.8876 (mmmm) cc_final: 0.8468 (tppp) REVERT: L 431 MET cc_start: 0.8165 (ptm) cc_final: 0.7627 (ppp) REVERT: L 460 ASN cc_start: 0.8703 (t0) cc_final: 0.8428 (t0) REVERT: M 245 ASN cc_start: 0.9326 (p0) cc_final: 0.9053 (p0) REVERT: M 353 MET cc_start: 0.8047 (ttt) cc_final: 0.7713 (ttt) REVERT: M 354 ASN cc_start: 0.8173 (m-40) cc_final: 0.7951 (m110) REVERT: M 379 MET cc_start: 0.8967 (mmm) cc_final: 0.7960 (mmm) REVERT: M 416 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8389 (mm-30) REVERT: M 422 LYS cc_start: 0.8868 (mmmm) cc_final: 0.8445 (tppp) REVERT: M 431 MET cc_start: 0.7829 (ptm) cc_final: 0.7550 (ppp) REVERT: M 460 ASN cc_start: 0.8733 (t0) cc_final: 0.8447 (t0) REVERT: N 239 GLU cc_start: 0.8353 (mp0) cc_final: 0.8148 (mp0) REVERT: N 245 ASN cc_start: 0.9363 (p0) cc_final: 0.9052 (p0) REVERT: N 353 MET cc_start: 0.7943 (ttt) cc_final: 0.7603 (ttt) REVERT: N 354 ASN cc_start: 0.8180 (m-40) cc_final: 0.7942 (m110) REVERT: N 379 MET cc_start: 0.8958 (mmm) cc_final: 0.7929 (mmm) REVERT: N 422 LYS cc_start: 0.8885 (mmmm) cc_final: 0.8478 (tppp) REVERT: N 431 MET cc_start: 0.8170 (ptm) cc_final: 0.7637 (ppp) REVERT: N 460 ASN cc_start: 0.8711 (t0) cc_final: 0.8450 (t0) REVERT: O 245 ASN cc_start: 0.9371 (p0) cc_final: 0.9086 (p0) REVERT: O 353 MET cc_start: 0.7953 (ttt) cc_final: 0.7660 (ttt) REVERT: O 379 MET cc_start: 0.8880 (mmm) cc_final: 0.7852 (mmm) REVERT: O 422 LYS cc_start: 0.8891 (mmmm) cc_final: 0.8461 (tppp) REVERT: O 431 MET cc_start: 0.8167 (ptm) cc_final: 0.7638 (ppp) REVERT: O 460 ASN cc_start: 0.8692 (t0) cc_final: 0.8439 (t0) REVERT: P 239 GLU cc_start: 0.8330 (mp0) cc_final: 0.8130 (mp0) REVERT: P 245 ASN cc_start: 0.9336 (p0) cc_final: 0.9056 (p0) REVERT: P 353 MET cc_start: 0.7967 (ttt) cc_final: 0.7644 (ttt) REVERT: P 379 MET cc_start: 0.8941 (mmm) cc_final: 0.7922 (mmm) REVERT: P 416 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8385 (mm-30) REVERT: P 422 LYS cc_start: 0.8890 (mmmm) cc_final: 0.8474 (tppp) REVERT: P 431 MET cc_start: 0.8160 (ptm) cc_final: 0.7635 (ppp) REVERT: P 460 ASN cc_start: 0.8730 (t0) cc_final: 0.8448 (t0) REVERT: Q 245 ASN cc_start: 0.9333 (p0) cc_final: 0.9003 (p0) REVERT: Q 353 MET cc_start: 0.7965 (ttt) cc_final: 0.7646 (ttt) REVERT: Q 379 MET cc_start: 0.8953 (mmm) cc_final: 0.7933 (mmm) REVERT: Q 422 LYS cc_start: 0.8893 (mmmm) cc_final: 0.8475 (tppp) REVERT: Q 431 MET cc_start: 0.8152 (ptm) cc_final: 0.7630 (ppp) REVERT: Q 460 ASN cc_start: 0.8711 (t0) cc_final: 0.8434 (t0) REVERT: R 245 ASN cc_start: 0.9365 (p0) cc_final: 0.9064 (p0) REVERT: R 353 MET cc_start: 0.7948 (ttt) cc_final: 0.7621 (ttt) REVERT: R 379 MET cc_start: 0.8944 (mmm) cc_final: 0.7910 (mmm) REVERT: R 422 LYS cc_start: 0.8894 (mmmm) cc_final: 0.8474 (tppp) REVERT: R 431 MET cc_start: 0.8171 (ptm) cc_final: 0.7640 (ppp) REVERT: R 460 ASN cc_start: 0.8673 (t0) cc_final: 0.8423 (t0) REVERT: S 245 ASN cc_start: 0.9307 (p0) cc_final: 0.9033 (p0) REVERT: S 295 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.7193 (p90) REVERT: S 353 MET cc_start: 0.8093 (ttt) cc_final: 0.7759 (ttt) REVERT: S 354 ASN cc_start: 0.8210 (m-40) cc_final: 0.7991 (m110) REVERT: S 379 MET cc_start: 0.8905 (mmm) cc_final: 0.7890 (mmm) REVERT: S 416 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8405 (mm-30) REVERT: S 422 LYS cc_start: 0.8815 (mmmm) cc_final: 0.8382 (tppp) REVERT: S 431 MET cc_start: 0.7826 (ptm) cc_final: 0.7546 (ppp) REVERT: S 460 ASN cc_start: 0.8754 (t0) cc_final: 0.8460 (t0) REVERT: T 239 GLU cc_start: 0.8372 (mp0) cc_final: 0.8168 (mp0) REVERT: T 245 ASN cc_start: 0.9347 (p0) cc_final: 0.9070 (p0) REVERT: T 353 MET cc_start: 0.7952 (ttt) cc_final: 0.7694 (ttt) REVERT: T 379 MET cc_start: 0.8967 (mmm) cc_final: 0.7948 (mmm) REVERT: T 416 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8382 (mm-30) REVERT: T 422 LYS cc_start: 0.8871 (mmmm) cc_final: 0.8448 (tppp) REVERT: T 431 MET cc_start: 0.8166 (ptm) cc_final: 0.7639 (ppp) REVERT: T 460 ASN cc_start: 0.8719 (t0) cc_final: 0.8425 (t0) REVERT: U 245 ASN cc_start: 0.9365 (p0) cc_final: 0.9069 (p0) REVERT: U 353 MET cc_start: 0.7946 (ttt) cc_final: 0.7668 (ttt) REVERT: U 379 MET cc_start: 0.8895 (mmm) cc_final: 0.7884 (mmm) REVERT: U 422 LYS cc_start: 0.8894 (mmmm) cc_final: 0.8471 (tppp) REVERT: U 431 MET cc_start: 0.8177 (ptm) cc_final: 0.7630 (ppp) REVERT: U 460 ASN cc_start: 0.8694 (t0) cc_final: 0.8433 (t0) REVERT: V 245 ASN cc_start: 0.9329 (p0) cc_final: 0.9055 (p0) REVERT: V 353 MET cc_start: 0.8060 (ttt) cc_final: 0.7720 (ttt) REVERT: V 354 ASN cc_start: 0.8179 (m-40) cc_final: 0.7963 (m110) REVERT: V 379 MET cc_start: 0.8941 (mmm) cc_final: 0.7920 (mmm) REVERT: V 416 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8404 (mm-30) REVERT: V 422 LYS cc_start: 0.8867 (mmmm) cc_final: 0.8441 (tppp) REVERT: V 431 MET cc_start: 0.8167 (ptm) cc_final: 0.7630 (ppp) REVERT: V 460 ASN cc_start: 0.8695 (t0) cc_final: 0.8438 (t0) REVERT: W 245 ASN cc_start: 0.9317 (p0) cc_final: 0.9072 (p0) REVERT: W 353 MET cc_start: 0.7963 (ttt) cc_final: 0.7693 (ttt) REVERT: W 379 MET cc_start: 0.8936 (mmm) cc_final: 0.7908 (mmm) REVERT: W 422 LYS cc_start: 0.8884 (mmmm) cc_final: 0.8461 (tppp) REVERT: W 431 MET cc_start: 0.8165 (ptm) cc_final: 0.7630 (ppp) REVERT: W 460 ASN cc_start: 0.8738 (t0) cc_final: 0.8451 (t0) REVERT: X 245 ASN cc_start: 0.9355 (p0) cc_final: 0.9080 (p0) REVERT: X 353 MET cc_start: 0.7970 (ttt) cc_final: 0.7641 (ttt) REVERT: X 379 MET cc_start: 0.8965 (mmm) cc_final: 0.7940 (mmm) REVERT: X 422 LYS cc_start: 0.8885 (mmmm) cc_final: 0.8452 (tppp) REVERT: X 431 MET cc_start: 0.8167 (ptm) cc_final: 0.7632 (ppp) REVERT: X 460 ASN cc_start: 0.8721 (t0) cc_final: 0.8450 (t0) outliers start: 130 outliers final: 79 residues processed: 874 average time/residue: 0.2411 time to fit residues: 358.3680 Evaluate side-chains 778 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 698 time to evaluate : 1.787 ------------------------------------------------------------------------------- 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 295 PHE 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 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 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 441 ILE Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain H residue 295 PHE 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 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: 1.9990 chunk 533 optimal weight: 2.9990 chunk 239 optimal weight: 2.9990 chunk 547 optimal weight: 5.9990 chunk 407 optimal weight: 5.9990 chunk 190 optimal weight: 0.9990 chunk 363 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 255 optimal weight: 7.9990 chunk 366 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.086407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.071294 restraints weight = 138484.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.073845 restraints weight = 68012.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.075418 restraints weight = 43975.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.076440 restraints weight = 33597.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.077072 restraints weight = 28124.010| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 43806 Z= 0.196 Angle : 0.627 5.297 59167 Z= 0.325 Chirality : 0.044 0.120 6840 Planarity : 0.005 0.045 7657 Dihedral : 4.944 46.440 6169 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.24 % Allowed : 17.11 % Favored : 80.66 % 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 aren not related in a simple way. whole: -1.49 (0.11), residues: 5568 helix: 0.75 (0.10), residues: 2256 sheet: -2.79 (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 D 452 TYR 0.015 0.002 TYR A 275 PHE 0.018 0.002 PHE S 392 HIS 0.003 0.001 HIS U 439 Details of bonding type rmsd covalent geometry : bond 0.00430 (43806) covalent geometry : angle 0.62657 (59167) hydrogen bonds : bond 0.03041 ( 2040) hydrogen bonds : angle 4.94390 ( 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 843 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 742 time to evaluate : 2.135 Fit side-chains revert: symmetry clash REVERT: A 295 PHE cc_start: 0.7251 (OUTLIER) cc_final: 0.6692 (p90) REVERT: A 353 MET cc_start: 0.7888 (ttt) cc_final: 0.7621 (ttt) REVERT: A 379 MET cc_start: 0.8844 (mmm) cc_final: 0.7708 (mmm) REVERT: A 416 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8449 (tp30) REVERT: A 422 LYS cc_start: 0.8887 (mmmm) cc_final: 0.8655 (tppp) REVERT: A 460 ASN cc_start: 0.8583 (t0) cc_final: 0.8275 (t0) REVERT: B 245 ASN cc_start: 0.9340 (p0) cc_final: 0.9086 (p0) REVERT: B 295 PHE cc_start: 0.7458 (OUTLIER) cc_final: 0.6922 (p90) REVERT: B 353 MET cc_start: 0.7915 (ttt) cc_final: 0.7638 (ttt) REVERT: B 379 MET cc_start: 0.8890 (mmm) cc_final: 0.7821 (mmm) REVERT: B 416 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8445 (tp30) REVERT: B 422 LYS cc_start: 0.8910 (mmmm) cc_final: 0.8697 (tppp) REVERT: B 460 ASN cc_start: 0.8509 (t0) cc_final: 0.8248 (t0) REVERT: C 239 GLU cc_start: 0.8358 (mp0) cc_final: 0.8086 (mp0) REVERT: C 245 ASN cc_start: 0.9339 (p0) cc_final: 0.9089 (p0) REVERT: C 295 PHE cc_start: 0.7203 (OUTLIER) cc_final: 0.6493 (p90) REVERT: C 353 MET cc_start: 0.7856 (ttt) cc_final: 0.7599 (ttt) REVERT: C 379 MET cc_start: 0.8876 (mmm) cc_final: 0.7787 (mmm) REVERT: C 416 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8482 (tp30) REVERT: C 422 LYS cc_start: 0.8916 (mmmm) cc_final: 0.8697 (tppp) REVERT: C 460 ASN cc_start: 0.8491 (t0) cc_final: 0.8195 (t0) REVERT: D 245 ASN cc_start: 0.9309 (p0) cc_final: 0.9043 (p0) REVERT: D 295 PHE cc_start: 0.7464 (OUTLIER) cc_final: 0.6925 (p90) REVERT: D 353 MET cc_start: 0.7936 (ttt) cc_final: 0.7691 (ttt) REVERT: D 379 MET cc_start: 0.8863 (mmm) cc_final: 0.7770 (mmm) REVERT: D 422 LYS cc_start: 0.8889 (mmmm) cc_final: 0.8666 (tppp) REVERT: D 430 MET cc_start: 0.7491 (mmm) cc_final: 0.7208 (mmm) REVERT: D 460 ASN cc_start: 0.8522 (t0) cc_final: 0.8271 (t0) REVERT: E 239 GLU cc_start: 0.8347 (mp0) cc_final: 0.8061 (mp0) REVERT: E 295 PHE cc_start: 0.7369 (OUTLIER) cc_final: 0.6747 (p90) REVERT: E 353 MET cc_start: 0.7836 (ttt) cc_final: 0.7565 (ttt) REVERT: E 379 MET cc_start: 0.8903 (mmm) cc_final: 0.7871 (mmm) REVERT: E 396 MET cc_start: 0.8002 (mmt) cc_final: 0.7689 (mmt) REVERT: E 422 LYS cc_start: 0.8894 (mmmm) cc_final: 0.8661 (tppp) REVERT: E 460 ASN cc_start: 0.8601 (t0) cc_final: 0.8252 (t0) REVERT: F 239 GLU cc_start: 0.8368 (mp0) cc_final: 0.8100 (mp0) REVERT: F 245 ASN cc_start: 0.9348 (p0) cc_final: 0.9126 (p0) REVERT: F 295 PHE cc_start: 0.7476 (OUTLIER) cc_final: 0.6888 (p90) REVERT: F 353 MET cc_start: 0.7888 (ttt) cc_final: 0.7540 (ttt) REVERT: F 354 ASN cc_start: 0.8136 (m-40) cc_final: 0.7878 (m110) REVERT: F 379 MET cc_start: 0.8895 (mmm) cc_final: 0.7832 (mmm) REVERT: F 416 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8437 (tp30) REVERT: F 422 LYS cc_start: 0.8923 (mmmm) cc_final: 0.8696 (tppp) REVERT: F 460 ASN cc_start: 0.8555 (t0) cc_final: 0.8219 (t0) REVERT: G 245 ASN cc_start: 0.9302 (p0) cc_final: 0.9036 (p0) REVERT: G 295 PHE cc_start: 0.7401 (OUTLIER) cc_final: 0.6778 (p90) REVERT: G 353 MET cc_start: 0.7899 (ttt) cc_final: 0.7640 (ttt) REVERT: G 379 MET cc_start: 0.8861 (mmm) cc_final: 0.7719 (mmm) REVERT: G 422 LYS cc_start: 0.8886 (mmmm) cc_final: 0.8660 (tppp) REVERT: G 460 ASN cc_start: 0.8556 (t0) cc_final: 0.8278 (t0) REVERT: H 239 GLU cc_start: 0.8362 (mp0) cc_final: 0.8086 (mp0) REVERT: H 245 ASN cc_start: 0.9336 (p0) cc_final: 0.9121 (p0) REVERT: H 295 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.6854 (p90) REVERT: H 353 MET cc_start: 0.7927 (ttt) cc_final: 0.7678 (ttt) REVERT: H 379 MET cc_start: 0.8891 (mmm) cc_final: 0.7875 (mmm) REVERT: H 396 MET cc_start: 0.8009 (mmt) cc_final: 0.7695 (mmt) REVERT: H 416 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8457 (tp30) REVERT: H 422 LYS cc_start: 0.8909 (mmmm) cc_final: 0.8684 (tppp) REVERT: H 460 ASN cc_start: 0.8622 (t0) cc_final: 0.8274 (t0) REVERT: I 239 GLU cc_start: 0.8367 (mp0) cc_final: 0.8092 (mp0) REVERT: I 245 ASN cc_start: 0.9350 (p0) cc_final: 0.9138 (p0) REVERT: I 295 PHE cc_start: 0.7465 (OUTLIER) cc_final: 0.6962 (p90) REVERT: I 353 MET cc_start: 0.7853 (ttt) cc_final: 0.7507 (ttt) REVERT: I 354 ASN cc_start: 0.8138 (m-40) cc_final: 0.7877 (m110) REVERT: I 379 MET cc_start: 0.8920 (mmm) cc_final: 0.7865 (mmm) REVERT: I 416 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8440 (tp30) REVERT: I 422 LYS cc_start: 0.8902 (mmmm) cc_final: 0.8691 (tppp) REVERT: I 460 ASN cc_start: 0.8549 (t0) cc_final: 0.8220 (t0) REVERT: J 245 ASN cc_start: 0.9344 (p0) cc_final: 0.9085 (p0) REVERT: J 295 PHE cc_start: 0.7395 (OUTLIER) cc_final: 0.6767 (p90) REVERT: J 353 MET cc_start: 0.7913 (ttt) cc_final: 0.7666 (ttt) REVERT: J 379 MET cc_start: 0.8907 (mmm) cc_final: 0.7807 (mmm) REVERT: J 422 LYS cc_start: 0.8890 (mmmm) cc_final: 0.8662 (tppp) REVERT: J 460 ASN cc_start: 0.8557 (t0) cc_final: 0.8196 (t0) REVERT: K 239 GLU cc_start: 0.8372 (mp0) cc_final: 0.8094 (mp0) REVERT: K 295 PHE cc_start: 0.7390 (OUTLIER) cc_final: 0.6845 (p90) REVERT: K 353 MET cc_start: 0.7907 (ttt) cc_final: 0.7686 (ttt) REVERT: K 379 MET cc_start: 0.8897 (mmm) cc_final: 0.7825 (mmm) REVERT: K 396 MET cc_start: 0.8016 (mmt) cc_final: 0.7705 (mmt) REVERT: K 416 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8458 (tp30) REVERT: K 422 LYS cc_start: 0.8907 (mmmm) cc_final: 0.8684 (tppp) REVERT: K 460 ASN cc_start: 0.8519 (t0) cc_final: 0.8169 (t0) REVERT: L 245 ASN cc_start: 0.9325 (p0) cc_final: 0.9063 (p0) REVERT: L 295 PHE cc_start: 0.7447 (OUTLIER) cc_final: 0.6987 (p90) REVERT: L 353 MET cc_start: 0.7895 (ttt) cc_final: 0.7625 (ttt) REVERT: L 379 MET cc_start: 0.8859 (mmm) cc_final: 0.7712 (mmm) REVERT: L 416 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8455 (tp30) REVERT: L 422 LYS cc_start: 0.8898 (mmmm) cc_final: 0.8682 (tppp) REVERT: L 460 ASN cc_start: 0.8555 (t0) cc_final: 0.8268 (t0) REVERT: M 245 ASN cc_start: 0.9295 (p0) cc_final: 0.9069 (p0) REVERT: M 295 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.6699 (p90) REVERT: M 353 MET cc_start: 0.7887 (ttt) cc_final: 0.7559 (ttt) REVERT: M 354 ASN cc_start: 0.8140 (m-40) cc_final: 0.7894 (m110) REVERT: M 379 MET cc_start: 0.8897 (mmm) cc_final: 0.7763 (mmm) REVERT: M 422 LYS cc_start: 0.8898 (mmmm) cc_final: 0.8666 (tppp) REVERT: M 460 ASN cc_start: 0.8486 (t0) cc_final: 0.8180 (t0) REVERT: N 245 ASN cc_start: 0.9339 (p0) cc_final: 0.9075 (p0) REVERT: N 295 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.6949 (p90) REVERT: N 353 MET cc_start: 0.7913 (ttt) cc_final: 0.7573 (ttt) REVERT: N 354 ASN cc_start: 0.8161 (m-40) cc_final: 0.7911 (m110) REVERT: N 379 MET cc_start: 0.8898 (mmm) cc_final: 0.7847 (mmm) REVERT: N 422 LYS cc_start: 0.8903 (mmmm) cc_final: 0.8687 (tppp) REVERT: N 460 ASN cc_start: 0.8596 (t0) cc_final: 0.8305 (t0) REVERT: O 239 GLU cc_start: 0.8333 (mp0) cc_final: 0.8052 (mp0) REVERT: O 245 ASN cc_start: 0.9340 (p0) cc_final: 0.9129 (p0) REVERT: O 295 PHE cc_start: 0.7193 (OUTLIER) cc_final: 0.6490 (p90) REVERT: O 353 MET cc_start: 0.7853 (ttt) cc_final: 0.7574 (ttt) REVERT: O 379 MET cc_start: 0.8876 (mmm) cc_final: 0.7807 (mmm) REVERT: O 416 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8466 (tp30) REVERT: O 422 LYS cc_start: 0.8922 (mmmm) cc_final: 0.8693 (tppp) REVERT: O 460 ASN cc_start: 0.8515 (t0) cc_final: 0.8245 (t0) REVERT: P 245 ASN cc_start: 0.9320 (p0) cc_final: 0.9057 (p0) REVERT: P 295 PHE cc_start: 0.7265 (OUTLIER) cc_final: 0.6574 (p90) REVERT: P 353 MET cc_start: 0.7930 (ttt) cc_final: 0.7693 (ttt) REVERT: P 379 MET cc_start: 0.8863 (mmm) cc_final: 0.7734 (mmm) REVERT: P 416 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8489 (tp30) REVERT: P 422 LYS cc_start: 0.8927 (mmmm) cc_final: 0.8707 (tppp) REVERT: P 460 ASN cc_start: 0.8520 (t0) cc_final: 0.8163 (t0) REVERT: Q 295 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.6774 (p90) REVERT: Q 353 MET cc_start: 0.7930 (ttt) cc_final: 0.7696 (ttt) REVERT: Q 379 MET cc_start: 0.8886 (mmm) cc_final: 0.7801 (mmm) REVERT: Q 416 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8479 (tp30) REVERT: Q 422 LYS cc_start: 0.8925 (mmmm) cc_final: 0.8705 (tppp) REVERT: Q 460 ASN cc_start: 0.8487 (t0) cc_final: 0.8186 (t0) REVERT: R 239 GLU cc_start: 0.8354 (mp0) cc_final: 0.8083 (mp0) REVERT: R 245 ASN cc_start: 0.9346 (p0) cc_final: 0.9090 (p0) REVERT: R 295 PHE cc_start: 0.7195 (OUTLIER) cc_final: 0.6493 (p90) REVERT: R 353 MET cc_start: 0.7913 (ttt) cc_final: 0.7670 (ttt) REVERT: R 379 MET cc_start: 0.8881 (mmm) cc_final: 0.7799 (mmm) REVERT: R 416 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8479 (tp30) REVERT: R 422 LYS cc_start: 0.8937 (mmmm) cc_final: 0.8718 (tppp) REVERT: R 460 ASN cc_start: 0.8539 (t0) cc_final: 0.8234 (t0) REVERT: S 245 ASN cc_start: 0.9255 (p0) cc_final: 0.9037 (p0) REVERT: S 295 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.6661 (p90) REVERT: S 353 MET cc_start: 0.7939 (ttt) cc_final: 0.7616 (ttt) REVERT: S 354 ASN cc_start: 0.8136 (m-40) cc_final: 0.7890 (m110) REVERT: S 379 MET cc_start: 0.8829 (mmm) cc_final: 0.7695 (mmm) REVERT: S 396 MET cc_start: 0.8177 (mmm) cc_final: 0.7807 (mmt) REVERT: S 416 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8463 (tp30) REVERT: S 460 ASN cc_start: 0.8559 (t0) cc_final: 0.8247 (t0) REVERT: T 245 ASN cc_start: 0.9340 (p0) cc_final: 0.9084 (p0) REVERT: T 295 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.6765 (p90) REVERT: T 353 MET cc_start: 0.7878 (ttt) cc_final: 0.7544 (ttt) REVERT: T 354 ASN cc_start: 0.8159 (m-40) cc_final: 0.7933 (m110) REVERT: T 379 MET cc_start: 0.8914 (mmm) cc_final: 0.7816 (mmm) REVERT: T 405 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7678 (pt0) REVERT: T 422 LYS cc_start: 0.8908 (mmmm) cc_final: 0.8684 (tppp) REVERT: T 460 ASN cc_start: 0.8561 (t0) cc_final: 0.8285 (t0) REVERT: U 239 GLU cc_start: 0.8358 (mp0) cc_final: 0.8083 (mp0) REVERT: U 245 ASN cc_start: 0.9347 (p0) cc_final: 0.9094 (p0) REVERT: U 295 PHE cc_start: 0.7222 (OUTLIER) cc_final: 0.6540 (p90) REVERT: U 353 MET cc_start: 0.7860 (ttt) cc_final: 0.7591 (ttt) REVERT: U 379 MET cc_start: 0.8914 (mmm) cc_final: 0.7887 (mmm) REVERT: U 416 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8465 (tp30) REVERT: U 422 LYS cc_start: 0.8917 (mmmm) cc_final: 0.8694 (tppp) REVERT: U 460 ASN cc_start: 0.8455 (t0) cc_final: 0.8185 (t0) REVERT: V 245 ASN cc_start: 0.9310 (p0) cc_final: 0.9051 (p0) REVERT: V 295 PHE cc_start: 0.7261 (OUTLIER) cc_final: 0.6632 (p90) REVERT: V 353 MET cc_start: 0.7908 (ttt) cc_final: 0.7583 (ttt) REVERT: V 354 ASN cc_start: 0.8141 (m-40) cc_final: 0.7899 (m110) REVERT: V 379 MET cc_start: 0.8876 (mmm) cc_final: 0.7774 (mmm) REVERT: V 416 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8481 (tp30) REVERT: V 422 LYS cc_start: 0.8906 (mmmm) cc_final: 0.8681 (tppp) REVERT: V 460 ASN cc_start: 0.8456 (t0) cc_final: 0.8186 (t0) REVERT: W 245 ASN cc_start: 0.9341 (p0) cc_final: 0.9133 (p0) REVERT: W 295 PHE cc_start: 0.7236 (OUTLIER) cc_final: 0.6546 (p90) REVERT: W 353 MET cc_start: 0.7859 (ttt) cc_final: 0.7609 (ttt) REVERT: W 379 MET cc_start: 0.8875 (mmm) cc_final: 0.7809 (mmm) REVERT: W 396 MET cc_start: 0.8007 (mmt) cc_final: 0.7693 (mmt) REVERT: W 416 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8466 (tp30) REVERT: W 422 LYS cc_start: 0.8894 (mmmm) cc_final: 0.8662 (tppp) REVERT: W 460 ASN cc_start: 0.8510 (t0) cc_final: 0.8201 (t0) REVERT: X 239 GLU cc_start: 0.8370 (mp0) cc_final: 0.8094 (mp0) REVERT: X 245 ASN cc_start: 0.9345 (p0) cc_final: 0.9093 (p0) REVERT: X 295 PHE cc_start: 0.7204 (OUTLIER) cc_final: 0.6501 (p90) REVERT: X 353 MET cc_start: 0.7915 (ttt) cc_final: 0.7667 (ttt) REVERT: X 379 MET cc_start: 0.8915 (mmm) cc_final: 0.7836 (mmm) REVERT: X 416 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8468 (tp30) REVERT: X 422 LYS cc_start: 0.8925 (mmmm) cc_final: 0.8696 (tppp) REVERT: X 460 ASN cc_start: 0.8592 (t0) cc_final: 0.8279 (t0) outliers start: 101 outliers final: 66 residues processed: 837 average time/residue: 0.2553 time to fit residues: 361.9368 Evaluate side-chains 798 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 707 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 409 LEU 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 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 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 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 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 409 LEU 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 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: 5.9990 chunk 162 optimal weight: 1.9990 chunk 199 optimal weight: 0.9980 chunk 173 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 357 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 195 optimal weight: 6.9990 chunk 369 optimal weight: 2.9990 chunk 293 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 J 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 405 GLN ** S 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 405 GLN ** V 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 405 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.087353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.072916 restraints weight = 137062.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.075390 restraints weight = 68909.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.076910 restraints weight = 44568.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.077884 restraints weight = 33708.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.078557 restraints weight = 28199.771| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 43806 Z= 0.155 Angle : 0.610 8.202 59167 Z= 0.313 Chirality : 0.044 0.120 6840 Planarity : 0.005 0.048 7657 Dihedral : 4.762 44.778 6169 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.70 % Allowed : 19.85 % 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 aren not related in a simple way. whole: -1.22 (0.11), residues: 5568 helix: 0.99 (0.10), residues: 2256 sheet: -2.64 (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 I 275 PHE 0.016 0.002 PHE S 392 HIS 0.003 0.001 HIS S 439 Details of bonding type rmsd covalent geometry : bond 0.00346 (43806) covalent geometry : angle 0.61010 (59167) hydrogen bonds : bond 0.02936 ( 2040) hydrogen bonds : angle 4.85081 ( 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 888 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 766 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 PHE cc_start: 0.7282 (OUTLIER) cc_final: 0.6678 (p90) REVERT: A 353 MET cc_start: 0.7839 (ttt) cc_final: 0.7570 (ttt) REVERT: A 379 MET cc_start: 0.8746 (mmm) cc_final: 0.7704 (mmm) REVERT: A 396 MET cc_start: 0.8107 (mmm) cc_final: 0.7769 (mmt) REVERT: A 422 LYS cc_start: 0.9012 (mmmm) cc_final: 0.8571 (tppp) REVERT: A 460 ASN cc_start: 0.8476 (t0) cc_final: 0.8123 (t0) REVERT: B 241 ARG cc_start: 0.8282 (mmp-170) cc_final: 0.7856 (mmp80) REVERT: B 270 GLU cc_start: 0.7818 (tp30) cc_final: 0.7360 (tp30) REVERT: B 295 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.6711 (p90) REVERT: B 310 GLN cc_start: 0.8016 (mt0) cc_final: 0.7766 (mt0) REVERT: B 344 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8689 (t) REVERT: B 353 MET cc_start: 0.7813 (ttt) cc_final: 0.7581 (ttt) REVERT: B 379 MET cc_start: 0.8838 (mmm) cc_final: 0.7703 (mmm) REVERT: B 396 MET cc_start: 0.8117 (mmm) cc_final: 0.7769 (mmt) REVERT: B 405 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7847 (pt0) REVERT: B 416 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8355 (tp30) REVERT: B 422 LYS cc_start: 0.9002 (mmmm) cc_final: 0.8572 (tppp) REVERT: B 460 ASN cc_start: 0.8475 (t0) cc_final: 0.8154 (t0) REVERT: C 241 ARG cc_start: 0.8342 (mmp-170) cc_final: 0.7906 (mmp80) REVERT: C 270 GLU cc_start: 0.7874 (tp30) cc_final: 0.7387 (tp30) REVERT: C 295 PHE cc_start: 0.7235 (OUTLIER) cc_final: 0.6470 (p90) REVERT: C 353 MET cc_start: 0.7858 (ttt) cc_final: 0.7603 (ttt) REVERT: C 379 MET cc_start: 0.8800 (mmm) cc_final: 0.7752 (mmm) REVERT: C 396 MET cc_start: 0.8129 (mmm) cc_final: 0.7809 (mmt) REVERT: C 405 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7739 (pt0) REVERT: C 422 LYS cc_start: 0.8961 (mmmm) cc_final: 0.8539 (tppp) REVERT: C 431 MET cc_start: 0.7770 (ppp) cc_final: 0.7471 (ppp) REVERT: C 460 ASN cc_start: 0.8470 (t0) cc_final: 0.8143 (t0) REVERT: D 245 ASN cc_start: 0.9301 (p0) cc_final: 0.9036 (p0) REVERT: D 295 PHE cc_start: 0.7428 (OUTLIER) cc_final: 0.6771 (p90) REVERT: D 310 GLN cc_start: 0.8024 (mt0) cc_final: 0.7770 (mt0) REVERT: D 344 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8732 (t) REVERT: D 353 MET cc_start: 0.7990 (ttt) cc_final: 0.7763 (ttt) REVERT: D 379 MET cc_start: 0.8785 (mmm) cc_final: 0.7669 (mmm) REVERT: D 396 MET cc_start: 0.8140 (mmm) cc_final: 0.7774 (mmt) REVERT: D 422 LYS cc_start: 0.8972 (mmmm) cc_final: 0.8547 (tppp) REVERT: D 430 MET cc_start: 0.7461 (mmm) cc_final: 0.7245 (mmm) REVERT: D 460 ASN cc_start: 0.8481 (t0) cc_final: 0.8178 (t0) REVERT: E 241 ARG cc_start: 0.8333 (mmp-170) cc_final: 0.7904 (mmp80) REVERT: E 270 GLU cc_start: 0.7870 (tp30) cc_final: 0.7355 (tp30) REVERT: E 295 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6617 (p90) REVERT: E 344 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8673 (t) REVERT: E 353 MET cc_start: 0.7786 (ttt) cc_final: 0.7527 (ttt) REVERT: E 379 MET cc_start: 0.8867 (mmm) cc_final: 0.7821 (mmm) REVERT: E 422 LYS cc_start: 0.8977 (mmmm) cc_final: 0.8537 (tppp) REVERT: E 431 MET cc_start: 0.7805 (ppp) cc_final: 0.7541 (ppp) REVERT: E 460 ASN cc_start: 0.8456 (t0) cc_final: 0.8128 (t0) REVERT: F 241 ARG cc_start: 0.8321 (mmp-170) cc_final: 0.7893 (mmp80) REVERT: F 245 ASN cc_start: 0.9355 (p0) cc_final: 0.9063 (p0) REVERT: F 270 GLU cc_start: 0.7816 (tp30) cc_final: 0.7325 (tp30) REVERT: F 295 PHE cc_start: 0.7294 (OUTLIER) cc_final: 0.6633 (p90) REVERT: F 310 GLN cc_start: 0.8072 (mt0) cc_final: 0.7804 (mt0) REVERT: F 344 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8664 (t) REVERT: F 353 MET cc_start: 0.7857 (ttt) cc_final: 0.7515 (ttt) REVERT: F 354 ASN cc_start: 0.8140 (m-40) cc_final: 0.7872 (m110) REVERT: F 379 MET cc_start: 0.8857 (mmm) cc_final: 0.7768 (mmm) REVERT: F 396 MET cc_start: 0.8143 (mmm) cc_final: 0.7809 (mmt) REVERT: F 416 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8355 (tp30) REVERT: F 422 LYS cc_start: 0.8974 (mmmm) cc_final: 0.8553 (tppp) REVERT: F 460 ASN cc_start: 0.8401 (t0) cc_final: 0.8053 (t0) REVERT: G 295 PHE cc_start: 0.7401 (OUTLIER) cc_final: 0.6706 (p90) REVERT: G 353 MET cc_start: 0.7810 (ttt) cc_final: 0.7567 (ttt) REVERT: G 379 MET cc_start: 0.8782 (mmm) cc_final: 0.7714 (mmm) REVERT: G 396 MET cc_start: 0.8145 (mmm) cc_final: 0.7781 (mmt) REVERT: G 422 LYS cc_start: 0.8979 (mmmm) cc_final: 0.8543 (tppp) REVERT: G 460 ASN cc_start: 0.8522 (t0) cc_final: 0.8197 (t0) REVERT: H 241 ARG cc_start: 0.8320 (mmp-170) cc_final: 0.7903 (mmp80) REVERT: H 245 ASN cc_start: 0.9364 (p0) cc_final: 0.9078 (p0) REVERT: H 270 GLU cc_start: 0.7865 (tp30) cc_final: 0.7325 (tp30) REVERT: H 295 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.6500 (p90) REVERT: H 353 MET cc_start: 0.7973 (ttt) cc_final: 0.7748 (ttt) REVERT: H 379 MET cc_start: 0.8831 (mmm) cc_final: 0.7779 (mmm) REVERT: H 416 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8367 (tp30) REVERT: H 422 LYS cc_start: 0.8942 (mmmm) cc_final: 0.8530 (tppp) REVERT: H 431 MET cc_start: 0.7796 (ppp) cc_final: 0.7530 (ppp) REVERT: H 460 ASN cc_start: 0.8436 (t0) cc_final: 0.8115 (t0) REVERT: I 241 ARG cc_start: 0.8342 (mmp-170) cc_final: 0.7917 (mmp80) REVERT: I 245 ASN cc_start: 0.9379 (p0) cc_final: 0.9096 (p0) REVERT: I 270 GLU cc_start: 0.7828 (tp30) cc_final: 0.7333 (tp30) REVERT: I 295 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.6629 (p90) REVERT: I 310 GLN cc_start: 0.8073 (mt0) cc_final: 0.7803 (mt0) REVERT: I 353 MET cc_start: 0.7818 (ttt) cc_final: 0.7477 (ttt) REVERT: I 354 ASN cc_start: 0.8122 (m-40) cc_final: 0.7849 (m110) REVERT: I 379 MET cc_start: 0.8880 (mmm) cc_final: 0.7799 (mmm) REVERT: I 396 MET cc_start: 0.8126 (mmm) cc_final: 0.7787 (mmt) REVERT: I 416 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8360 (tp30) REVERT: I 422 LYS cc_start: 0.8943 (mmmm) cc_final: 0.8530 (tppp) REVERT: I 460 ASN cc_start: 0.8423 (t0) cc_final: 0.8095 (t0) REVERT: J 295 PHE cc_start: 0.7390 (OUTLIER) cc_final: 0.6641 (p90) REVERT: J 353 MET cc_start: 0.7956 (ttt) cc_final: 0.7744 (ttt) REVERT: J 379 MET cc_start: 0.8800 (mmm) cc_final: 0.7723 (mmm) REVERT: J 396 MET cc_start: 0.8125 (mmm) cc_final: 0.7792 (mmt) REVERT: J 422 LYS cc_start: 0.8971 (mmmm) cc_final: 0.8529 (tppp) REVERT: J 430 MET cc_start: 0.7579 (mmm) cc_final: 0.7340 (mmm) REVERT: J 460 ASN cc_start: 0.8423 (t0) cc_final: 0.8107 (t0) REVERT: K 241 ARG cc_start: 0.8318 (mmp-170) cc_final: 0.7895 (mmp80) REVERT: K 270 GLU cc_start: 0.7865 (tp30) cc_final: 0.7360 (tp30) REVERT: K 295 PHE cc_start: 0.7402 (OUTLIER) cc_final: 0.6654 (p90) REVERT: K 353 MET cc_start: 0.7998 (ttt) cc_final: 0.7780 (ttt) REVERT: K 379 MET cc_start: 0.8812 (mmm) cc_final: 0.7814 (mmm) REVERT: K 416 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8365 (tp30) REVERT: K 422 LYS cc_start: 0.8943 (mmmm) cc_final: 0.8525 (tppp) REVERT: K 431 MET cc_start: 0.7817 (ppp) cc_final: 0.7555 (ppp) REVERT: K 460 ASN cc_start: 0.8394 (t0) cc_final: 0.8079 (t0) REVERT: L 241 ARG cc_start: 0.8284 (mmp-170) cc_final: 0.7841 (mmp80) REVERT: L 245 ASN cc_start: 0.9317 (p0) cc_final: 0.9056 (p0) REVERT: L 270 GLU cc_start: 0.7830 (tp30) cc_final: 0.7329 (tp30) REVERT: L 295 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.6794 (p90) REVERT: L 353 MET cc_start: 0.7814 (ttt) cc_final: 0.7553 (ttt) REVERT: L 379 MET cc_start: 0.8810 (mmm) cc_final: 0.7677 (mmm) REVERT: L 396 MET cc_start: 0.8148 (mmm) cc_final: 0.7794 (mmt) REVERT: L 416 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8364 (tp30) REVERT: L 422 LYS cc_start: 0.8936 (mmmm) cc_final: 0.8525 (tppp) REVERT: L 460 ASN cc_start: 0.8461 (t0) cc_final: 0.8136 (t0) REVERT: M 270 GLU cc_start: 0.7819 (tp30) cc_final: 0.7353 (tp30) REVERT: M 295 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.6853 (p90) REVERT: M 353 MET cc_start: 0.7858 (ttt) cc_final: 0.7517 (ttt) REVERT: M 354 ASN cc_start: 0.8125 (m-40) cc_final: 0.7833 (m110) REVERT: M 379 MET cc_start: 0.8792 (mmm) cc_final: 0.7730 (mmm) REVERT: M 396 MET cc_start: 0.8135 (mmm) cc_final: 0.7785 (mmt) REVERT: M 422 LYS cc_start: 0.8932 (mmmm) cc_final: 0.8500 (tppp) REVERT: M 460 ASN cc_start: 0.8458 (t0) cc_final: 0.8130 (t0) REVERT: N 245 ASN cc_start: 0.9331 (p0) cc_final: 0.9090 (p0) REVERT: N 270 GLU cc_start: 0.7834 (tp30) cc_final: 0.7324 (tp30) REVERT: N 295 PHE cc_start: 0.7279 (OUTLIER) cc_final: 0.6623 (p90) REVERT: N 310 GLN cc_start: 0.8018 (mt0) cc_final: 0.7761 (mt0) REVERT: N 353 MET cc_start: 0.7843 (ttt) cc_final: 0.7522 (ttt) REVERT: N 354 ASN cc_start: 0.8147 (m-40) cc_final: 0.7859 (m110) REVERT: N 379 MET cc_start: 0.8846 (mmm) cc_final: 0.7735 (mmm) REVERT: N 396 MET cc_start: 0.8139 (mmm) cc_final: 0.7804 (mmt) REVERT: N 422 LYS cc_start: 0.8986 (mmmm) cc_final: 0.8560 (tppp) REVERT: N 460 ASN cc_start: 0.8462 (t0) cc_final: 0.8144 (t0) REVERT: O 241 ARG cc_start: 0.8338 (mmp-170) cc_final: 0.7916 (mmp80) REVERT: O 245 ASN cc_start: 0.9368 (p0) cc_final: 0.9084 (p0) REVERT: O 270 GLU cc_start: 0.7876 (tp30) cc_final: 0.7376 (tp30) REVERT: O 295 PHE cc_start: 0.7236 (OUTLIER) cc_final: 0.6477 (p90) REVERT: O 344 VAL cc_start: 0.8930 (OUTLIER) cc_final: 0.8729 (t) REVERT: O 353 MET cc_start: 0.7804 (ttt) cc_final: 0.7534 (ttt) REVERT: O 379 MET cc_start: 0.8804 (mmm) cc_final: 0.7718 (mmm) REVERT: O 396 MET cc_start: 0.8140 (mmm) cc_final: 0.7804 (mmt) REVERT: O 422 LYS cc_start: 0.8940 (mmmm) cc_final: 0.8519 (tppp) REVERT: O 460 ASN cc_start: 0.8427 (t0) cc_final: 0.8117 (t0) REVERT: P 270 GLU cc_start: 0.7819 (tp30) cc_final: 0.7352 (tp30) REVERT: P 295 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.6661 (p90) REVERT: P 344 VAL cc_start: 0.8909 (OUTLIER) cc_final: 0.8701 (t) REVERT: P 353 MET cc_start: 0.7980 (ttt) cc_final: 0.7764 (ttt) REVERT: P 379 MET cc_start: 0.8816 (mmm) cc_final: 0.7705 (mmm) REVERT: P 396 MET cc_start: 0.8143 (mmm) cc_final: 0.7797 (mmt) REVERT: P 422 LYS cc_start: 0.8967 (mmmm) cc_final: 0.8544 (tppp) REVERT: P 460 ASN cc_start: 0.8437 (t0) cc_final: 0.8118 (t0) REVERT: Q 270 GLU cc_start: 0.7836 (tp30) cc_final: 0.7353 (tp30) REVERT: Q 295 PHE cc_start: 0.7397 (OUTLIER) cc_final: 0.6700 (p90) REVERT: Q 353 MET cc_start: 0.7983 (ttt) cc_final: 0.7777 (ttt) REVERT: Q 379 MET cc_start: 0.8786 (mmm) cc_final: 0.7724 (mmm) REVERT: Q 396 MET cc_start: 0.8132 (mmm) cc_final: 0.7808 (mmt) REVERT: Q 422 LYS cc_start: 0.8966 (mmmm) cc_final: 0.8547 (tppp) REVERT: Q 460 ASN cc_start: 0.8463 (t0) cc_final: 0.8138 (t0) REVERT: R 241 ARG cc_start: 0.8283 (mmp-170) cc_final: 0.7856 (mmp80) REVERT: R 270 GLU cc_start: 0.7885 (tp30) cc_final: 0.7392 (tp30) REVERT: R 295 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6563 (p90) REVERT: R 310 GLN cc_start: 0.8013 (mt0) cc_final: 0.7766 (mt0) REVERT: R 353 MET cc_start: 0.7961 (ttt) cc_final: 0.7755 (ttt) REVERT: R 379 MET cc_start: 0.8832 (mmm) cc_final: 0.7739 (mmm) REVERT: R 396 MET cc_start: 0.8141 (mmm) cc_final: 0.7809 (mmt) REVERT: R 422 LYS cc_start: 0.8974 (mmmm) cc_final: 0.8559 (tppp) REVERT: R 460 ASN cc_start: 0.8435 (t0) cc_final: 0.8126 (t0) REVERT: S 295 PHE cc_start: 0.7412 (OUTLIER) cc_final: 0.6586 (p90) REVERT: S 353 MET cc_start: 0.7943 (ttt) cc_final: 0.7623 (ttt) REVERT: S 354 ASN cc_start: 0.8126 (m-40) cc_final: 0.7833 (m110) REVERT: S 379 MET cc_start: 0.8712 (mmm) cc_final: 0.7662 (mmm) REVERT: S 460 ASN cc_start: 0.8467 (t0) cc_final: 0.8136 (t0) REVERT: T 241 ARG cc_start: 0.8289 (mmp-170) cc_final: 0.7863 (mmp80) REVERT: T 270 GLU cc_start: 0.7828 (tp30) cc_final: 0.7331 (tp30) REVERT: T 295 PHE cc_start: 0.7408 (OUTLIER) cc_final: 0.6711 (p90) REVERT: T 344 VAL cc_start: 0.8862 (OUTLIER) cc_final: 0.8651 (t) REVERT: T 353 MET cc_start: 0.7826 (ttt) cc_final: 0.7488 (ttt) REVERT: T 354 ASN cc_start: 0.8147 (m-40) cc_final: 0.7893 (m110) REVERT: T 379 MET cc_start: 0.8860 (mmm) cc_final: 0.7738 (mmm) REVERT: T 396 MET cc_start: 0.8139 (mmm) cc_final: 0.7803 (mmt) REVERT: T 405 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7835 (pt0) REVERT: T 422 LYS cc_start: 0.8938 (mmmm) cc_final: 0.8523 (tppp) REVERT: T 460 ASN cc_start: 0.8516 (t0) cc_final: 0.8195 (t0) REVERT: U 241 ARG cc_start: 0.8304 (mmp-170) cc_final: 0.7884 (mmp80) REVERT: U 270 GLU cc_start: 0.7821 (tp30) cc_final: 0.7312 (tp30) REVERT: U 295 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.6626 (p90) REVERT: U 344 VAL cc_start: 0.8919 (OUTLIER) cc_final: 0.8718 (t) REVERT: U 353 MET cc_start: 0.7818 (ttt) cc_final: 0.7546 (ttt) REVERT: U 379 MET cc_start: 0.8836 (mmm) cc_final: 0.7737 (mmm) REVERT: U 396 MET cc_start: 0.8141 (mmm) cc_final: 0.7812 (mmt) REVERT: U 422 LYS cc_start: 0.8950 (mmmm) cc_final: 0.8534 (tppp) REVERT: U 460 ASN cc_start: 0.8436 (t0) cc_final: 0.8141 (t0) REVERT: V 270 GLU cc_start: 0.7819 (tp30) cc_final: 0.7314 (tp30) REVERT: V 295 PHE cc_start: 0.7298 (OUTLIER) cc_final: 0.6700 (p90) REVERT: V 353 MET cc_start: 0.7861 (ttt) cc_final: 0.7539 (ttt) REVERT: V 354 ASN cc_start: 0.8123 (m-40) cc_final: 0.7830 (m110) REVERT: V 379 MET cc_start: 0.8774 (mmm) cc_final: 0.7714 (mmm) REVERT: V 396 MET cc_start: 0.8136 (mmm) cc_final: 0.7770 (mmt) REVERT: V 422 LYS cc_start: 0.8933 (mmmm) cc_final: 0.8517 (tppp) REVERT: V 460 ASN cc_start: 0.8436 (t0) cc_final: 0.8140 (t0) REVERT: W 241 ARG cc_start: 0.8286 (mmp-170) cc_final: 0.7861 (mmp80) REVERT: W 245 ASN cc_start: 0.9333 (p0) cc_final: 0.9041 (p0) REVERT: W 270 GLU cc_start: 0.7877 (tp30) cc_final: 0.7373 (tp30) REVERT: W 295 PHE cc_start: 0.7351 (OUTLIER) cc_final: 0.6633 (p90) REVERT: W 353 MET cc_start: 0.7819 (ttt) cc_final: 0.7547 (ttt) REVERT: W 379 MET cc_start: 0.8805 (mmm) cc_final: 0.7689 (mmm) REVERT: W 422 LYS cc_start: 0.8940 (mmmm) cc_final: 0.8513 (tppp) REVERT: W 431 MET cc_start: 0.7796 (ppp) cc_final: 0.7534 (ppp) REVERT: W 460 ASN cc_start: 0.8486 (t0) cc_final: 0.8153 (t0) REVERT: X 241 ARG cc_start: 0.8309 (mmp-170) cc_final: 0.7873 (mmp80) REVERT: X 270 GLU cc_start: 0.7830 (tp30) cc_final: 0.7324 (tp30) REVERT: X 295 PHE cc_start: 0.7242 (OUTLIER) cc_final: 0.6478 (p90) REVERT: X 310 GLN cc_start: 0.8020 (mt0) cc_final: 0.7765 (mt0) REVERT: X 353 MET cc_start: 0.7957 (ttt) cc_final: 0.7744 (ttt) REVERT: X 379 MET cc_start: 0.8867 (mmm) cc_final: 0.7741 (mmm) REVERT: X 396 MET cc_start: 0.8145 (mmm) cc_final: 0.7810 (mmt) REVERT: X 405 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7849 (pt0) REVERT: X 422 LYS cc_start: 0.8961 (mmmm) cc_final: 0.8540 (tppp) REVERT: X 460 ASN cc_start: 0.8477 (t0) cc_final: 0.8138 (t0) outliers start: 122 outliers final: 62 residues processed: 887 average time/residue: 0.2590 time to fit residues: 383.1342 Evaluate side-chains 809 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 711 time to evaluate : 1.819 ------------------------------------------------------------------------------- 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 344 VAL 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 344 VAL 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 344 VAL 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 409 LEU 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 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 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 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 441 ILE Chi-restraints excluded: chain N residue 464 ILE Chi-restraints excluded: chain O residue 295 PHE Chi-restraints excluded: chain O residue 344 VAL 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 344 VAL 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 344 VAL 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 344 VAL 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: 2.9990 chunk 271 optimal weight: 6.9990 chunk 82 optimal weight: 0.0970 chunk 362 optimal weight: 3.9990 chunk 411 optimal weight: 2.9990 chunk 260 optimal weight: 5.9990 chunk 367 optimal weight: 0.9990 chunk 187 optimal weight: 0.7980 chunk 162 optimal weight: 5.9990 chunk 293 optimal weight: 0.9980 chunk 523 optimal weight: 8.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 405 GLN C 405 GLN ** G 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 405 GLN P 405 GLN U 405 GLN W 405 GLN X 405 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.088837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.071560 restraints weight = 132882.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.073520 restraints weight = 70127.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.074869 restraints weight = 49009.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.075696 restraints weight = 39463.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.076125 restraints weight = 34461.108| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3939 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= 0.138 Angle : 0.613 8.557 59167 Z= 0.311 Chirality : 0.044 0.119 6840 Planarity : 0.004 0.046 7657 Dihedral : 4.641 43.990 6169 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.97 % Allowed : 19.03 % Favored : 77.00 % 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 aren not related in a simple way. whole: -1.07 (0.11), residues: 5568 helix: 1.10 (0.10), residues: 2256 sheet: -2.50 (0.13), residues: 1152 loop : -1.55 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 452 TYR 0.015 0.002 TYR L 275 PHE 0.014 0.002 PHE A 392 HIS 0.002 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00313 (43806) covalent geometry : angle 0.61273 (59167) hydrogen bonds : bond 0.02845 ( 2040) hydrogen bonds : angle 4.74670 ( 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 900 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 721 time to evaluate : 1.790 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: A 241 ARG cc_start: 0.8446 (mmp-170) cc_final: 0.7968 (mmp80) REVERT: A 247 MET cc_start: 0.9046 (ppp) cc_final: 0.8719 (ppp) REVERT: A 270 GLU cc_start: 0.7752 (tp30) cc_final: 0.6939 (tp30) REVERT: A 275 TYR cc_start: 0.8032 (t80) cc_final: 0.7422 (t80) REVERT: A 295 PHE cc_start: 0.7170 (OUTLIER) cc_final: 0.6324 (p90) REVERT: A 353 MET cc_start: 0.7774 (ttt) cc_final: 0.7564 (ttt) REVERT: A 379 MET cc_start: 0.8761 (mmm) cc_final: 0.7710 (mmm) REVERT: A 396 MET cc_start: 0.8115 (mmm) cc_final: 0.7760 (mmt) REVERT: A 460 ASN cc_start: 0.8384 (t0) cc_final: 0.8020 (t0) REVERT: B 270 GLU cc_start: 0.7599 (tp30) cc_final: 0.6783 (tp30) REVERT: B 295 PHE cc_start: 0.7146 (OUTLIER) cc_final: 0.6410 (p90) REVERT: B 344 VAL cc_start: 0.8890 (OUTLIER) cc_final: 0.8670 (t) REVERT: B 353 MET cc_start: 0.7835 (ttt) cc_final: 0.7536 (ttt) REVERT: B 379 MET cc_start: 0.8878 (mmm) cc_final: 0.7724 (mmm) REVERT: B 396 MET cc_start: 0.8141 (mmm) cc_final: 0.7785 (mmt) REVERT: B 405 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7857 (pt0) REVERT: B 416 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8133 (tp30) REVERT: B 460 ASN cc_start: 0.8354 (t0) cc_final: 0.7994 (t0) REVERT: C 270 GLU cc_start: 0.7701 (tp30) cc_final: 0.7271 (tp30) REVERT: C 295 PHE cc_start: 0.7149 (OUTLIER) cc_final: 0.6307 (p90) REVERT: C 353 MET cc_start: 0.7797 (ttt) cc_final: 0.7513 (ttt) REVERT: C 379 MET cc_start: 0.8840 (mmm) cc_final: 0.7789 (mmm) REVERT: C 396 MET cc_start: 0.8177 (mmm) cc_final: 0.7838 (mmt) REVERT: C 431 MET cc_start: 0.7531 (ppp) cc_final: 0.7299 (ppp) REVERT: C 460 ASN cc_start: 0.8381 (t0) cc_final: 0.8031 (t0) REVERT: D 241 ARG cc_start: 0.8461 (mmp-170) cc_final: 0.7976 (mmp80) REVERT: D 295 PHE cc_start: 0.7301 (OUTLIER) cc_final: 0.6501 (p90) REVERT: D 344 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8780 (t) REVERT: D 353 MET cc_start: 0.7784 (ttt) cc_final: 0.7580 (ttt) REVERT: D 379 MET cc_start: 0.8808 (mmm) cc_final: 0.7665 (mmm) REVERT: D 396 MET cc_start: 0.8137 (mmm) cc_final: 0.7737 (mmt) REVERT: D 430 MET cc_start: 0.7647 (mmm) cc_final: 0.7367 (mmm) REVERT: D 460 ASN cc_start: 0.8360 (t0) cc_final: 0.8021 (t0) REVERT: E 270 GLU cc_start: 0.7632 (tp30) cc_final: 0.7177 (tp30) REVERT: E 295 PHE cc_start: 0.7118 (OUTLIER) cc_final: 0.6363 (p90) REVERT: E 344 VAL cc_start: 0.8884 (OUTLIER) cc_final: 0.8674 (t) REVERT: E 353 MET cc_start: 0.7754 (ttt) cc_final: 0.7443 (ttt) REVERT: E 379 MET cc_start: 0.8889 (mmm) cc_final: 0.7791 (mmm) REVERT: E 431 MET cc_start: 0.7590 (ppp) cc_final: 0.7366 (ppp) REVERT: E 460 ASN cc_start: 0.8368 (t0) cc_final: 0.8056 (t0) REVERT: F 270 GLU cc_start: 0.7591 (tp30) cc_final: 0.7183 (tp30) REVERT: F 295 PHE cc_start: 0.7160 (OUTLIER) cc_final: 0.6421 (p90) REVERT: F 344 VAL cc_start: 0.8895 (OUTLIER) cc_final: 0.8681 (t) REVERT: F 353 MET cc_start: 0.7860 (ttt) cc_final: 0.7483 (ttt) REVERT: F 354 ASN cc_start: 0.8175 (m-40) cc_final: 0.7888 (m110) REVERT: F 379 MET cc_start: 0.8887 (mmm) cc_final: 0.7736 (mmm) REVERT: F 396 MET cc_start: 0.8169 (mmm) cc_final: 0.7817 (mmt) REVERT: F 416 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8147 (tp30) REVERT: F 460 ASN cc_start: 0.8360 (t0) cc_final: 0.8006 (t0) REVERT: G 270 GLU cc_start: 0.7736 (tp30) cc_final: 0.6874 (tp30) REVERT: G 295 PHE cc_start: 0.7282 (OUTLIER) cc_final: 0.6455 (p90) REVERT: G 379 MET cc_start: 0.8786 (mmm) cc_final: 0.7724 (mmm) REVERT: G 396 MET cc_start: 0.8170 (mmm) cc_final: 0.7800 (mmt) REVERT: G 460 ASN cc_start: 0.8409 (t0) cc_final: 0.8051 (t0) REVERT: H 270 GLU cc_start: 0.7614 (tp30) cc_final: 0.7167 (tp30) REVERT: H 295 PHE cc_start: 0.7120 (OUTLIER) cc_final: 0.6388 (p90) REVERT: H 353 MET cc_start: 0.7806 (ttt) cc_final: 0.7600 (ttt) REVERT: H 379 MET cc_start: 0.8778 (mmm) cc_final: 0.7762 (mmm) REVERT: H 416 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8165 (tp30) REVERT: H 431 MET cc_start: 0.7573 (ppp) cc_final: 0.7349 (ppp) REVERT: H 460 ASN cc_start: 0.8361 (t0) cc_final: 0.8037 (t0) REVERT: I 270 GLU cc_start: 0.7667 (tp30) cc_final: 0.7253 (tp30) REVERT: I 295 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.6524 (p90) REVERT: I 310 GLN cc_start: 0.8103 (mt0) cc_final: 0.7798 (mt0) REVERT: I 353 MET cc_start: 0.7668 (ttt) cc_final: 0.7266 (ttt) REVERT: I 354 ASN cc_start: 0.8176 (m-40) cc_final: 0.7892 (m110) REVERT: I 379 MET cc_start: 0.8867 (mmm) cc_final: 0.7813 (mmm) REVERT: I 396 MET cc_start: 0.8164 (mmm) cc_final: 0.7801 (mmt) REVERT: I 416 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8186 (tp30) REVERT: I 460 ASN cc_start: 0.8348 (t0) cc_final: 0.7987 (t0) REVERT: J 241 ARG cc_start: 0.8502 (mmp-170) cc_final: 0.7997 (mmp80) REVERT: J 270 GLU cc_start: 0.7750 (tp30) cc_final: 0.7482 (tp30) REVERT: J 295 PHE cc_start: 0.7130 (OUTLIER) cc_final: 0.6293 (p90) REVERT: J 379 MET cc_start: 0.8832 (mmm) cc_final: 0.7754 (mmm) REVERT: J 396 MET cc_start: 0.8147 (mmm) cc_final: 0.7746 (mmt) REVERT: J 430 MET cc_start: 0.7612 (mmm) cc_final: 0.7333 (mmm) REVERT: J 460 ASN cc_start: 0.8350 (t0) cc_final: 0.8037 (t0) REVERT: K 270 GLU cc_start: 0.7674 (tp30) cc_final: 0.7215 (tp30) REVERT: K 295 PHE cc_start: 0.7149 (OUTLIER) cc_final: 0.6404 (p90) REVERT: K 379 MET cc_start: 0.8845 (mmm) cc_final: 0.7839 (mmm) REVERT: K 416 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8180 (tp30) REVERT: K 431 MET cc_start: 0.7594 (ppp) cc_final: 0.7371 (ppp) REVERT: K 460 ASN cc_start: 0.8315 (t0) cc_final: 0.8001 (t0) REVERT: L 251 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8893 (mp) REVERT: L 270 GLU cc_start: 0.7653 (tp30) cc_final: 0.7242 (tp30) REVERT: L 295 PHE cc_start: 0.7147 (OUTLIER) cc_final: 0.6401 (p90) REVERT: L 379 MET cc_start: 0.8762 (mmm) cc_final: 0.7657 (mmm) REVERT: L 396 MET cc_start: 0.8144 (mmm) cc_final: 0.7775 (mmt) REVERT: L 416 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8172 (tp30) REVERT: L 460 ASN cc_start: 0.8385 (t0) cc_final: 0.8033 (t0) REVERT: M 241 ARG cc_start: 0.8454 (mmp-170) cc_final: 0.7975 (mmp80) REVERT: M 270 GLU cc_start: 0.7662 (tp30) cc_final: 0.7231 (tp30) REVERT: M 295 PHE cc_start: 0.7319 (OUTLIER) cc_final: 0.6530 (p90) REVERT: M 353 MET cc_start: 0.7738 (ttt) cc_final: 0.7444 (ttt) REVERT: M 354 ASN cc_start: 0.8155 (m-40) cc_final: 0.7851 (m110) REVERT: M 379 MET cc_start: 0.8811 (mmm) cc_final: 0.7758 (mmm) REVERT: M 396 MET cc_start: 0.8147 (mmm) cc_final: 0.7777 (mmt) REVERT: M 419 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8256 (tp) REVERT: M 460 ASN cc_start: 0.8333 (t0) cc_final: 0.7961 (t0) REVERT: N 239 GLU cc_start: 0.8467 (mp0) cc_final: 0.8121 (mp0) REVERT: N 251 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8885 (mp) REVERT: N 270 GLU cc_start: 0.7672 (tp30) cc_final: 0.7228 (tp30) REVERT: N 295 PHE cc_start: 0.7124 (OUTLIER) cc_final: 0.6459 (p90) REVERT: N 353 MET cc_start: 0.7879 (ttt) cc_final: 0.7483 (ttt) REVERT: N 354 ASN cc_start: 0.8171 (m-40) cc_final: 0.7901 (m110) REVERT: N 379 MET cc_start: 0.8828 (mmm) cc_final: 0.7729 (mmm) REVERT: N 396 MET cc_start: 0.8180 (mmm) cc_final: 0.7828 (mmt) REVERT: N 460 ASN cc_start: 0.8390 (t0) cc_final: 0.8041 (t0) REVERT: O 239 GLU cc_start: 0.8513 (mp0) cc_final: 0.8198 (mp0) REVERT: O 270 GLU cc_start: 0.7670 (tp30) cc_final: 0.7259 (tp30) REVERT: O 295 PHE cc_start: 0.7130 (OUTLIER) cc_final: 0.6389 (p90) REVERT: O 344 VAL cc_start: 0.8927 (OUTLIER) cc_final: 0.8718 (t) REVERT: O 379 MET cc_start: 0.8781 (mmm) cc_final: 0.7677 (mmm) REVERT: O 396 MET cc_start: 0.8190 (mmm) cc_final: 0.7829 (mmt) REVERT: O 460 ASN cc_start: 0.8308 (t0) cc_final: 0.7985 (t0) REVERT: P 241 ARG cc_start: 0.8463 (mmp-170) cc_final: 0.7980 (mmp80) REVERT: P 270 GLU cc_start: 0.7657 (tp30) cc_final: 0.7248 (tp30) REVERT: P 273 MET cc_start: 0.7274 (mtp) cc_final: 0.7030 (mtp) REVERT: P 295 PHE cc_start: 0.7285 (OUTLIER) cc_final: 0.6504 (p90) REVERT: P 344 VAL cc_start: 0.8947 (OUTLIER) cc_final: 0.8739 (t) REVERT: P 379 MET cc_start: 0.8872 (mmm) cc_final: 0.7737 (mmm) REVERT: P 396 MET cc_start: 0.8145 (mmm) cc_final: 0.7772 (mmt) REVERT: P 460 ASN cc_start: 0.8357 (t0) cc_final: 0.8039 (t0) REVERT: Q 241 ARG cc_start: 0.8442 (mmp-170) cc_final: 0.7970 (mmp80) REVERT: Q 270 GLU cc_start: 0.7644 (tp30) cc_final: 0.7251 (tp30) REVERT: Q 273 MET cc_start: 0.7233 (mtp) cc_final: 0.6996 (mtp) REVERT: Q 295 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6472 (p90) REVERT: Q 379 MET cc_start: 0.8801 (mmm) cc_final: 0.7738 (mmm) REVERT: Q 396 MET cc_start: 0.8175 (mmm) cc_final: 0.7812 (mmt) REVERT: Q 460 ASN cc_start: 0.8387 (t0) cc_final: 0.8032 (t0) REVERT: R 270 GLU cc_start: 0.7655 (tp30) cc_final: 0.7255 (tp30) REVERT: R 273 MET cc_start: 0.7207 (mtp) cc_final: 0.6989 (mtp) REVERT: R 295 PHE cc_start: 0.7133 (OUTLIER) cc_final: 0.6395 (p90) REVERT: R 379 MET cc_start: 0.8802 (mmm) cc_final: 0.7712 (mmm) REVERT: R 396 MET cc_start: 0.8182 (mmm) cc_final: 0.7831 (mmt) REVERT: R 460 ASN cc_start: 0.8343 (t0) cc_final: 0.8017 (t0) REVERT: S 241 ARG cc_start: 0.8469 (mmp-170) cc_final: 0.7994 (mmp80) REVERT: S 270 GLU cc_start: 0.7733 (tp30) cc_final: 0.7339 (tp30) REVERT: S 273 MET cc_start: 0.7168 (mtp) cc_final: 0.6946 (mtp) REVERT: S 295 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6340 (p90) REVERT: S 353 MET cc_start: 0.7888 (ttt) cc_final: 0.7606 (ttt) REVERT: S 354 ASN cc_start: 0.8163 (m-40) cc_final: 0.7856 (m110) REVERT: S 379 MET cc_start: 0.8710 (mmm) cc_final: 0.7663 (mmm) REVERT: S 396 MET cc_start: 0.8235 (mmm) cc_final: 0.8001 (mmm) REVERT: S 419 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8250 (tp) REVERT: S 460 ASN cc_start: 0.8380 (t0) cc_final: 0.8022 (t0) REVERT: T 239 GLU cc_start: 0.8488 (mp0) cc_final: 0.8143 (mp0) REVERT: T 270 GLU cc_start: 0.7660 (tp30) cc_final: 0.7233 (tp30) REVERT: T 295 PHE cc_start: 0.7294 (OUTLIER) cc_final: 0.6466 (p90) REVERT: T 344 VAL cc_start: 0.8856 (OUTLIER) cc_final: 0.8631 (t) REVERT: T 353 MET cc_start: 0.7777 (ttt) cc_final: 0.7388 (ttt) REVERT: T 354 ASN cc_start: 0.8174 (m-40) cc_final: 0.7904 (m110) REVERT: T 379 MET cc_start: 0.8896 (mmm) cc_final: 0.7760 (mmm) REVERT: T 396 MET cc_start: 0.8183 (mmm) cc_final: 0.7824 (mmt) REVERT: T 419 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8223 (tp) REVERT: T 460 ASN cc_start: 0.8367 (t0) cc_final: 0.7995 (t0) REVERT: U 270 GLU cc_start: 0.7674 (tp30) cc_final: 0.7252 (tp30) REVERT: U 273 MET cc_start: 0.7179 (mtp) cc_final: 0.6960 (mtp) REVERT: U 295 PHE cc_start: 0.7230 (OUTLIER) cc_final: 0.6394 (p90) REVERT: U 344 VAL cc_start: 0.8918 (OUTLIER) cc_final: 0.8704 (t) REVERT: U 379 MET cc_start: 0.8819 (mmm) cc_final: 0.7712 (mmm) REVERT: U 396 MET cc_start: 0.8186 (mmm) cc_final: 0.7819 (mmt) REVERT: U 460 ASN cc_start: 0.8311 (t0) cc_final: 0.8017 (t0) REVERT: V 241 ARG cc_start: 0.8481 (mmp-170) cc_final: 0.7987 (mmp80) REVERT: V 270 GLU cc_start: 0.7655 (tp30) cc_final: 0.7215 (tp30) REVERT: V 295 PHE cc_start: 0.7186 (OUTLIER) cc_final: 0.6440 (p90) REVERT: V 353 MET cc_start: 0.7847 (ttt) cc_final: 0.7546 (ttt) REVERT: V 354 ASN cc_start: 0.8156 (m-40) cc_final: 0.7852 (m110) REVERT: V 379 MET cc_start: 0.8800 (mmm) cc_final: 0.7733 (mmm) REVERT: V 396 MET cc_start: 0.8153 (mmm) cc_final: 0.7767 (mmt) REVERT: V 419 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8208 (tp) REVERT: V 460 ASN cc_start: 0.8307 (t0) cc_final: 0.7976 (t0) REVERT: W 270 GLU cc_start: 0.7673 (tp30) cc_final: 0.7212 (tp30) REVERT: W 295 PHE cc_start: 0.7245 (OUTLIER) cc_final: 0.6462 (p90) REVERT: W 353 MET cc_start: 0.7725 (ttt) cc_final: 0.7391 (ttt) REVERT: W 379 MET cc_start: 0.8763 (mmm) cc_final: 0.7682 (mmm) REVERT: W 431 MET cc_start: 0.7573 (ppp) cc_final: 0.7350 (ppp) REVERT: W 460 ASN cc_start: 0.8369 (t0) cc_final: 0.8024 (t0) REVERT: X 270 GLU cc_start: 0.7682 (tp30) cc_final: 0.7267 (tp30) REVERT: X 273 MET cc_start: 0.7188 (mtp) cc_final: 0.6966 (mtp) REVERT: X 295 PHE cc_start: 0.7142 (OUTLIER) cc_final: 0.6410 (p90) REVERT: X 379 MET cc_start: 0.8868 (mmm) cc_final: 0.7769 (mmm) REVERT: X 396 MET cc_start: 0.8171 (mmm) cc_final: 0.7813 (mmt) REVERT: X 405 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7845 (pt0) REVERT: X 460 ASN cc_start: 0.8384 (t0) cc_final: 0.8034 (t0) outliers start: 179 outliers final: 85 residues processed: 900 average time/residue: 0.2484 time to fit residues: 377.4193 Evaluate side-chains 824 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 699 time to evaluate : 1.496 ------------------------------------------------------------------------------- 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 344 VAL 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 344 VAL 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 344 VAL 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 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 251 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 419 ILE Chi-restraints excluded: chain M residue 441 ILE Chi-restraints excluded: chain M residue 464 ILE Chi-restraints excluded: chain N residue 251 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 344 VAL 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 344 VAL 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 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 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 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 344 VAL 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 344 VAL 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: 0.9980 chunk 59 optimal weight: 0.0000 chunk 57 optimal weight: 0.7980 chunk 446 optimal weight: 4.9990 chunk 260 optimal weight: 4.9990 chunk 181 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 chunk 337 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 252 optimal weight: 0.8980 chunk 360 optimal weight: 4.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 E 405 GLN ** G 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 405 GLN J 405 GLN ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 405 GLN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.087195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.072409 restraints weight = 130242.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.074406 restraints weight = 70079.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.075732 restraints weight = 48670.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.076527 restraints weight = 38859.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.077104 restraints weight = 34124.015| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3934 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= 0.123 Angle : 0.637 12.395 59167 Z= 0.322 Chirality : 0.044 0.131 6840 Planarity : 0.004 0.044 7657 Dihedral : 4.546 43.614 6169 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.83 % Allowed : 19.48 % Favored : 76.69 % 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 aren not related in a simple way. whole: -1.02 (0.11), residues: 5568 helix: 1.08 (0.11), residues: 2256 sheet: -2.40 (0.13), residues: 1152 loop : -1.48 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 452 TYR 0.015 0.001 TYR D 275 PHE 0.013 0.002 PHE T 392 HIS 0.003 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00279 (43806) covalent geometry : angle 0.63654 (59167) hydrogen bonds : bond 0.02764 ( 2040) hydrogen bonds : angle 4.67757 ( 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 919 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 746 time to evaluate : 1.747 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 241 ARG cc_start: 0.8380 (mmp-170) cc_final: 0.7863 (mmp80) REVERT: A 295 PHE cc_start: 0.7109 (OUTLIER) cc_final: 0.6366 (p90) REVERT: A 309 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8830 (tp) REVERT: A 379 MET cc_start: 0.8656 (mmm) cc_final: 0.7631 (mmm) REVERT: A 396 MET cc_start: 0.8099 (mmm) cc_final: 0.7726 (mmt) REVERT: A 430 MET cc_start: 0.8191 (mmm) cc_final: 0.6903 (mmp) REVERT: A 460 ASN cc_start: 0.8274 (t0) cc_final: 0.7913 (t0) REVERT: B 247 MET cc_start: 0.9049 (ppp) cc_final: 0.8648 (ppp) REVERT: B 273 MET cc_start: 0.6954 (mtp) cc_final: 0.6750 (mtp) REVERT: B 295 PHE cc_start: 0.7081 (OUTLIER) cc_final: 0.6340 (p90) REVERT: B 344 VAL cc_start: 0.8912 (OUTLIER) cc_final: 0.8681 (t) REVERT: B 379 MET cc_start: 0.8749 (mmm) cc_final: 0.7611 (mmm) REVERT: B 396 MET cc_start: 0.8159 (mmm) cc_final: 0.7749 (mmt) REVERT: B 416 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8179 (tp30) REVERT: B 430 MET cc_start: 0.8062 (mmm) cc_final: 0.7065 (mmt) REVERT: B 460 ASN cc_start: 0.8212 (t0) cc_final: 0.7822 (t0) REVERT: C 239 GLU cc_start: 0.8503 (mp0) cc_final: 0.8085 (mp0) REVERT: C 247 MET cc_start: 0.9036 (ppp) cc_final: 0.8643 (ppp) REVERT: C 295 PHE cc_start: 0.7102 (OUTLIER) cc_final: 0.6312 (p90) REVERT: C 379 MET cc_start: 0.8740 (mmm) cc_final: 0.7707 (mmm) REVERT: C 396 MET cc_start: 0.8125 (mmm) cc_final: 0.7777 (mmt) REVERT: C 460 ASN cc_start: 0.8302 (t0) cc_final: 0.7911 (t0) REVERT: D 241 ARG cc_start: 0.8372 (mmp-170) cc_final: 0.7867 (mmp80) REVERT: D 273 MET cc_start: 0.7075 (mtp) cc_final: 0.6767 (mtp) REVERT: D 295 PHE cc_start: 0.7069 (OUTLIER) cc_final: 0.6342 (p90) REVERT: D 344 VAL cc_start: 0.8987 (OUTLIER) cc_final: 0.8778 (t) REVERT: D 353 MET cc_start: 0.7664 (ttt) cc_final: 0.7416 (ttt) REVERT: D 379 MET cc_start: 0.8703 (mmm) cc_final: 0.7581 (mmm) REVERT: D 460 ASN cc_start: 0.8251 (t0) cc_final: 0.7877 (t0) REVERT: E 239 GLU cc_start: 0.8519 (mp0) cc_final: 0.8277 (mp0) REVERT: E 270 GLU cc_start: 0.7573 (tp30) cc_final: 0.6730 (tp30) REVERT: E 295 PHE cc_start: 0.7060 (OUTLIER) cc_final: 0.6389 (p90) REVERT: E 344 VAL cc_start: 0.8879 (OUTLIER) cc_final: 0.8656 (t) REVERT: E 379 MET cc_start: 0.8776 (mmm) cc_final: 0.7729 (mmm) REVERT: E 396 MET cc_start: 0.8079 (mmm) cc_final: 0.7782 (mmt) REVERT: E 431 MET cc_start: 0.7625 (ppp) cc_final: 0.7388 (ppp) REVERT: E 460 ASN cc_start: 0.8288 (t0) cc_final: 0.7926 (t0) REVERT: F 239 GLU cc_start: 0.8543 (mp0) cc_final: 0.8320 (mp0) REVERT: F 295 PHE cc_start: 0.7127 (OUTLIER) cc_final: 0.6401 (p90) REVERT: F 344 VAL cc_start: 0.8911 (OUTLIER) cc_final: 0.8685 (t) REVERT: F 354 ASN cc_start: 0.8122 (m-40) cc_final: 0.7764 (m110) REVERT: F 379 MET cc_start: 0.8787 (mmm) cc_final: 0.7684 (mmm) REVERT: F 416 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8198 (tp30) REVERT: F 460 ASN cc_start: 0.8264 (t0) cc_final: 0.7904 (t0) REVERT: G 247 MET cc_start: 0.9056 (ppp) cc_final: 0.8663 (ppp) REVERT: G 295 PHE cc_start: 0.7052 (OUTLIER) cc_final: 0.6373 (p90) REVERT: G 379 MET cc_start: 0.8696 (mmm) cc_final: 0.7655 (mmm) REVERT: G 460 ASN cc_start: 0.8282 (t0) cc_final: 0.7894 (t0) REVERT: H 239 GLU cc_start: 0.8506 (mp0) cc_final: 0.8273 (mp0) REVERT: H 270 GLU cc_start: 0.7562 (tp30) cc_final: 0.6723 (tp30) REVERT: H 275 TYR cc_start: 0.8017 (t80) cc_final: 0.7366 (t80) REVERT: H 295 PHE cc_start: 0.7104 (OUTLIER) cc_final: 0.6312 (p90) REVERT: H 353 MET cc_start: 0.7663 (ttt) cc_final: 0.7420 (ttt) REVERT: H 379 MET cc_start: 0.8630 (mmm) cc_final: 0.7662 (mmm) REVERT: H 396 MET cc_start: 0.8090 (mmm) cc_final: 0.7795 (mmt) REVERT: H 416 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8178 (tp30) REVERT: H 431 MET cc_start: 0.7638 (ppp) cc_final: 0.7381 (ppp) REVERT: H 460 ASN cc_start: 0.8371 (t0) cc_final: 0.7959 (t0) REVERT: I 239 GLU cc_start: 0.8547 (mp0) cc_final: 0.8311 (mp0) REVERT: I 295 PHE cc_start: 0.7139 (OUTLIER) cc_final: 0.6473 (p90) REVERT: I 354 ASN cc_start: 0.8160 (m-40) cc_final: 0.7790 (m110) REVERT: I 379 MET cc_start: 0.8753 (mmm) cc_final: 0.7722 (mmm) REVERT: I 416 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8217 (tp30) REVERT: I 460 ASN cc_start: 0.8248 (t0) cc_final: 0.7888 (t0) REVERT: J 241 ARG cc_start: 0.8367 (mmp-170) cc_final: 0.7857 (mmp80) REVERT: J 247 MET cc_start: 0.9027 (ppp) cc_final: 0.8425 (ppp) REVERT: J 270 GLU cc_start: 0.7710 (tp30) cc_final: 0.6961 (tp30) REVERT: J 273 MET cc_start: 0.7056 (mtp) cc_final: 0.6763 (mtp) REVERT: J 295 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.6341 (p90) REVERT: J 309 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8815 (tp) REVERT: J 379 MET cc_start: 0.8771 (mmm) cc_final: 0.7710 (mmm) REVERT: J 460 ASN cc_start: 0.8377 (t0) cc_final: 0.7954 (t0) REVERT: K 239 GLU cc_start: 0.8508 (mp0) cc_final: 0.8282 (mp0) REVERT: K 270 GLU cc_start: 0.7598 (tp30) cc_final: 0.6758 (tp30) REVERT: K 295 PHE cc_start: 0.7081 (OUTLIER) cc_final: 0.6340 (p90) REVERT: K 379 MET cc_start: 0.8709 (mmm) cc_final: 0.7733 (mmm) REVERT: K 396 MET cc_start: 0.8048 (mmm) cc_final: 0.7756 (mmt) REVERT: K 416 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8163 (tp30) REVERT: K 431 MET cc_start: 0.7667 (ppp) cc_final: 0.7377 (ppp) REVERT: K 460 ASN cc_start: 0.8302 (t0) cc_final: 0.7898 (t0) REVERT: L 275 TYR cc_start: 0.7989 (t80) cc_final: 0.7294 (t80) REVERT: L 295 PHE cc_start: 0.7113 (OUTLIER) cc_final: 0.6382 (p90) REVERT: L 379 MET cc_start: 0.8629 (mmm) cc_final: 0.7570 (mmm) REVERT: L 416 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8213 (tp30) REVERT: L 460 ASN cc_start: 0.8304 (t0) cc_final: 0.7914 (t0) REVERT: M 239 GLU cc_start: 0.8348 (mp0) cc_final: 0.8102 (mp0) REVERT: M 241 ARG cc_start: 0.8392 (mmp-170) cc_final: 0.7924 (mmp80) REVERT: M 247 MET cc_start: 0.9045 (ppp) cc_final: 0.8658 (ppp) REVERT: M 295 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.6524 (p90) REVERT: M 354 ASN cc_start: 0.8140 (m-40) cc_final: 0.7763 (m110) REVERT: M 379 MET cc_start: 0.8717 (mmm) cc_final: 0.7682 (mmm) REVERT: M 460 ASN cc_start: 0.8287 (t0) cc_final: 0.7881 (t0) REVERT: N 239 GLU cc_start: 0.8415 (mp0) cc_final: 0.8085 (mp0) REVERT: N 270 GLU cc_start: 0.7623 (tp30) cc_final: 0.7171 (tp30) REVERT: N 295 PHE cc_start: 0.7106 (OUTLIER) cc_final: 0.6375 (p90) REVERT: N 354 ASN cc_start: 0.8140 (m-40) cc_final: 0.7789 (m110) REVERT: N 379 MET cc_start: 0.8717 (mmm) cc_final: 0.7642 (mmm) REVERT: N 460 ASN cc_start: 0.8346 (t0) cc_final: 0.7971 (t0) REVERT: O 239 GLU cc_start: 0.8547 (mp0) cc_final: 0.8308 (mp0) REVERT: O 273 MET cc_start: 0.7110 (mtp) cc_final: 0.6801 (mtp) REVERT: O 295 PHE cc_start: 0.7081 (OUTLIER) cc_final: 0.6286 (p90) REVERT: O 344 VAL cc_start: 0.8943 (OUTLIER) cc_final: 0.8726 (t) REVERT: O 379 MET cc_start: 0.8660 (mmm) cc_final: 0.7583 (mmm) REVERT: O 460 ASN cc_start: 0.8295 (t0) cc_final: 0.7939 (t0) REVERT: P 241 ARG cc_start: 0.8340 (mmp-170) cc_final: 0.7894 (mmp80) REVERT: P 247 MET cc_start: 0.9052 (ppp) cc_final: 0.8669 (ppp) REVERT: P 273 MET cc_start: 0.7243 (mtp) cc_final: 0.6958 (mtp) REVERT: P 295 PHE cc_start: 0.7208 (OUTLIER) cc_final: 0.6481 (p90) REVERT: P 344 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8740 (t) REVERT: P 379 MET cc_start: 0.8768 (mmm) cc_final: 0.7644 (mmm) REVERT: P 460 ASN cc_start: 0.8341 (t0) cc_final: 0.7913 (t0) REVERT: Q 273 MET cc_start: 0.7240 (mtp) cc_final: 0.6961 (mtp) REVERT: Q 295 PHE cc_start: 0.7039 (OUTLIER) cc_final: 0.6305 (p90) REVERT: Q 379 MET cc_start: 0.8697 (mmm) cc_final: 0.7658 (mmm) REVERT: Q 460 ASN cc_start: 0.8302 (t0) cc_final: 0.7914 (t0) REVERT: R 239 GLU cc_start: 0.8510 (mp0) cc_final: 0.8063 (mp0) REVERT: R 247 MET cc_start: 0.9051 (ppp) cc_final: 0.8660 (ppp) REVERT: R 295 PHE cc_start: 0.7056 (OUTLIER) cc_final: 0.6291 (p90) REVERT: R 379 MET cc_start: 0.8713 (mmm) cc_final: 0.7673 (mmm) REVERT: R 460 ASN cc_start: 0.8255 (t0) cc_final: 0.7900 (t0) REVERT: S 295 PHE cc_start: 0.7218 (OUTLIER) cc_final: 0.6258 (p90) REVERT: S 354 ASN cc_start: 0.8139 (m-40) cc_final: 0.7773 (m110) REVERT: S 379 MET cc_start: 0.8607 (mmm) cc_final: 0.7589 (mmm) REVERT: S 396 MET cc_start: 0.8184 (mmm) cc_final: 0.7915 (mmm) REVERT: S 431 MET cc_start: 0.7743 (ttt) cc_final: 0.7534 (ppp) REVERT: S 460 ASN cc_start: 0.8220 (t0) cc_final: 0.7847 (t0) REVERT: T 239 GLU cc_start: 0.8421 (mp0) cc_final: 0.8071 (mp0) REVERT: T 247 MET cc_start: 0.9034 (ppp) cc_final: 0.8553 (ppp) REVERT: T 295 PHE cc_start: 0.7081 (OUTLIER) cc_final: 0.6334 (p90) REVERT: T 344 VAL cc_start: 0.8930 (OUTLIER) cc_final: 0.8703 (t) REVERT: T 379 MET cc_start: 0.8810 (mmm) cc_final: 0.7668 (mmm) REVERT: T 405 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7802 (pt0) REVERT: T 460 ASN cc_start: 0.8279 (t0) cc_final: 0.7889 (t0) REVERT: U 239 GLU cc_start: 0.8514 (mp0) cc_final: 0.8116 (mp0) REVERT: U 247 MET cc_start: 0.9033 (ppp) cc_final: 0.8637 (ppp) REVERT: U 295 PHE cc_start: 0.6983 (OUTLIER) cc_final: 0.6163 (p90) REVERT: U 344 VAL cc_start: 0.8923 (OUTLIER) cc_final: 0.8709 (t) REVERT: U 379 MET cc_start: 0.8700 (mmm) cc_final: 0.7582 (mmm) REVERT: U 460 ASN cc_start: 0.8220 (t0) cc_final: 0.7867 (t0) REVERT: V 241 ARG cc_start: 0.8378 (mmp-170) cc_final: 0.7865 (mmp80) REVERT: V 247 MET cc_start: 0.9041 (ppp) cc_final: 0.8654 (ppp) REVERT: V 295 PHE cc_start: 0.7131 (OUTLIER) cc_final: 0.6341 (p90) REVERT: V 354 ASN cc_start: 0.8097 (m-40) cc_final: 0.7723 (m110) REVERT: V 379 MET cc_start: 0.8687 (mmm) cc_final: 0.7643 (mmm) REVERT: V 460 ASN cc_start: 0.8254 (t0) cc_final: 0.7911 (t0) REVERT: W 270 GLU cc_start: 0.7591 (tp30) cc_final: 0.6746 (tp30) REVERT: W 295 PHE cc_start: 0.7197 (OUTLIER) cc_final: 0.6455 (p90) REVERT: W 379 MET cc_start: 0.8641 (mmm) cc_final: 0.7600 (mmm) REVERT: W 396 MET cc_start: 0.8107 (mmm) cc_final: 0.7801 (mmt) REVERT: W 431 MET cc_start: 0.7596 (ppp) cc_final: 0.7395 (ppp) REVERT: W 460 ASN cc_start: 0.8292 (t0) cc_final: 0.7887 (t0) REVERT: X 239 GLU cc_start: 0.8511 (mp0) cc_final: 0.8094 (mp0) REVERT: X 247 MET cc_start: 0.9038 (ppp) cc_final: 0.8653 (ppp) REVERT: X 295 PHE cc_start: 0.7063 (OUTLIER) cc_final: 0.6302 (p90) REVERT: X 379 MET cc_start: 0.8763 (mmm) cc_final: 0.7685 (mmm) REVERT: X 460 ASN cc_start: 0.8309 (t0) cc_final: 0.7924 (t0) outliers start: 173 outliers final: 93 residues processed: 907 average time/residue: 0.2379 time to fit residues: 364.2634 Evaluate side-chains 861 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 733 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 309 LEU 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 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 344 VAL 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 344 VAL 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 344 VAL 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 242 VAL 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 309 LEU 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 441 ILE Chi-restraints excluded: chain N residue 464 ILE Chi-restraints excluded: chain O residue 295 PHE Chi-restraints excluded: chain O residue 344 VAL 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 344 VAL 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 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 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 344 VAL 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 344 VAL 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: 0.9990 chunk 236 optimal weight: 0.8980 chunk 426 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 435 optimal weight: 0.6980 chunk 453 optimal weight: 4.9990 chunk 326 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 458 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 344 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN ** G 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 405 GLN S 405 GLN ** U 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.088993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.075072 restraints weight = 136538.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.077323 restraints weight = 67145.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.078822 restraints weight = 44399.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.079772 restraints weight = 33697.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.080420 restraints weight = 27963.915| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3989 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 : 0.673 12.925 59167 Z= 0.334 Chirality : 0.045 0.151 6840 Planarity : 0.004 0.041 7657 Dihedral : 4.503 42.357 6169 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.08 % Allowed : 21.54 % 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 aren not related in a simple way. whole: -1.07 (0.11), residues: 5568 helix: 0.95 (0.11), residues: 2256 sheet: -2.31 (0.14), residues: 1152 loop : -1.48 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 417 TYR 0.017 0.001 TYR X 275 PHE 0.013 0.001 PHE F 392 HIS 0.002 0.001 HIS E 412 Details of bonding type rmsd covalent geometry : bond 0.00300 (43806) covalent geometry : angle 0.67257 (59167) hydrogen bonds : bond 0.02804 ( 2040) hydrogen bonds : angle 4.65822 ( 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 905 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 766 time to evaluate : 1.769 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: A 295 PHE cc_start: 0.7149 (OUTLIER) cc_final: 0.6344 (p90) REVERT: A 379 MET cc_start: 0.8699 (mmm) cc_final: 0.7682 (mmm) REVERT: A 396 MET cc_start: 0.8058 (mmm) cc_final: 0.7733 (mmt) REVERT: A 460 ASN cc_start: 0.8183 (t0) cc_final: 0.7792 (t0) REVERT: B 295 PHE cc_start: 0.7057 (OUTLIER) cc_final: 0.6357 (p90) REVERT: B 344 VAL cc_start: 0.8900 (OUTLIER) cc_final: 0.8673 (t) REVERT: B 353 MET cc_start: 0.7526 (tpp) cc_final: 0.7025 (ttt) REVERT: B 379 MET cc_start: 0.8732 (mmm) cc_final: 0.7627 (mmm) REVERT: B 396 MET cc_start: 0.8083 (mmm) cc_final: 0.7724 (mmt) REVERT: B 416 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8252 (tp30) REVERT: B 460 ASN cc_start: 0.8244 (t0) cc_final: 0.7815 (t0) REVERT: C 239 GLU cc_start: 0.8529 (mp0) cc_final: 0.8073 (mp0) REVERT: C 295 PHE cc_start: 0.7079 (OUTLIER) cc_final: 0.6271 (p90) REVERT: C 353 MET cc_start: 0.7477 (tpp) cc_final: 0.7006 (ttt) REVERT: C 379 MET cc_start: 0.8722 (mmm) cc_final: 0.7676 (mmm) REVERT: C 396 MET cc_start: 0.8133 (mmm) cc_final: 0.7743 (mmt) REVERT: C 405 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7789 (pt0) REVERT: C 460 ASN cc_start: 0.8193 (t0) cc_final: 0.7766 (t0) REVERT: D 273 MET cc_start: 0.7080 (mtp) cc_final: 0.6750 (mtp) REVERT: D 295 PHE cc_start: 0.7054 (OUTLIER) cc_final: 0.6287 (p90) REVERT: D 344 VAL cc_start: 0.8931 (OUTLIER) cc_final: 0.8702 (t) REVERT: D 353 MET cc_start: 0.7662 (ttt) cc_final: 0.7433 (ttt) REVERT: D 379 MET cc_start: 0.8728 (mmm) cc_final: 0.7588 (mmm) REVERT: D 396 MET cc_start: 0.8101 (mmm) cc_final: 0.7593 (mmt) REVERT: D 460 ASN cc_start: 0.8176 (t0) cc_final: 0.7827 (t0) REVERT: E 239 GLU cc_start: 0.8443 (mp0) cc_final: 0.8233 (mp0) REVERT: E 295 PHE cc_start: 0.7058 (OUTLIER) cc_final: 0.6330 (p90) REVERT: E 353 MET cc_start: 0.7466 (tpp) cc_final: 0.6979 (ttt) REVERT: E 396 MET cc_start: 0.8048 (mmm) cc_final: 0.7720 (mmt) REVERT: E 430 MET cc_start: 0.8193 (mmm) cc_final: 0.7613 (mmm) REVERT: E 460 ASN cc_start: 0.8272 (t0) cc_final: 0.7858 (t0) REVERT: F 247 MET cc_start: 0.8918 (ppp) cc_final: 0.8474 (ppp) REVERT: F 295 PHE cc_start: 0.7126 (OUTLIER) cc_final: 0.6350 (p90) REVERT: F 344 VAL cc_start: 0.8907 (OUTLIER) cc_final: 0.8684 (t) REVERT: F 353 MET cc_start: 0.7567 (tpp) cc_final: 0.7066 (ttt) REVERT: F 379 MET cc_start: 0.8788 (mmm) cc_final: 0.7670 (mmm) REVERT: F 396 MET cc_start: 0.8150 (mmm) cc_final: 0.7640 (mmt) REVERT: F 416 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8252 (tp30) REVERT: F 460 ASN cc_start: 0.8155 (t0) cc_final: 0.7724 (t0) REVERT: G 295 PHE cc_start: 0.7088 (OUTLIER) cc_final: 0.6426 (p90) REVERT: G 379 MET cc_start: 0.8729 (mmm) cc_final: 0.7704 (mmm) REVERT: G 396 MET cc_start: 0.8125 (mmm) cc_final: 0.7621 (mmt) REVERT: G 460 ASN cc_start: 0.8239 (t0) cc_final: 0.7759 (t0) REVERT: H 247 MET cc_start: 0.8918 (ppp) cc_final: 0.8436 (ppp) REVERT: H 295 PHE cc_start: 0.7142 (OUTLIER) cc_final: 0.6504 (p90) REVERT: H 353 MET cc_start: 0.7640 (ttt) cc_final: 0.7397 (ttt) REVERT: H 379 MET cc_start: 0.8742 (mmm) cc_final: 0.7728 (mmm) REVERT: H 396 MET cc_start: 0.8058 (mmm) cc_final: 0.7736 (mmt) REVERT: H 416 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8280 (tp30) REVERT: H 430 MET cc_start: 0.8087 (mmm) cc_final: 0.7493 (mmm) REVERT: H 460 ASN cc_start: 0.8292 (t0) cc_final: 0.7856 (t0) REVERT: I 247 MET cc_start: 0.8925 (ppp) cc_final: 0.8489 (ppp) REVERT: I 295 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.6412 (p90) REVERT: I 379 MET cc_start: 0.8760 (mmm) cc_final: 0.7741 (mmm) REVERT: I 396 MET cc_start: 0.8145 (mmm) cc_final: 0.7643 (mmt) REVERT: I 416 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8249 (tp30) REVERT: I 460 ASN cc_start: 0.8148 (t0) cc_final: 0.7712 (t0) REVERT: J 247 MET cc_start: 0.9010 (ppp) cc_final: 0.8538 (ppp) REVERT: J 270 GLU cc_start: 0.7446 (tp30) cc_final: 0.6874 (tp30) REVERT: J 273 MET cc_start: 0.6999 (mtp) cc_final: 0.6640 (mtp) REVERT: J 295 PHE cc_start: 0.7039 (OUTLIER) cc_final: 0.6321 (p90) REVERT: J 309 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8788 (tp) REVERT: J 379 MET cc_start: 0.8766 (mmm) cc_final: 0.7716 (mmm) REVERT: J 396 MET cc_start: 0.8143 (mmm) cc_final: 0.7620 (mmt) REVERT: J 405 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7802 (pt0) REVERT: J 430 MET cc_start: 0.8080 (mmm) cc_final: 0.7538 (mmm) REVERT: J 460 ASN cc_start: 0.8223 (t0) cc_final: 0.7807 (t0) REVERT: K 295 PHE cc_start: 0.7111 (OUTLIER) cc_final: 0.6405 (p90) REVERT: K 379 MET cc_start: 0.8786 (mmm) cc_final: 0.7829 (mmm) REVERT: K 396 MET cc_start: 0.8037 (mmm) cc_final: 0.7695 (mmt) REVERT: K 416 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8269 (tp30) REVERT: K 430 MET cc_start: 0.8071 (mmm) cc_final: 0.7429 (mmm) REVERT: K 460 ASN cc_start: 0.8180 (t0) cc_final: 0.7753 (t0) REVERT: L 247 MET cc_start: 0.8939 (ppp) cc_final: 0.8524 (ppp) REVERT: L 295 PHE cc_start: 0.7077 (OUTLIER) cc_final: 0.6296 (p90) REVERT: L 353 MET cc_start: 0.7571 (tpp) cc_final: 0.7104 (ttt) REVERT: L 379 MET cc_start: 0.8677 (mmm) cc_final: 0.7622 (mmm) REVERT: L 396 MET cc_start: 0.8146 (mmm) cc_final: 0.7634 (mmt) REVERT: L 416 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8261 (tp30) REVERT: L 460 ASN cc_start: 0.8254 (t0) cc_final: 0.7822 (t0) REVERT: M 239 GLU cc_start: 0.8273 (mp0) cc_final: 0.8043 (mp0) REVERT: M 241 ARG cc_start: 0.8257 (mmp-170) cc_final: 0.7828 (mmp80) REVERT: M 295 PHE cc_start: 0.7208 (OUTLIER) cc_final: 0.6390 (p90) REVERT: M 353 MET cc_start: 0.7479 (tpp) cc_final: 0.6988 (ttt) REVERT: M 354 ASN cc_start: 0.8030 (m-40) cc_final: 0.7780 (m110) REVERT: M 379 MET cc_start: 0.8752 (mmm) cc_final: 0.7724 (mmm) REVERT: M 396 MET cc_start: 0.8149 (mmm) cc_final: 0.7630 (mmt) REVERT: M 460 ASN cc_start: 0.8195 (t0) cc_final: 0.7743 (t0) REVERT: N 239 GLU cc_start: 0.8301 (mp0) cc_final: 0.8020 (mp0) REVERT: N 247 MET cc_start: 0.8972 (ppp) cc_final: 0.8578 (ppp) REVERT: N 295 PHE cc_start: 0.7086 (OUTLIER) cc_final: 0.6392 (p90) REVERT: N 354 ASN cc_start: 0.8022 (m-40) cc_final: 0.7717 (m110) REVERT: N 379 MET cc_start: 0.8733 (mmm) cc_final: 0.7677 (mmm) REVERT: N 396 MET cc_start: 0.8110 (mmm) cc_final: 0.7631 (mmt) REVERT: N 430 MET cc_start: 0.8037 (mmm) cc_final: 0.7458 (mmm) REVERT: N 460 ASN cc_start: 0.8244 (t0) cc_final: 0.7822 (t0) REVERT: O 247 MET cc_start: 0.8915 (ppp) cc_final: 0.8477 (ppp) REVERT: O 295 PHE cc_start: 0.7007 (OUTLIER) cc_final: 0.6176 (p90) REVERT: O 344 VAL cc_start: 0.8881 (OUTLIER) cc_final: 0.8648 (t) REVERT: O 379 MET cc_start: 0.8739 (mmm) cc_final: 0.7666 (mmm) REVERT: O 396 MET cc_start: 0.8152 (mmm) cc_final: 0.7644 (mmt) REVERT: O 460 ASN cc_start: 0.8164 (t0) cc_final: 0.7813 (t0) REVERT: P 295 PHE cc_start: 0.7059 (OUTLIER) cc_final: 0.6271 (p90) REVERT: P 344 VAL cc_start: 0.8911 (OUTLIER) cc_final: 0.8680 (t) REVERT: P 379 MET cc_start: 0.8770 (mmm) cc_final: 0.7661 (mmm) REVERT: P 396 MET cc_start: 0.8148 (mmm) cc_final: 0.7625 (mmt) REVERT: P 460 ASN cc_start: 0.8249 (t0) cc_final: 0.7828 (t0) REVERT: Q 295 PHE cc_start: 0.7045 (OUTLIER) cc_final: 0.6346 (p90) REVERT: Q 379 MET cc_start: 0.8710 (mmm) cc_final: 0.7682 (mmm) REVERT: Q 396 MET cc_start: 0.8150 (mmm) cc_final: 0.7642 (mmt) REVERT: Q 460 ASN cc_start: 0.8246 (t0) cc_final: 0.7829 (t0) REVERT: R 239 GLU cc_start: 0.8480 (mp0) cc_final: 0.8004 (mp0) REVERT: R 295 PHE cc_start: 0.7100 (OUTLIER) cc_final: 0.6378 (p90) REVERT: R 379 MET cc_start: 0.8706 (mmm) cc_final: 0.7658 (mmm) REVERT: R 396 MET cc_start: 0.8164 (mmm) cc_final: 0.7651 (mmt) REVERT: R 460 ASN cc_start: 0.8192 (t0) cc_final: 0.7774 (t0) REVERT: S 247 MET cc_start: 0.9081 (ppp) cc_final: 0.8344 (ppp) REVERT: S 295 PHE cc_start: 0.7107 (OUTLIER) cc_final: 0.6318 (p90) REVERT: S 353 MET cc_start: 0.7537 (tpp) cc_final: 0.7066 (ttt) REVERT: S 354 ASN cc_start: 0.8033 (m-40) cc_final: 0.7782 (m110) REVERT: S 379 MET cc_start: 0.8691 (mmm) cc_final: 0.7664 (mmm) REVERT: S 460 ASN cc_start: 0.8184 (t0) cc_final: 0.7804 (t0) REVERT: T 239 GLU cc_start: 0.8308 (mp0) cc_final: 0.8010 (mp0) REVERT: T 247 MET cc_start: 0.8981 (ppp) cc_final: 0.8587 (ppp) REVERT: T 295 PHE cc_start: 0.7103 (OUTLIER) cc_final: 0.6377 (p90) REVERT: T 344 VAL cc_start: 0.8886 (OUTLIER) cc_final: 0.8654 (t) REVERT: T 353 MET cc_start: 0.7503 (tpp) cc_final: 0.7043 (ttt) REVERT: T 379 MET cc_start: 0.8810 (mmm) cc_final: 0.7688 (mmm) REVERT: T 396 MET cc_start: 0.8134 (mmm) cc_final: 0.7630 (mmt) REVERT: T 460 ASN cc_start: 0.8273 (t0) cc_final: 0.7855 (t0) REVERT: U 239 GLU cc_start: 0.8546 (mp0) cc_final: 0.8086 (mp0) REVERT: U 295 PHE cc_start: 0.7048 (OUTLIER) cc_final: 0.6225 (p90) REVERT: U 344 VAL cc_start: 0.8873 (OUTLIER) cc_final: 0.8631 (t) REVERT: U 379 MET cc_start: 0.8726 (mmm) cc_final: 0.7617 (mmm) REVERT: U 396 MET cc_start: 0.8155 (mmm) cc_final: 0.7641 (mmt) REVERT: U 405 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7780 (pt0) REVERT: U 460 ASN cc_start: 0.8195 (t0) cc_final: 0.7777 (t0) REVERT: V 295 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.6344 (p90) REVERT: V 353 MET cc_start: 0.7514 (tpp) cc_final: 0.7011 (ttt) REVERT: V 354 ASN cc_start: 0.8031 (m-40) cc_final: 0.7785 (m110) REVERT: V 379 MET cc_start: 0.8730 (mmm) cc_final: 0.7697 (mmm) REVERT: V 396 MET cc_start: 0.8136 (mmm) cc_final: 0.7630 (mmt) REVERT: V 460 ASN cc_start: 0.8240 (t0) cc_final: 0.7833 (t0) REVERT: W 247 MET cc_start: 0.8905 (ppp) cc_final: 0.8464 (ppp) REVERT: W 295 PHE cc_start: 0.7089 (OUTLIER) cc_final: 0.6347 (p90) REVERT: W 379 MET cc_start: 0.8709 (mmm) cc_final: 0.7666 (mmm) REVERT: W 396 MET cc_start: 0.8077 (mmm) cc_final: 0.7770 (mmt) REVERT: W 430 MET cc_start: 0.8183 (mmm) cc_final: 0.7586 (mmm) REVERT: W 460 ASN cc_start: 0.8277 (t0) cc_final: 0.7845 (t0) REVERT: X 239 GLU cc_start: 0.8490 (mp0) cc_final: 0.8022 (mp0) REVERT: X 295 PHE cc_start: 0.7093 (OUTLIER) cc_final: 0.6376 (p90) REVERT: X 379 MET cc_start: 0.8763 (mmm) cc_final: 0.7706 (mmm) REVERT: X 396 MET cc_start: 0.8143 (mmm) cc_final: 0.7646 (mmt) REVERT: X 460 ASN cc_start: 0.8215 (t0) cc_final: 0.7803 (t0) outliers start: 139 outliers final: 94 residues processed: 880 average time/residue: 0.2493 time to fit residues: 372.8184 Evaluate side-chains 835 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 706 time to evaluate : 1.864 ------------------------------------------------------------------------------- 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 344 VAL 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 344 VAL 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 242 VAL 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 242 VAL 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 309 LEU Chi-restraints excluded: chain J residue 311 ASP 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 441 ILE Chi-restraints excluded: chain N residue 464 ILE Chi-restraints excluded: chain O residue 295 PHE Chi-restraints excluded: chain O residue 344 VAL 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 344 VAL 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 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 344 VAL 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 344 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 175 optimal weight: 6.9990 chunk 284 optimal weight: 3.9990 chunk 486 optimal weight: 3.9990 chunk 524 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 241 optimal weight: 4.9990 chunk 504 optimal weight: 0.9990 chunk 520 optimal weight: 5.9990 chunk 490 optimal weight: 0.6980 chunk 491 optimal weight: 1.9990 chunk 163 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN ** G 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 405 GLN S 405 GLN ** U 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.089243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.072430 restraints weight = 145139.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.074900 restraints weight = 72442.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.076374 restraints weight = 47345.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.077318 restraints weight = 36328.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.077960 restraints weight = 30765.712| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 43806 Z= 0.172 Angle : 0.691 14.808 59167 Z= 0.348 Chirality : 0.045 0.130 6840 Planarity : 0.004 0.045 7657 Dihedral : 4.644 43.868 6169 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.10 % Allowed : 21.52 % 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 aren not related in a simple way. whole: -1.16 (0.11), residues: 5568 helix: 0.87 (0.11), residues: 2256 sheet: -2.41 (0.14), residues: 1152 loop : -1.49 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG V 417 TYR 0.014 0.002 TYR T 275 PHE 0.015 0.002 PHE S 392 HIS 0.003 0.001 HIS S 439 Details of bonding type rmsd covalent geometry : bond 0.00380 (43806) covalent geometry : angle 0.69085 (59167) hydrogen bonds : bond 0.02917 ( 2040) hydrogen bonds : angle 4.76103 ( 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 853 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 713 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.6508 (p90) REVERT: A 379 MET cc_start: 0.8790 (mmm) cc_final: 0.7737 (mmm) REVERT: A 460 ASN cc_start: 0.8324 (t0) cc_final: 0.7914 (t0) REVERT: B 295 PHE cc_start: 0.7252 (OUTLIER) cc_final: 0.6408 (p90) REVERT: B 344 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8670 (t) REVERT: B 353 MET cc_start: 0.7565 (tpp) cc_final: 0.7175 (ttt) REVERT: B 379 MET cc_start: 0.8843 (mmm) cc_final: 0.7668 (mmm) REVERT: B 396 MET cc_start: 0.8140 (mmm) cc_final: 0.7748 (mmt) REVERT: B 416 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8281 (tp30) REVERT: B 460 ASN cc_start: 0.8388 (t0) cc_final: 0.7976 (t0) REVERT: C 239 GLU cc_start: 0.8521 (mp0) cc_final: 0.8119 (mp0) REVERT: C 295 PHE cc_start: 0.7253 (OUTLIER) cc_final: 0.6377 (p90) REVERT: C 353 MET cc_start: 0.7616 (tpp) cc_final: 0.7236 (ttt) REVERT: C 379 MET cc_start: 0.8828 (mmm) cc_final: 0.7776 (mmm) REVERT: C 460 ASN cc_start: 0.8279 (t0) cc_final: 0.7894 (t0) REVERT: D 295 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.6407 (p90) REVERT: D 344 VAL cc_start: 0.8923 (OUTLIER) cc_final: 0.8704 (t) REVERT: D 353 MET cc_start: 0.7829 (ttt) cc_final: 0.7609 (ttt) REVERT: D 379 MET cc_start: 0.8805 (mmm) cc_final: 0.7630 (mmm) REVERT: D 396 MET cc_start: 0.8149 (mmm) cc_final: 0.7604 (mmt) REVERT: D 460 ASN cc_start: 0.8309 (t0) cc_final: 0.7955 (t0) REVERT: E 239 GLU cc_start: 0.8565 (mp0) cc_final: 0.8147 (mp0) REVERT: E 295 PHE cc_start: 0.7266 (OUTLIER) cc_final: 0.6485 (p90) REVERT: E 353 MET cc_start: 0.7606 (tpp) cc_final: 0.7227 (ttt) REVERT: E 379 MET cc_start: 0.8900 (mmm) cc_final: 0.7903 (mmm) REVERT: E 396 MET cc_start: 0.8126 (mmm) cc_final: 0.7825 (mmt) REVERT: E 430 MET cc_start: 0.7928 (mmm) cc_final: 0.6626 (mmp) REVERT: E 460 ASN cc_start: 0.8321 (t0) cc_final: 0.7941 (t0) REVERT: F 295 PHE cc_start: 0.7304 (OUTLIER) cc_final: 0.6519 (p90) REVERT: F 344 VAL cc_start: 0.8885 (OUTLIER) cc_final: 0.8632 (t) REVERT: F 353 MET cc_start: 0.7591 (tpp) cc_final: 0.7113 (ttt) REVERT: F 354 ASN cc_start: 0.8084 (m-40) cc_final: 0.7827 (m110) REVERT: F 379 MET cc_start: 0.8867 (mmm) cc_final: 0.7704 (mmm) REVERT: F 396 MET cc_start: 0.8129 (mmm) cc_final: 0.7603 (mmt) REVERT: F 416 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8160 (tp30) REVERT: F 460 ASN cc_start: 0.8331 (t0) cc_final: 0.7968 (t0) REVERT: G 295 PHE cc_start: 0.7275 (OUTLIER) cc_final: 0.6397 (p90) REVERT: G 379 MET cc_start: 0.8819 (mmm) cc_final: 0.7785 (mmm) REVERT: G 396 MET cc_start: 0.8198 (mmm) cc_final: 0.7933 (mmm) REVERT: G 460 ASN cc_start: 0.8396 (t0) cc_final: 0.7972 (t0) REVERT: H 247 MET cc_start: 0.8982 (ppp) cc_final: 0.8560 (ppp) REVERT: H 295 PHE cc_start: 0.7280 (OUTLIER) cc_final: 0.6503 (p90) REVERT: H 353 MET cc_start: 0.7745 (ttt) cc_final: 0.7519 (ttt) REVERT: H 379 MET cc_start: 0.8847 (mmm) cc_final: 0.7844 (mmm) REVERT: H 396 MET cc_start: 0.8150 (mmm) cc_final: 0.7835 (mmt) REVERT: H 416 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8277 (tp30) REVERT: H 460 ASN cc_start: 0.8417 (t0) cc_final: 0.7985 (t0) REVERT: I 247 MET cc_start: 0.8989 (ppp) cc_final: 0.8568 (ppp) REVERT: I 295 PHE cc_start: 0.7279 (OUTLIER) cc_final: 0.6494 (p90) REVERT: I 379 MET cc_start: 0.8856 (mmm) cc_final: 0.7805 (mmm) REVERT: I 396 MET cc_start: 0.8164 (mmm) cc_final: 0.7638 (mmt) REVERT: I 416 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8167 (tp30) REVERT: I 460 ASN cc_start: 0.8318 (t0) cc_final: 0.7949 (t0) REVERT: J 270 GLU cc_start: 0.7509 (tp30) cc_final: 0.7092 (tp30) REVERT: J 295 PHE cc_start: 0.7229 (OUTLIER) cc_final: 0.6398 (p90) REVERT: J 379 MET cc_start: 0.8854 (mmm) cc_final: 0.7813 (mmm) REVERT: J 396 MET cc_start: 0.8173 (mmm) cc_final: 0.7899 (mmm) REVERT: J 430 MET cc_start: 0.8131 (mmm) cc_final: 0.7637 (mmm) REVERT: J 460 ASN cc_start: 0.8374 (t0) cc_final: 0.7958 (t0) REVERT: K 295 PHE cc_start: 0.7303 (OUTLIER) cc_final: 0.6534 (p90) REVERT: K 379 MET cc_start: 0.8868 (mmm) cc_final: 0.7887 (mmm) REVERT: K 396 MET cc_start: 0.8121 (mmm) cc_final: 0.7823 (mmt) REVERT: K 416 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8223 (tp30) REVERT: K 460 ASN cc_start: 0.8373 (t0) cc_final: 0.7966 (t0) REVERT: L 295 PHE cc_start: 0.7274 (OUTLIER) cc_final: 0.6500 (p90) REVERT: L 353 MET cc_start: 0.7615 (tpp) cc_final: 0.7216 (ttt) REVERT: L 379 MET cc_start: 0.8785 (mmm) cc_final: 0.7697 (mmm) REVERT: L 396 MET cc_start: 0.8169 (mmm) cc_final: 0.7636 (mmt) REVERT: L 416 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8175 (tp30) REVERT: L 460 ASN cc_start: 0.8426 (t0) cc_final: 0.8000 (t0) REVERT: M 239 GLU cc_start: 0.8352 (mp0) cc_final: 0.8104 (mp0) REVERT: M 270 GLU cc_start: 0.8113 (tp30) cc_final: 0.7809 (tp30) REVERT: M 295 PHE cc_start: 0.7301 (OUTLIER) cc_final: 0.6483 (p90) REVERT: M 353 MET cc_start: 0.7626 (tpp) cc_final: 0.7229 (ttt) REVERT: M 354 ASN cc_start: 0.8126 (m-40) cc_final: 0.7881 (m110) REVERT: M 379 MET cc_start: 0.8836 (mmm) cc_final: 0.7812 (mmm) REVERT: M 396 MET cc_start: 0.8154 (mmm) cc_final: 0.7659 (mmt) REVERT: M 460 ASN cc_start: 0.8360 (t0) cc_final: 0.7945 (t0) REVERT: N 295 PHE cc_start: 0.7261 (OUTLIER) cc_final: 0.6483 (p90) REVERT: N 354 ASN cc_start: 0.8093 (m-40) cc_final: 0.7767 (m110) REVERT: N 379 MET cc_start: 0.8819 (mmm) cc_final: 0.7754 (mmm) REVERT: N 396 MET cc_start: 0.8135 (mmm) cc_final: 0.7877 (mmm) REVERT: N 460 ASN cc_start: 0.8417 (t0) cc_final: 0.8011 (t0) REVERT: O 295 PHE cc_start: 0.7209 (OUTLIER) cc_final: 0.6351 (p90) REVERT: O 344 VAL cc_start: 0.8930 (OUTLIER) cc_final: 0.8703 (t) REVERT: O 379 MET cc_start: 0.8841 (mmm) cc_final: 0.7665 (mmm) REVERT: O 396 MET cc_start: 0.8199 (mmm) cc_final: 0.7650 (mmt) REVERT: O 460 ASN cc_start: 0.8289 (t0) cc_final: 0.7953 (t0) REVERT: P 295 PHE cc_start: 0.7272 (OUTLIER) cc_final: 0.6506 (p90) REVERT: P 344 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8663 (t) REVERT: P 379 MET cc_start: 0.8823 (mmm) cc_final: 0.7669 (mmm) REVERT: P 396 MET cc_start: 0.8190 (mmm) cc_final: 0.7633 (mmt) REVERT: P 460 ASN cc_start: 0.8373 (t0) cc_final: 0.7965 (t0) REVERT: Q 295 PHE cc_start: 0.7256 (OUTLIER) cc_final: 0.6503 (p90) REVERT: Q 379 MET cc_start: 0.8789 (mmm) cc_final: 0.7747 (mmm) REVERT: Q 396 MET cc_start: 0.8202 (mmm) cc_final: 0.7651 (mmt) REVERT: Q 460 ASN cc_start: 0.8372 (t0) cc_final: 0.7972 (t0) REVERT: R 239 GLU cc_start: 0.8524 (mp0) cc_final: 0.8123 (mp0) REVERT: R 295 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6499 (p90) REVERT: R 379 MET cc_start: 0.8806 (mmm) cc_final: 0.7746 (mmm) REVERT: R 396 MET cc_start: 0.8148 (mmm) cc_final: 0.7638 (mmt) REVERT: R 460 ASN cc_start: 0.8382 (t0) cc_final: 0.7990 (t0) REVERT: S 295 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.6361 (p90) REVERT: S 353 MET cc_start: 0.7632 (tpp) cc_final: 0.7341 (ttt) REVERT: S 354 ASN cc_start: 0.8135 (m-40) cc_final: 0.7880 (m110) REVERT: S 379 MET cc_start: 0.8770 (mmm) cc_final: 0.7720 (mmm) REVERT: S 396 MET cc_start: 0.8156 (mmm) cc_final: 0.7867 (mmm) REVERT: S 460 ASN cc_start: 0.8312 (t0) cc_final: 0.7944 (t0) REVERT: T 239 GLU cc_start: 0.8398 (mp0) cc_final: 0.8193 (mp0) REVERT: T 270 GLU cc_start: 0.8108 (tp30) cc_final: 0.7810 (tp30) REVERT: T 295 PHE cc_start: 0.7282 (OUTLIER) cc_final: 0.6426 (p90) REVERT: T 344 VAL cc_start: 0.8883 (OUTLIER) cc_final: 0.8651 (t) REVERT: T 353 MET cc_start: 0.7631 (tpp) cc_final: 0.7271 (ttt) REVERT: T 354 ASN cc_start: 0.8128 (m-40) cc_final: 0.7898 (m110) REVERT: T 379 MET cc_start: 0.8875 (mmm) cc_final: 0.7729 (mmm) REVERT: T 396 MET cc_start: 0.8148 (mmm) cc_final: 0.7662 (mmt) REVERT: T 460 ASN cc_start: 0.8406 (t0) cc_final: 0.7987 (t0) REVERT: U 239 GLU cc_start: 0.8539 (mp0) cc_final: 0.8144 (mp0) REVERT: U 295 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.6371 (p90) REVERT: U 344 VAL cc_start: 0.8915 (OUTLIER) cc_final: 0.8689 (t) REVERT: U 379 MET cc_start: 0.8864 (mmm) cc_final: 0.7705 (mmm) REVERT: U 396 MET cc_start: 0.8201 (mmm) cc_final: 0.7673 (mmt) REVERT: U 460 ASN cc_start: 0.8374 (t0) cc_final: 0.7992 (t0) REVERT: V 270 GLU cc_start: 0.8112 (tp30) cc_final: 0.7817 (tp30) REVERT: V 295 PHE cc_start: 0.7280 (OUTLIER) cc_final: 0.6481 (p90) REVERT: V 353 MET cc_start: 0.7650 (tpp) cc_final: 0.7331 (ttt) REVERT: V 354 ASN cc_start: 0.8086 (m-40) cc_final: 0.7838 (m110) REVERT: V 379 MET cc_start: 0.8807 (mmm) cc_final: 0.7742 (mmm) REVERT: V 396 MET cc_start: 0.8157 (mmm) cc_final: 0.7647 (mmt) REVERT: V 460 ASN cc_start: 0.8360 (t0) cc_final: 0.7979 (t0) REVERT: W 295 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.6486 (p90) REVERT: W 379 MET cc_start: 0.8788 (mmm) cc_final: 0.7711 (mmm) REVERT: W 396 MET cc_start: 0.8158 (mmm) cc_final: 0.7825 (mmt) REVERT: W 460 ASN cc_start: 0.8425 (t0) cc_final: 0.8021 (t0) REVERT: X 239 GLU cc_start: 0.8566 (mp0) cc_final: 0.8168 (mp0) REVERT: X 295 PHE cc_start: 0.7263 (OUTLIER) cc_final: 0.6496 (p90) REVERT: X 379 MET cc_start: 0.8846 (mmm) cc_final: 0.7788 (mmm) REVERT: X 396 MET cc_start: 0.8118 (mmm) cc_final: 0.7601 (mmt) REVERT: X 460 ASN cc_start: 0.8447 (t0) cc_final: 0.8044 (t0) outliers start: 140 outliers final: 88 residues processed: 837 average time/residue: 0.2502 time to fit residues: 356.2481 Evaluate side-chains 823 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 704 time to evaluate : 1.796 ------------------------------------------------------------------------------- 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 344 VAL 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 344 VAL 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 311 ASP 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 419 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 344 VAL 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 344 VAL 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 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 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 344 VAL 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 344 VAL 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 497 optimal weight: 10.0000 chunk 520 optimal weight: 9.9990 chunk 286 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 392 optimal weight: 6.9990 chunk 296 optimal weight: 0.0060 chunk 406 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 224 optimal weight: 0.8980 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 405 GLN C 405 GLN ** G 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 405 GLN J 405 GLN ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 405 GLN P 405 GLN ** U 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 405 GLN V 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 = 0.3787 r_free = 0.3787 target = 0.090552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.073769 restraints weight = 145853.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.076235 restraints weight = 72943.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.077714 restraints weight = 47861.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.078698 restraints weight = 36711.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.079313 restraints weight = 30968.314| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4138 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= 0.136 Angle : 0.678 12.256 59167 Z= 0.339 Chirality : 0.045 0.160 6840 Planarity : 0.004 0.045 7657 Dihedral : 4.619 43.777 6169 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.88 % Allowed : 21.83 % Favored : 75.29 % 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 aren not related in a simple way. whole: -1.11 (0.11), residues: 5568 helix: 0.89 (0.11), residues: 2256 sheet: -2.36 (0.14), residues: 1152 loop : -1.45 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 417 TYR 0.014 0.001 TYR T 275 PHE 0.014 0.002 PHE L 392 HIS 0.003 0.001 HIS F 412 Details of bonding type rmsd covalent geometry : bond 0.00308 (43806) covalent geometry : angle 0.67776 (59167) hydrogen bonds : bond 0.02826 ( 2040) hydrogen bonds : angle 4.68962 ( 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 867 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 737 time to evaluate : 1.792 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: A 295 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.6400 (p90) REVERT: A 353 MET cc_start: 0.7845 (ttt) cc_final: 0.7217 (ttm) REVERT: A 379 MET cc_start: 0.8746 (mmm) cc_final: 0.7703 (mmm) REVERT: A 396 MET cc_start: 0.8033 (mmm) cc_final: 0.7619 (mmt) REVERT: A 460 ASN cc_start: 0.8165 (t0) cc_final: 0.7769 (t0) REVERT: B 295 PHE cc_start: 0.7170 (OUTLIER) cc_final: 0.6323 (p90) REVERT: B 344 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8638 (t) REVERT: B 353 MET cc_start: 0.7463 (tpp) cc_final: 0.6995 (ttt) REVERT: B 379 MET cc_start: 0.8804 (mmm) cc_final: 0.7656 (mmm) REVERT: B 416 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8300 (tp30) REVERT: B 460 ASN cc_start: 0.8249 (t0) cc_final: 0.7872 (t0) REVERT: C 239 GLU cc_start: 0.8545 (mp0) cc_final: 0.8084 (mp0) REVERT: C 295 PHE cc_start: 0.7163 (OUTLIER) cc_final: 0.6311 (p90) REVERT: C 353 MET cc_start: 0.7520 (tpp) cc_final: 0.7121 (ttt) REVERT: C 379 MET cc_start: 0.8790 (mmm) cc_final: 0.7745 (mmm) REVERT: C 396 MET cc_start: 0.8074 (mmm) cc_final: 0.7620 (mmt) REVERT: C 460 ASN cc_start: 0.8214 (t0) cc_final: 0.7802 (t0) REVERT: D 295 PHE cc_start: 0.7184 (OUTLIER) cc_final: 0.6344 (p90) REVERT: D 344 VAL cc_start: 0.8910 (OUTLIER) cc_final: 0.8673 (t) REVERT: D 379 MET cc_start: 0.8770 (mmm) cc_final: 0.7622 (mmm) REVERT: D 396 MET cc_start: 0.8134 (mmm) cc_final: 0.7541 (mmt) REVERT: D 460 ASN cc_start: 0.8165 (t0) cc_final: 0.7813 (t0) REVERT: E 295 PHE cc_start: 0.7167 (OUTLIER) cc_final: 0.6306 (p90) REVERT: E 353 MET cc_start: 0.7482 (tpp) cc_final: 0.7088 (ttt) REVERT: E 379 MET cc_start: 0.8854 (mmm) cc_final: 0.7862 (mmm) REVERT: E 396 MET cc_start: 0.8072 (mmm) cc_final: 0.7719 (mmt) REVERT: E 460 ASN cc_start: 0.8229 (t0) cc_final: 0.7802 (t0) REVERT: F 295 PHE cc_start: 0.7236 (OUTLIER) cc_final: 0.6387 (p90) REVERT: F 344 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8644 (t) REVERT: F 353 MET cc_start: 0.7539 (tpp) cc_final: 0.7022 (ttt) REVERT: F 354 ASN cc_start: 0.8063 (m-40) cc_final: 0.7823 (m110) REVERT: F 379 MET cc_start: 0.8844 (mmm) cc_final: 0.7722 (mmm) REVERT: F 396 MET cc_start: 0.8138 (mmm) cc_final: 0.7634 (mmt) REVERT: F 416 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8161 (tp30) REVERT: F 431 MET cc_start: 0.8041 (ttt) cc_final: 0.7756 (ppp) REVERT: F 460 ASN cc_start: 0.8175 (t0) cc_final: 0.7811 (t0) REVERT: G 295 PHE cc_start: 0.7187 (OUTLIER) cc_final: 0.6377 (p90) REVERT: G 379 MET cc_start: 0.8761 (mmm) cc_final: 0.7740 (mmm) REVERT: G 396 MET cc_start: 0.8162 (mmm) cc_final: 0.7610 (mmt) REVERT: G 460 ASN cc_start: 0.8264 (t0) cc_final: 0.7849 (t0) REVERT: H 270 GLU cc_start: 0.7424 (tp30) cc_final: 0.7140 (tm-30) REVERT: H 295 PHE cc_start: 0.7172 (OUTLIER) cc_final: 0.6395 (p90) REVERT: H 379 MET cc_start: 0.8791 (mmm) cc_final: 0.7801 (mmm) REVERT: H 396 MET cc_start: 0.8083 (mmm) cc_final: 0.7696 (mmt) REVERT: H 416 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8272 (tp30) REVERT: H 430 MET cc_start: 0.7686 (mmt) cc_final: 0.7275 (mmm) REVERT: H 460 ASN cc_start: 0.8273 (t0) cc_final: 0.7854 (t0) REVERT: I 295 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6465 (p90) REVERT: I 354 ASN cc_start: 0.8043 (m-40) cc_final: 0.7733 (m110) REVERT: I 379 MET cc_start: 0.8820 (mmm) cc_final: 0.7801 (mmm) REVERT: I 396 MET cc_start: 0.8126 (mmm) cc_final: 0.7620 (mmt) REVERT: I 416 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8013 (mm-30) REVERT: I 431 MET cc_start: 0.8022 (ttt) cc_final: 0.7753 (ppp) REVERT: I 460 ASN cc_start: 0.8166 (t0) cc_final: 0.7796 (t0) REVERT: J 270 GLU cc_start: 0.7473 (tp30) cc_final: 0.7065 (tp30) REVERT: J 295 PHE cc_start: 0.7209 (OUTLIER) cc_final: 0.6368 (p90) REVERT: J 379 MET cc_start: 0.8812 (mmm) cc_final: 0.7775 (mmm) REVERT: J 396 MET cc_start: 0.8145 (mmm) cc_final: 0.7565 (mmt) REVERT: J 430 MET cc_start: 0.8099 (mmm) cc_final: 0.7754 (mmm) REVERT: J 460 ASN cc_start: 0.8294 (t0) cc_final: 0.7888 (t0) REVERT: K 270 GLU cc_start: 0.7427 (tp30) cc_final: 0.7167 (tm-30) REVERT: K 295 PHE cc_start: 0.7207 (OUTLIER) cc_final: 0.6373 (p90) REVERT: K 379 MET cc_start: 0.8812 (mmm) cc_final: 0.7836 (mmm) REVERT: K 396 MET cc_start: 0.8063 (mmm) cc_final: 0.7671 (mmt) REVERT: K 416 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8260 (tp30) REVERT: K 430 MET cc_start: 0.7691 (mmt) cc_final: 0.7252 (mmm) REVERT: K 460 ASN cc_start: 0.8269 (t0) cc_final: 0.7857 (t0) REVERT: L 295 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.6378 (p90) REVERT: L 379 MET cc_start: 0.8727 (mmm) cc_final: 0.7646 (mmm) REVERT: L 396 MET cc_start: 0.8132 (mmm) cc_final: 0.7600 (mmt) REVERT: L 416 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8024 (mm-30) REVERT: L 460 ASN cc_start: 0.8285 (t0) cc_final: 0.7876 (t0) REVERT: M 239 GLU cc_start: 0.8307 (mp0) cc_final: 0.8054 (mp0) REVERT: M 270 GLU cc_start: 0.7762 (tp30) cc_final: 0.7102 (tp30) REVERT: M 295 PHE cc_start: 0.7202 (OUTLIER) cc_final: 0.6343 (p90) REVERT: M 353 MET cc_start: 0.7520 (tpp) cc_final: 0.7082 (ttt) REVERT: M 354 ASN cc_start: 0.8072 (m-40) cc_final: 0.7841 (m110) REVERT: M 379 MET cc_start: 0.8810 (mmm) cc_final: 0.7789 (mmm) REVERT: M 396 MET cc_start: 0.8124 (mmm) cc_final: 0.7573 (mmt) REVERT: M 460 ASN cc_start: 0.8275 (t0) cc_final: 0.7875 (t0) REVERT: N 295 PHE cc_start: 0.7197 (OUTLIER) cc_final: 0.6340 (p90) REVERT: N 353 MET cc_start: 0.7610 (tpp) cc_final: 0.7023 (ttt) REVERT: N 354 ASN cc_start: 0.8023 (m-40) cc_final: 0.7776 (m110) REVERT: N 379 MET cc_start: 0.8792 (mmm) cc_final: 0.7764 (mmm) REVERT: N 396 MET cc_start: 0.8140 (mmm) cc_final: 0.7611 (mmt) REVERT: N 460 ASN cc_start: 0.8310 (t0) cc_final: 0.7917 (t0) REVERT: O 295 PHE cc_start: 0.7167 (OUTLIER) cc_final: 0.6243 (p90) REVERT: O 344 VAL cc_start: 0.8904 (OUTLIER) cc_final: 0.8650 (t) REVERT: O 379 MET cc_start: 0.8814 (mmm) cc_final: 0.7692 (mmm) REVERT: O 396 MET cc_start: 0.8164 (mmm) cc_final: 0.7605 (mmt) REVERT: O 460 ASN cc_start: 0.8212 (t0) cc_final: 0.7850 (t0) REVERT: P 295 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6399 (p90) REVERT: P 344 VAL cc_start: 0.8873 (OUTLIER) cc_final: 0.8630 (t) REVERT: P 379 MET cc_start: 0.8776 (mmm) cc_final: 0.7646 (mmm) REVERT: P 396 MET cc_start: 0.8166 (mmm) cc_final: 0.7585 (mmt) REVERT: P 460 ASN cc_start: 0.8290 (t0) cc_final: 0.7901 (t0) REVERT: Q 295 PHE cc_start: 0.7218 (OUTLIER) cc_final: 0.6389 (p90) REVERT: Q 379 MET cc_start: 0.8763 (mmm) cc_final: 0.7736 (mmm) REVERT: Q 396 MET cc_start: 0.8154 (mmm) cc_final: 0.7565 (mmt) REVERT: Q 460 ASN cc_start: 0.8285 (t0) cc_final: 0.7910 (t0) REVERT: R 295 PHE cc_start: 0.7195 (OUTLIER) cc_final: 0.6449 (p90) REVERT: R 379 MET cc_start: 0.8765 (mmm) cc_final: 0.7733 (mmm) REVERT: R 396 MET cc_start: 0.8155 (mmm) cc_final: 0.7591 (mmt) REVERT: R 460 ASN cc_start: 0.8277 (t0) cc_final: 0.7889 (t0) REVERT: S 270 GLU cc_start: 0.8076 (tp30) cc_final: 0.7847 (tp30) REVERT: S 295 PHE cc_start: 0.7185 (OUTLIER) cc_final: 0.6339 (p90) REVERT: S 353 MET cc_start: 0.7557 (tpp) cc_final: 0.7146 (ttt) REVERT: S 354 ASN cc_start: 0.8103 (m-40) cc_final: 0.7861 (m110) REVERT: S 379 MET cc_start: 0.8706 (mmm) cc_final: 0.7670 (mmm) REVERT: S 396 MET cc_start: 0.8100 (mmm) cc_final: 0.7810 (mmm) REVERT: S 460 ASN cc_start: 0.8208 (t0) cc_final: 0.7789 (t0) REVERT: T 239 GLU cc_start: 0.8336 (mp0) cc_final: 0.8031 (mp0) REVERT: T 270 GLU cc_start: 0.7769 (tp30) cc_final: 0.7096 (tp30) REVERT: T 295 PHE cc_start: 0.7209 (OUTLIER) cc_final: 0.6358 (p90) REVERT: T 344 VAL cc_start: 0.8856 (OUTLIER) cc_final: 0.8588 (t) REVERT: T 353 MET cc_start: 0.7549 (tpp) cc_final: 0.7072 (ttt) REVERT: T 354 ASN cc_start: 0.8102 (m-40) cc_final: 0.7888 (m110) REVERT: T 379 MET cc_start: 0.8836 (mmm) cc_final: 0.7694 (mmm) REVERT: T 396 MET cc_start: 0.8108 (mmm) cc_final: 0.7569 (mmt) REVERT: T 460 ASN cc_start: 0.8277 (t0) cc_final: 0.7884 (t0) REVERT: U 295 PHE cc_start: 0.7180 (OUTLIER) cc_final: 0.6319 (p90) REVERT: U 379 MET cc_start: 0.8816 (mmm) cc_final: 0.7685 (mmm) REVERT: U 396 MET cc_start: 0.8186 (mmm) cc_final: 0.7601 (mmt) REVERT: U 460 ASN cc_start: 0.8281 (t0) cc_final: 0.7895 (t0) REVERT: V 270 GLU cc_start: 0.7766 (tp30) cc_final: 0.7135 (tp30) REVERT: V 295 PHE cc_start: 0.7198 (OUTLIER) cc_final: 0.6358 (p90) REVERT: V 353 MET cc_start: 0.7560 (tpp) cc_final: 0.7121 (ttt) REVERT: V 354 ASN cc_start: 0.8107 (m-40) cc_final: 0.7868 (m110) REVERT: V 379 MET cc_start: 0.8765 (mmm) cc_final: 0.7714 (mmm) REVERT: V 396 MET cc_start: 0.8109 (mmm) cc_final: 0.7573 (mmt) REVERT: V 460 ASN cc_start: 0.8267 (t0) cc_final: 0.7904 (t0) REVERT: W 295 PHE cc_start: 0.7193 (OUTLIER) cc_final: 0.6347 (p90) REVERT: W 353 MET cc_start: 0.7601 (tpp) cc_final: 0.7129 (ttt) REVERT: W 379 MET cc_start: 0.8757 (mmm) cc_final: 0.7718 (mmm) REVERT: W 396 MET cc_start: 0.8099 (mmm) cc_final: 0.7721 (mmt) REVERT: W 460 ASN cc_start: 0.8329 (t0) cc_final: 0.7943 (t0) REVERT: X 295 PHE cc_start: 0.7195 (OUTLIER) cc_final: 0.6375 (p90) REVERT: X 379 MET cc_start: 0.8812 (mmm) cc_final: 0.7764 (mmm) REVERT: X 396 MET cc_start: 0.8162 (mmm) cc_final: 0.7607 (mmt) REVERT: X 460 ASN cc_start: 0.8280 (t0) cc_final: 0.7886 (t0) outliers start: 130 outliers final: 87 residues processed: 842 average time/residue: 0.2421 time to fit residues: 346.5168 Evaluate side-chains 838 residues out of total 4536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 721 time to evaluate : 1.815 ------------------------------------------------------------------------------- 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 344 VAL 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 344 VAL 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 311 ASP 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 344 VAL 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 344 VAL 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 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 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 344 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 401 optimal weight: 5.9990 chunk 367 optimal weight: 1.9990 chunk 420 optimal weight: 0.7980 chunk 418 optimal weight: 4.9990 chunk 322 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 483 optimal weight: 10.0000 chunk 337 optimal weight: 0.8980 chunk 458 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 236 optimal weight: 0.6980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 405 GLN F 405 GLN ** G 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 405 GLN L 405 GLN ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 405 GLN R 405 GLN ** U 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 405 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.089270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.072265 restraints weight = 146723.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.074723 restraints weight = 73332.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.076213 restraints weight = 48281.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.077177 restraints weight = 37156.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.077844 restraints weight = 31522.775| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 43806 Z= 0.182 Angle : 0.705 14.723 59167 Z= 0.356 Chirality : 0.045 0.127 6840 Planarity : 0.004 0.043 7657 Dihedral : 4.705 44.951 6169 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.84 % Allowed : 20.87 % Favored : 76.29 % 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 aren not related in a simple way. whole: -1.19 (0.11), residues: 5568 helix: 0.84 (0.11), residues: 2256 sheet: -2.46 (0.14), residues: 1152 loop : -1.47 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 417 TYR 0.014 0.002 TYR B 275 PHE 0.016 0.002 PHE Q 392 HIS 0.003 0.001 HIS S 439 Details of bonding type rmsd covalent geometry : bond 0.00404 (43806) covalent geometry : angle 0.70472 (59167) hydrogen bonds : bond 0.02952 ( 2040) hydrogen bonds : angle 4.75186 ( 5904) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8092.42 seconds wall clock time: 140 minutes 25.66 seconds (8425.66 seconds total)