Starting phenix.real_space_refine on Fri Jul 3 13:59:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m6r_23705/07_2026/7m6r_23705.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m6r_23705/07_2026/7m6r_23705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7m6r_23705/07_2026/7m6r_23705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m6r_23705/07_2026/7m6r_23705.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7m6r_23705/07_2026/7m6r_23705.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m6r_23705/07_2026/7m6r_23705.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m6r_23705/07_2026/7m6r_23705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m6r_23705/07_2026/7m6r_23705.map" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.043 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 100 5.16 5 C 9290 2.51 5 N 2335 2.21 5 O 2575 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14300 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2841 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 333} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2841 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 333} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2841 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 333} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2841 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 333} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 2841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2841 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 333} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.81, per 1000 atoms: 0.20 Number of scatterers: 14300 At special positions: 0 Unit cell: (96.8, 93.5, 139.7, 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 100 16.00 O 2575 8.00 N 2335 7.00 C 9290 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 176 " distance=2.04 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 176 " distance=2.04 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 176 " distance=2.04 Simple disulfide: pdb=" SG CYS D 162 " - pdb=" SG CYS D 176 " distance=2.04 Simple disulfide: pdb=" SG CYS E 162 " - pdb=" SG CYS E 176 " distance=2.04 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 62 " " NAG B 802 " - " ASN B 62 " " NAG C 802 " - " ASN C 62 " " NAG D 802 " - " ASN D 62 " " NAG E 802 " - " ASN E 62 " Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 754.8 milliseconds 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3360 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 25 sheets defined 38.7% alpha, 35.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 33 through 43 removed outlier: 3.546A pdb=" N PHE A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 Processing helix chain 'A' and resid 251 through 268 Processing helix chain 'A' and resid 273 through 295 removed outlier: 3.836A pdb=" N VAL A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY A 278 " --> pdb=" O PRO A 274 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 336 removed outlier: 3.658A pdb=" N LEU A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 323 " --> pdb=" O PHE A 319 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 440 removed outlier: 3.702A pdb=" N LYS A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Proline residue: A 419 - end of helix removed outlier: 3.593A pdb=" N PHE A 422 " --> pdb=" O PHE A 418 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 428 " --> pdb=" O ILE A 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 43 removed outlier: 3.547A pdb=" N PHE B 37 " --> pdb=" O PRO B 33 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 251 Processing helix chain 'B' and resid 251 through 268 Processing helix chain 'B' and resid 273 through 295 removed outlier: 3.836A pdb=" N VAL B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY B 278 " --> pdb=" O PRO B 274 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLY B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 336 removed outlier: 3.659A pdb=" N LEU B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 323 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 440 removed outlier: 3.703A pdb=" N LYS B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) Proline residue: B 419 - end of helix removed outlier: 3.594A pdb=" N PHE B 422 " --> pdb=" O PHE B 418 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE B 428 " --> pdb=" O ILE B 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 43 removed outlier: 3.547A pdb=" N PHE C 37 " --> pdb=" O PRO C 33 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 251 Processing helix chain 'C' and resid 251 through 268 Processing helix chain 'C' and resid 273 through 295 removed outlier: 3.836A pdb=" N VAL C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY C 278 " --> pdb=" O PRO C 274 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY C 280 " --> pdb=" O ARG C 276 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 336 removed outlier: 3.658A pdb=" N LEU C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 323 " --> pdb=" O PHE C 319 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR C 325 " --> pdb=" O ALA C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 440 removed outlier: 3.703A pdb=" N LYS C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) Proline residue: C 419 - end of helix removed outlier: 3.594A pdb=" N PHE C 422 " --> pdb=" O PHE C 418 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE C 427 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE C 428 " --> pdb=" O ILE C 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 43 removed outlier: 3.547A pdb=" N PHE D 37 " --> pdb=" O PRO D 33 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 Processing helix chain 'D' and resid 251 through 268 Processing helix chain 'D' and resid 273 through 295 removed outlier: 3.836A pdb=" N VAL D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY D 278 " --> pdb=" O PRO D 274 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU D 279 " --> pdb=" O ALA D 275 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY D 280 " --> pdb=" O ARG D 276 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR D 283 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 336 removed outlier: 3.659A pdb=" N LEU D 322 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 323 " --> pdb=" O PHE D 319 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 440 removed outlier: 3.703A pdb=" N LYS D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) Proline residue: D 419 - end of helix removed outlier: 3.593A pdb=" N PHE D 422 " --> pdb=" O PHE D 418 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE D 427 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE D 428 " --> pdb=" O ILE D 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 43 removed outlier: 3.546A pdb=" N PHE E 37 " --> pdb=" O PRO E 33 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 251 Processing helix chain 'E' and resid 251 through 268 Processing helix chain 'E' and resid 273 through 295 removed outlier: 3.836A pdb=" N VAL E 277 " --> pdb=" O ALA E 273 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY E 278 " --> pdb=" O PRO E 274 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU E 279 " --> pdb=" O ALA E 275 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY E 280 " --> pdb=" O ARG E 276 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR E 283 " --> pdb=" O LEU E 279 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG E 295 " --> pdb=" O SER E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 336 removed outlier: 3.659A pdb=" N LEU E 322 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU E 323 " --> pdb=" O PHE E 319 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 440 removed outlier: 3.703A pdb=" N LYS E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) Proline residue: E 419 - end of helix removed outlier: 3.594A pdb=" N PHE E 422 " --> pdb=" O PHE E 418 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE E 427 " --> pdb=" O LEU E 423 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE E 428 " --> pdb=" O ILE E 424 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 106 through 109 removed outlier: 4.628A pdb=" N LEU A 142 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N VAL A 63 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 132 removed outlier: 3.656A pdb=" N VAL A 159 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA A 130 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N THR A 157 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N PHE A 132 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N ARG A 155 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 123 through 124 Processing sheet with id=AA4, first strand: chain 'A' and resid 123 through 124 removed outlier: 3.601A pdb=" N ARG A 220 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA6, first strand: chain 'B' and resid 106 through 109 removed outlier: 4.628A pdb=" N LEU B 142 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VAL B 63 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 127 through 132 removed outlier: 3.657A pdb=" N VAL B 159 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA B 130 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N THR B 157 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N PHE B 132 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ARG B 155 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AA9, first strand: chain 'B' and resid 123 through 124 removed outlier: 3.600A pdb=" N ARG B 220 " --> pdb=" O GLU B 235 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AB2, first strand: chain 'C' and resid 106 through 109 removed outlier: 4.628A pdb=" N LEU C 142 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N VAL C 63 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 127 through 132 removed outlier: 3.658A pdb=" N VAL C 159 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA C 130 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N THR C 157 " --> pdb=" O ALA C 130 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N PHE C 132 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ARG C 155 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 123 through 124 Processing sheet with id=AB5, first strand: chain 'C' and resid 123 through 124 removed outlier: 3.600A pdb=" N ARG C 220 " --> pdb=" O GLU C 235 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AB7, first strand: chain 'D' and resid 106 through 109 removed outlier: 4.628A pdb=" N LEU D 142 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VAL D 63 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 127 through 132 removed outlier: 3.658A pdb=" N VAL D 159 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA D 130 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N THR D 157 " --> pdb=" O ALA D 130 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N PHE D 132 " --> pdb=" O ARG D 155 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ARG D 155 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 123 through 124 Processing sheet with id=AC1, first strand: chain 'D' and resid 123 through 124 removed outlier: 3.600A pdb=" N ARG D 220 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AC3, first strand: chain 'E' and resid 106 through 109 removed outlier: 4.628A pdb=" N LEU E 142 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASP E 81 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N SER E 74 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N VAL E 63 " --> pdb=" O GLU E 193 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 127 through 132 removed outlier: 3.658A pdb=" N VAL E 159 " --> pdb=" O LYS E 128 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA E 130 " --> pdb=" O THR E 157 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N THR E 157 " --> pdb=" O ALA E 130 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N PHE E 132 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N ARG E 155 " --> pdb=" O PHE E 132 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASP E 81 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N SER E 74 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 123 through 124 Processing sheet with id=AC6, first strand: chain 'E' and resid 123 through 124 removed outlier: 3.601A pdb=" N ARG E 220 " --> pdb=" O GLU E 235 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 224 through 225 810 hydrogen bonds defined for protein. 2385 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3798 1.33 - 1.46: 3060 1.46 - 1.58: 7617 1.58 - 1.70: 0 1.70 - 1.82: 170 Bond restraints: 14645 Sorted by residual: bond pdb=" C ILE A 436 " pdb=" N ARG A 437 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.31e-02 5.83e+03 3.92e+00 bond pdb=" C ILE E 436 " pdb=" N ARG E 437 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.31e-02 5.83e+03 3.84e+00 bond pdb=" C ILE D 436 " pdb=" N ARG D 437 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.31e-02 5.83e+03 3.84e+00 bond pdb=" C ILE B 436 " pdb=" N ARG B 437 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.31e-02 5.83e+03 3.78e+00 bond pdb=" C ILE C 436 " pdb=" N ARG C 437 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.31e-02 5.83e+03 3.71e+00 ... (remaining 14640 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 18395 2.14 - 4.27: 1167 4.27 - 6.41: 218 6.41 - 8.55: 60 8.55 - 10.69: 5 Bond angle restraints: 19845 Sorted by residual: angle pdb=" N LEU E 190 " pdb=" CA LEU E 190 " pdb=" C LEU E 190 " ideal model delta sigma weight residual 111.39 116.61 -5.22 1.38e+00 5.25e-01 1.43e+01 angle pdb=" N LEU B 190 " pdb=" CA LEU B 190 " pdb=" C LEU B 190 " ideal model delta sigma weight residual 111.39 116.56 -5.17 1.38e+00 5.25e-01 1.40e+01 angle pdb=" N LEU A 190 " pdb=" CA LEU A 190 " pdb=" C LEU A 190 " ideal model delta sigma weight residual 111.39 116.53 -5.14 1.38e+00 5.25e-01 1.39e+01 angle pdb=" N LEU D 190 " pdb=" CA LEU D 190 " pdb=" C LEU D 190 " ideal model delta sigma weight residual 111.39 116.53 -5.14 1.38e+00 5.25e-01 1.39e+01 angle pdb=" N LEU C 190 " pdb=" CA LEU C 190 " pdb=" C LEU C 190 " ideal model delta sigma weight residual 111.39 116.52 -5.13 1.38e+00 5.25e-01 1.38e+01 ... (remaining 19840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.58: 8055 16.58 - 33.16: 529 33.16 - 49.74: 116 49.74 - 66.33: 15 66.33 - 82.91: 10 Dihedral angle restraints: 8725 sinusoidal: 3550 harmonic: 5175 Sorted by residual: dihedral pdb=" CA ASP C 39 " pdb=" CB ASP C 39 " pdb=" CG ASP C 39 " pdb=" OD1 ASP C 39 " ideal model delta sinusoidal sigma weight residual -30.00 -89.86 59.86 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CA ASP E 39 " pdb=" CB ASP E 39 " pdb=" CG ASP E 39 " pdb=" OD1 ASP E 39 " ideal model delta sinusoidal sigma weight residual -30.00 -89.82 59.82 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP B 39 " pdb=" CB ASP B 39 " pdb=" CG ASP B 39 " pdb=" OD1 ASP B 39 " ideal model delta sinusoidal sigma weight residual -30.00 -89.81 59.81 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 8722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1855 0.095 - 0.190: 331 0.190 - 0.284: 34 0.284 - 0.379: 5 0.379 - 0.474: 5 Chirality restraints: 2230 Sorted by residual: chirality pdb=" CB ILE C 281 " pdb=" CA ILE C 281 " pdb=" CG1 ILE C 281 " pdb=" CG2 ILE C 281 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.61e+00 chirality pdb=" CB ILE B 281 " pdb=" CA ILE B 281 " pdb=" CG1 ILE B 281 " pdb=" CG2 ILE B 281 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" CB ILE D 281 " pdb=" CA ILE D 281 " pdb=" CG1 ILE D 281 " pdb=" CG2 ILE D 281 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.51e+00 ... (remaining 2227 not shown) Planarity restraints: 2490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 323 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.78e+00 pdb=" C LEU D 323 " 0.051 2.00e-02 2.50e+03 pdb=" O LEU D 323 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU D 324 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 323 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.69e+00 pdb=" C LEU B 323 " -0.051 2.00e-02 2.50e+03 pdb=" O LEU B 323 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU B 324 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 323 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.63e+00 pdb=" C LEU A 323 " -0.051 2.00e-02 2.50e+03 pdb=" O LEU A 323 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU A 324 " 0.017 2.00e-02 2.50e+03 ... (remaining 2487 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 4506 2.85 - 3.36: 13698 3.36 - 3.87: 22774 3.87 - 4.39: 24696 4.39 - 4.90: 42749 Nonbonded interactions: 108423 Sorted by model distance: nonbonded pdb=" OG1 THR D 186 " pdb=" OD1 ASN D 188 " model vdw 2.333 3.040 nonbonded pdb=" OG1 THR B 186 " pdb=" OD1 ASN B 188 " model vdw 2.333 3.040 nonbonded pdb=" OG1 THR E 186 " pdb=" OD1 ASN E 188 " model vdw 2.333 3.040 nonbonded pdb=" OG1 THR C 186 " pdb=" OD1 ASN C 188 " model vdw 2.333 3.040 nonbonded pdb=" OG1 THR A 186 " pdb=" OD1 ASN A 188 " model vdw 2.333 3.040 ... (remaining 108418 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 32 through 440) selection = (chain 'B' and resid 32 through 440) selection = (chain 'C' and resid 32 through 440) selection = (chain 'D' and resid 32 through 440) selection = (chain 'E' and resid 32 through 440) } 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: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.970 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 14655 Z= 0.364 Angle : 1.206 10.687 19870 Z= 0.684 Chirality : 0.076 0.474 2230 Planarity : 0.009 0.071 2485 Dihedral : 12.288 82.907 5350 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.64 % Allowed : 3.44 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.20), residues: 1730 helix: 1.85 (0.20), residues: 665 sheet: 0.20 (0.28), residues: 360 loop : -2.12 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG D 276 TYR 0.021 0.004 TYR D 325 PHE 0.023 0.004 PHE C 192 TRP 0.040 0.004 TRP B 430 HIS 0.008 0.002 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00759 / 0.36 (14645) covalent geometry : angle 1.20416 / 0.68 (19845) SS BOND : bond 0.00918 / 0.54 ( 5) SS BOND : angle 1.10106 / 0.60 ( 10) hydrogen bonds : bond 0.19192 / 12.38 ( 675) hydrogen bonds : angle 6.89472 / 4.74 ( 2385) link_NAG-ASN : bond 0.00174 / 0.10 ( 5) link_NAG-ASN : angle 2.60278 / 1.46 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 627 time to evaluate : 0.553 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 81 ASP cc_start: 0.7778 (p0) cc_final: 0.7463 (p0) REVERT: A 104 ASP cc_start: 0.8809 (p0) cc_final: 0.8351 (p0) REVERT: A 109 LEU cc_start: 0.9113 (mm) cc_final: 0.8879 (mp) REVERT: A 114 LEU cc_start: 0.8673 (mt) cc_final: 0.8298 (tp) REVERT: A 119 LYS cc_start: 0.9040 (mtmm) cc_final: 0.8754 (mtmt) REVERT: A 127 GLU cc_start: 0.7020 (tm-30) cc_final: 0.6160 (tm-30) REVERT: A 140 LYS cc_start: 0.8805 (mttp) cc_final: 0.8202 (mtmm) REVERT: A 142 LEU cc_start: 0.8720 (tp) cc_final: 0.8393 (tt) REVERT: A 153 SER cc_start: 0.9150 (t) cc_final: 0.8492 (p) REVERT: A 154 ILE cc_start: 0.8833 (mm) cc_final: 0.8423 (mm) REVERT: A 190 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.7906 (tt) REVERT: A 193 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7861 (mm-30) REVERT: A 195 ASP cc_start: 0.8457 (t0) cc_final: 0.8199 (t0) REVERT: A 214 LYS cc_start: 0.8805 (mmtp) cc_final: 0.8447 (mmmm) REVERT: A 235 GLU cc_start: 0.7755 (tt0) cc_final: 0.7296 (tt0) REVERT: A 237 ARG cc_start: 0.7913 (mtt-85) cc_final: 0.7151 (mtt180) REVERT: A 241 GLU cc_start: 0.7200 (mp0) cc_final: 0.6559 (mp0) REVERT: A 287 MET cc_start: 0.8889 (tpp) cc_final: 0.8435 (tpp) REVERT: A 291 SER cc_start: 0.9281 (t) cc_final: 0.9063 (p) REVERT: A 314 CYS cc_start: 0.8168 (p) cc_final: 0.7317 (p) REVERT: A 322 LEU cc_start: 0.9410 (mt) cc_final: 0.9132 (mp) REVERT: A 399 MET cc_start: 0.5193 (mpp) cc_final: 0.4917 (mpp) REVERT: A 403 PHE cc_start: 0.7465 (m-80) cc_final: 0.6890 (m-80) REVERT: A 406 ARG cc_start: 0.7880 (ttm170) cc_final: 0.7535 (mmp-170) REVERT: B 66 ASN cc_start: 0.7954 (t0) cc_final: 0.7736 (t0) REVERT: B 77 GLU cc_start: 0.7966 (pm20) cc_final: 0.7744 (pm20) REVERT: B 90 GLN cc_start: 0.8929 (pt0) cc_final: 0.8701 (pt0) REVERT: B 102 TYR cc_start: 0.8206 (m-10) cc_final: 0.7995 (m-10) REVERT: B 104 ASP cc_start: 0.8685 (p0) cc_final: 0.7648 (p0) REVERT: B 105 ASP cc_start: 0.8609 (p0) cc_final: 0.8402 (p0) REVERT: B 114 LEU cc_start: 0.8495 (mt) cc_final: 0.8220 (mm) REVERT: B 140 LYS cc_start: 0.8814 (mttp) cc_final: 0.8276 (mtmm) REVERT: B 146 LYS cc_start: 0.8904 (ttmm) cc_final: 0.8571 (tppp) REVERT: B 166 LEU cc_start: 0.9113 (mt) cc_final: 0.8788 (mp) REVERT: B 174 GLN cc_start: 0.8305 (mm-40) cc_final: 0.7990 (mm-40) REVERT: B 179 GLN cc_start: 0.8670 (mt0) cc_final: 0.8433 (mt0) REVERT: B 181 GLU cc_start: 0.6807 (pm20) cc_final: 0.6053 (pm20) REVERT: B 190 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8115 (tp) REVERT: B 193 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7722 (mm-30) REVERT: B 201 GLN cc_start: 0.7843 (mp10) cc_final: 0.7374 (mp10) REVERT: B 214 LYS cc_start: 0.8786 (mmtp) cc_final: 0.7985 (mmmm) REVERT: B 237 ARG cc_start: 0.7974 (mtt-85) cc_final: 0.7666 (mtt90) REVERT: B 241 GLU cc_start: 0.7064 (mp0) cc_final: 0.6220 (mp0) REVERT: B 287 MET cc_start: 0.8958 (tpp) cc_final: 0.8520 (tpp) REVERT: B 303 TYR cc_start: 0.8207 (p90) cc_final: 0.7586 (p90) REVERT: B 314 CYS cc_start: 0.8106 (p) cc_final: 0.7105 (p) REVERT: B 322 LEU cc_start: 0.9430 (mt) cc_final: 0.9209 (mp) REVERT: B 324 GLU cc_start: 0.8284 (pp20) cc_final: 0.7969 (mm-30) REVERT: B 325 TYR cc_start: 0.8920 (t80) cc_final: 0.8673 (t80) REVERT: B 328 VAL cc_start: 0.9020 (p) cc_final: 0.8733 (m) REVERT: B 406 ARG cc_start: 0.7905 (ttm170) cc_final: 0.7460 (mmp-170) REVERT: C 36 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8135 (mt-10) REVERT: C 80 MET cc_start: 0.8058 (mmm) cc_final: 0.7396 (mmt) REVERT: C 81 ASP cc_start: 0.7638 (p0) cc_final: 0.7290 (p0) REVERT: C 90 GLN cc_start: 0.8933 (pt0) cc_final: 0.8688 (pt0) REVERT: C 104 ASP cc_start: 0.8840 (p0) cc_final: 0.8068 (p0) REVERT: C 113 MET cc_start: 0.8601 (pmm) cc_final: 0.7924 (pmm) REVERT: C 114 LEU cc_start: 0.8526 (mt) cc_final: 0.8048 (tp) REVERT: C 119 LYS cc_start: 0.8929 (mtmm) cc_final: 0.8560 (mtmm) REVERT: C 137 THR cc_start: 0.9066 (p) cc_final: 0.8858 (m) REVERT: C 140 LYS cc_start: 0.8694 (mttp) cc_final: 0.8135 (mtmm) REVERT: C 154 ILE cc_start: 0.8906 (mm) cc_final: 0.8668 (mm) REVERT: C 190 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8026 (tp) REVERT: C 235 GLU cc_start: 0.7802 (tt0) cc_final: 0.7505 (tt0) REVERT: C 241 GLU cc_start: 0.7260 (mp0) cc_final: 0.6695 (mp0) REVERT: C 251 MET cc_start: 0.8214 (mpp) cc_final: 0.7973 (mpp) REVERT: C 287 MET cc_start: 0.8982 (tpp) cc_final: 0.8551 (tpp) REVERT: C 291 SER cc_start: 0.9207 (t) cc_final: 0.8976 (p) REVERT: C 300 LYS cc_start: 0.8966 (mttp) cc_final: 0.8520 (mmtp) REVERT: C 314 CYS cc_start: 0.7858 (p) cc_final: 0.7101 (p) REVERT: C 406 ARG cc_start: 0.8047 (ttm170) cc_final: 0.7633 (mmp-170) REVERT: C 410 ILE cc_start: 0.8718 (mm) cc_final: 0.8457 (mm) REVERT: C 429 TYR cc_start: 0.9327 (t80) cc_final: 0.9081 (t80) REVERT: D 49 ASP cc_start: 0.8889 (t0) cc_final: 0.8608 (t0) REVERT: D 81 ASP cc_start: 0.7939 (p0) cc_final: 0.7652 (p0) REVERT: D 90 GLN cc_start: 0.8951 (pt0) cc_final: 0.8700 (pt0) REVERT: D 104 ASP cc_start: 0.8774 (p0) cc_final: 0.8207 (p0) REVERT: D 114 LEU cc_start: 0.8642 (mt) cc_final: 0.8238 (mm) REVERT: D 127 GLU cc_start: 0.6861 (tm-30) cc_final: 0.6012 (tm-30) REVERT: D 138 ASP cc_start: 0.8500 (p0) cc_final: 0.7434 (p0) REVERT: D 140 LYS cc_start: 0.8768 (mttp) cc_final: 0.7825 (mtmm) REVERT: D 154 ILE cc_start: 0.9039 (mm) cc_final: 0.8837 (mm) REVERT: D 181 GLU cc_start: 0.6838 (pm20) cc_final: 0.6037 (pm20) REVERT: D 190 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8395 (tp) REVERT: D 214 LYS cc_start: 0.8813 (mmtp) cc_final: 0.8435 (mmmm) REVERT: D 224 LYS cc_start: 0.9190 (mmtm) cc_final: 0.8757 (mmtm) REVERT: D 235 GLU cc_start: 0.7941 (tt0) cc_final: 0.7612 (tt0) REVERT: D 241 GLU cc_start: 0.7279 (mp0) cc_final: 0.6651 (mp0) REVERT: D 260 ILE cc_start: 0.8914 (mt) cc_final: 0.8690 (tp) REVERT: D 287 MET cc_start: 0.8859 (tpp) cc_final: 0.8537 (tpp) REVERT: D 291 SER cc_start: 0.9169 (t) cc_final: 0.8891 (p) REVERT: D 314 CYS cc_start: 0.8057 (p) cc_final: 0.7162 (p) REVERT: D 406 ARG cc_start: 0.7860 (ttm170) cc_final: 0.7319 (mmp-170) REVERT: E 66 ASN cc_start: 0.7745 (t0) cc_final: 0.7454 (t0) REVERT: E 81 ASP cc_start: 0.8092 (p0) cc_final: 0.7783 (p0) REVERT: E 90 GLN cc_start: 0.8909 (pt0) cc_final: 0.8705 (pt0) REVERT: E 104 ASP cc_start: 0.8793 (p0) cc_final: 0.8483 (p0) REVERT: E 114 LEU cc_start: 0.8530 (mt) cc_final: 0.8139 (tp) REVERT: E 154 ILE cc_start: 0.8922 (mm) cc_final: 0.8593 (mm) REVERT: E 169 PHE cc_start: 0.8964 (t80) cc_final: 0.8706 (t80) REVERT: E 181 GLU cc_start: 0.6695 (pm20) cc_final: 0.6256 (pm20) REVERT: E 190 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8383 (tp) REVERT: E 201 GLN cc_start: 0.8096 (mp10) cc_final: 0.7764 (mp10) REVERT: E 214 LYS cc_start: 0.8889 (mmtp) cc_final: 0.8497 (mmmm) REVERT: E 224 LYS cc_start: 0.9113 (mmtm) cc_final: 0.8710 (mmtm) REVERT: E 235 GLU cc_start: 0.7730 (tt0) cc_final: 0.7510 (tt0) REVERT: E 241 GLU cc_start: 0.7123 (mp0) cc_final: 0.6439 (mp0) REVERT: E 315 LEU cc_start: 0.9299 (mt) cc_final: 0.9098 (tp) REVERT: E 322 LEU cc_start: 0.9500 (mt) cc_final: 0.9262 (mp) REVERT: E 406 ARG cc_start: 0.7817 (ttm170) cc_final: 0.7554 (mmp-170) REVERT: E 433 TYR cc_start: 0.8900 (m-80) cc_final: 0.8675 (m-80) outliers start: 10 outliers final: 2 residues processed: 632 average time/residue: 0.1070 time to fit residues: 99.0920 Evaluate side-chains 521 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 514 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 268 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 250 GLN B 250 GLN D 239 HIS E 179 GLN E 250 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.101959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.083370 restraints weight = 32455.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.086618 restraints weight = 14831.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.088632 restraints weight = 8298.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.089879 restraints weight = 5327.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.090665 restraints weight = 3848.709| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 14655 Z= 0.172 Angle : 0.786 12.148 19870 Z= 0.410 Chirality : 0.049 0.196 2230 Planarity : 0.005 0.056 2485 Dihedral : 5.450 37.683 1924 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.18 % Allowed : 12.61 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.20), residues: 1730 helix: 2.35 (0.20), residues: 630 sheet: 0.75 (0.28), residues: 360 loop : -1.80 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 409 TYR 0.022 0.002 TYR D 99 PHE 0.021 0.002 PHE E 56 TRP 0.012 0.001 TRP E 310 HIS 0.004 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (14645) covalent geometry : angle 0.76687 / 0.40 (19845) SS BOND : bond 0.01089 / 0.56 ( 5) SS BOND : angle 7.74574 / 3.89 ( 10) hydrogen bonds : bond 0.05497 / 3.69 ( 675) hydrogen bonds : angle 5.01421 / 3.43 ( 2385) link_NAG-ASN : bond 0.00075 / 0.06 ( 5) link_NAG-ASN : angle 1.15373 / 0.62 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 503 time to evaluate : 0.447 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 77 GLU cc_start: 0.8063 (pm20) cc_final: 0.7784 (pm20) REVERT: A 81 ASP cc_start: 0.7658 (p0) cc_final: 0.7422 (p0) REVERT: A 114 LEU cc_start: 0.8719 (mt) cc_final: 0.8364 (tp) REVERT: A 119 LYS cc_start: 0.9076 (mtmm) cc_final: 0.8809 (mtmt) REVERT: A 138 ASP cc_start: 0.8351 (p0) cc_final: 0.7968 (p0) REVERT: A 140 LYS cc_start: 0.8900 (mttp) cc_final: 0.8341 (mtmm) REVERT: A 142 LEU cc_start: 0.8717 (tp) cc_final: 0.8513 (tt) REVERT: A 146 LYS cc_start: 0.8921 (ttmm) cc_final: 0.8691 (tppp) REVERT: A 190 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8066 (tp) REVERT: A 193 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7828 (mm-30) REVERT: A 197 LYS cc_start: 0.8637 (mmtp) cc_final: 0.8324 (mmtt) REVERT: A 214 LYS cc_start: 0.8687 (mmtp) cc_final: 0.8432 (mmmm) REVERT: A 235 GLU cc_start: 0.7849 (tt0) cc_final: 0.7558 (tt0) REVERT: A 237 ARG cc_start: 0.7859 (mtt-85) cc_final: 0.7497 (mtt-85) REVERT: A 241 GLU cc_start: 0.7186 (mp0) cc_final: 0.6533 (mp0) REVERT: A 270 MET cc_start: 0.7865 (ppp) cc_final: 0.7346 (ppp) REVERT: A 287 MET cc_start: 0.8806 (tpp) cc_final: 0.8414 (tpp) REVERT: A 291 SER cc_start: 0.9369 (t) cc_final: 0.9153 (p) REVERT: A 322 LEU cc_start: 0.9377 (mt) cc_final: 0.9141 (mp) REVERT: A 329 ASN cc_start: 0.8686 (t0) cc_final: 0.8457 (t0) REVERT: A 406 ARG cc_start: 0.7850 (ttm170) cc_final: 0.7455 (mmt180) REVERT: A 428 PHE cc_start: 0.8859 (OUTLIER) cc_final: 0.8618 (t80) REVERT: A 431 ILE cc_start: 0.8410 (mm) cc_final: 0.8117 (pt) REVERT: B 42 MET cc_start: 0.8628 (pmm) cc_final: 0.8362 (pmm) REVERT: B 81 ASP cc_start: 0.7840 (p0) cc_final: 0.7510 (p0) REVERT: B 113 MET cc_start: 0.8369 (pmm) cc_final: 0.7626 (pmm) REVERT: B 140 LYS cc_start: 0.8867 (mttp) cc_final: 0.8259 (mtmm) REVERT: B 146 LYS cc_start: 0.8874 (ttmm) cc_final: 0.8571 (tppp) REVERT: B 177 ILE cc_start: 0.8983 (mm) cc_final: 0.8546 (mt) REVERT: B 179 GLN cc_start: 0.8632 (mt0) cc_final: 0.8253 (mt0) REVERT: B 181 GLU cc_start: 0.6688 (pm20) cc_final: 0.5883 (pm20) REVERT: B 190 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8360 (tp) REVERT: B 193 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7686 (mm-30) REVERT: B 214 LYS cc_start: 0.8661 (mmtp) cc_final: 0.8361 (mmmm) REVERT: B 287 MET cc_start: 0.8719 (tpp) cc_final: 0.8378 (tpp) REVERT: B 322 LEU cc_start: 0.9364 (mt) cc_final: 0.9133 (mp) REVERT: B 324 GLU cc_start: 0.8364 (pp20) cc_final: 0.8135 (mm-30) REVERT: B 325 TYR cc_start: 0.9019 (t80) cc_final: 0.8761 (t80) REVERT: C 81 ASP cc_start: 0.7466 (p0) cc_final: 0.7247 (p0) REVERT: C 104 ASP cc_start: 0.8873 (p0) cc_final: 0.8425 (p0) REVERT: C 114 LEU cc_start: 0.8512 (mt) cc_final: 0.7906 (tp) REVERT: C 119 LYS cc_start: 0.9026 (mtmm) cc_final: 0.8499 (mttm) REVERT: C 127 GLU cc_start: 0.6559 (tm-30) cc_final: 0.6356 (tm-30) REVERT: C 140 LYS cc_start: 0.8787 (mttp) cc_final: 0.8191 (mtmm) REVERT: C 142 LEU cc_start: 0.8700 (tp) cc_final: 0.8388 (tt) REVERT: C 190 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8257 (tp) REVERT: C 195 ASP cc_start: 0.8363 (t0) cc_final: 0.8151 (t0) REVERT: C 197 LYS cc_start: 0.8755 (mmtm) cc_final: 0.8420 (ptpp) REVERT: C 235 GLU cc_start: 0.7660 (tt0) cc_final: 0.6937 (tt0) REVERT: C 237 ARG cc_start: 0.8063 (mtt-85) cc_final: 0.7408 (mtt-85) REVERT: C 241 GLU cc_start: 0.7326 (mp0) cc_final: 0.6724 (mp0) REVERT: C 263 TRP cc_start: 0.6525 (t60) cc_final: 0.6287 (t60) REVERT: C 287 MET cc_start: 0.8942 (tpp) cc_final: 0.8569 (tpp) REVERT: C 291 SER cc_start: 0.9259 (t) cc_final: 0.8984 (p) REVERT: C 406 ARG cc_start: 0.7989 (ttm170) cc_final: 0.7502 (mmp-170) REVERT: C 410 ILE cc_start: 0.8724 (mm) cc_final: 0.8438 (mm) REVERT: C 431 ILE cc_start: 0.8498 (mm) cc_final: 0.8154 (pt) REVERT: D 41 LEU cc_start: 0.9256 (tp) cc_final: 0.8961 (tp) REVERT: D 81 ASP cc_start: 0.7931 (p0) cc_final: 0.7621 (p0) REVERT: D 113 MET cc_start: 0.8383 (pmm) cc_final: 0.7614 (pmm) REVERT: D 114 LEU cc_start: 0.8594 (mt) cc_final: 0.8309 (mt) REVERT: D 138 ASP cc_start: 0.8058 (p0) cc_final: 0.7040 (p0) REVERT: D 140 LYS cc_start: 0.8828 (mttp) cc_final: 0.8008 (mtmm) REVERT: D 190 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8514 (tp) REVERT: D 193 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7693 (mm-30) REVERT: D 210 GLN cc_start: 0.7972 (mp10) cc_final: 0.7670 (mp10) REVERT: D 214 LYS cc_start: 0.8723 (mmtp) cc_final: 0.8477 (mmmm) REVERT: D 235 GLU cc_start: 0.7879 (tt0) cc_final: 0.7479 (tt0) REVERT: D 237 ARG cc_start: 0.8103 (mtt-85) cc_final: 0.7696 (mtt-85) REVERT: D 241 GLU cc_start: 0.7220 (mp0) cc_final: 0.6568 (mp0) REVERT: D 260 ILE cc_start: 0.8937 (mt) cc_final: 0.8661 (tp) REVERT: D 287 MET cc_start: 0.8686 (tpp) cc_final: 0.8418 (tpp) REVERT: D 291 SER cc_start: 0.9256 (t) cc_final: 0.8954 (p) REVERT: D 399 MET cc_start: 0.6077 (mpp) cc_final: 0.4875 (mpp) REVERT: D 403 PHE cc_start: 0.7191 (m-80) cc_final: 0.6652 (m-80) REVERT: D 406 ARG cc_start: 0.7783 (ttm170) cc_final: 0.7493 (mmp-170) REVERT: E 101 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7565 (mm-30) REVERT: E 102 TYR cc_start: 0.8720 (m-80) cc_final: 0.8145 (m-80) REVERT: E 144 ILE cc_start: 0.9281 (mt) cc_final: 0.9018 (mm) REVERT: E 169 PHE cc_start: 0.8619 (t80) cc_final: 0.8312 (t80) REVERT: E 190 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8551 (tp) REVERT: E 193 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7556 (mm-30) REVERT: E 214 LYS cc_start: 0.8736 (mmtp) cc_final: 0.8489 (mmmm) REVERT: E 235 GLU cc_start: 0.7763 (tt0) cc_final: 0.7214 (tt0) REVERT: E 237 ARG cc_start: 0.7932 (mtt-85) cc_final: 0.7553 (mtt-85) REVERT: E 241 GLU cc_start: 0.7110 (mp0) cc_final: 0.6313 (mp0) REVERT: E 287 MET cc_start: 0.8933 (tpp) cc_final: 0.8616 (tmm) REVERT: E 315 LEU cc_start: 0.9354 (mt) cc_final: 0.9062 (tp) REVERT: E 322 LEU cc_start: 0.9431 (mt) cc_final: 0.9205 (mp) REVERT: E 422 PHE cc_start: 0.8659 (t80) cc_final: 0.8328 (t80) outliers start: 50 outliers final: 25 residues processed: 522 average time/residue: 0.1116 time to fit residues: 85.5457 Evaluate side-chains 524 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 493 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 233 CYS Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 418 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 172 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 112 optimal weight: 0.0870 chunk 132 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 239 HIS C 250 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.100613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.082011 restraints weight = 32800.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.085142 restraints weight = 15446.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.087083 restraints weight = 8762.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.088292 restraints weight = 5680.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.089057 restraints weight = 4135.020| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14655 Z= 0.146 Angle : 0.702 7.872 19870 Z= 0.363 Chirality : 0.047 0.202 2230 Planarity : 0.004 0.049 2485 Dihedral : 5.152 42.832 1922 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.06 % Allowed : 15.92 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.20), residues: 1730 helix: 2.30 (0.20), residues: 630 sheet: 0.90 (0.27), residues: 360 loop : -1.76 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 409 TYR 0.016 0.002 TYR D 429 PHE 0.020 0.001 PHE A 169 TRP 0.009 0.001 TRP D 310 HIS 0.005 0.001 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (14645) covalent geometry : angle 0.70053 / 0.36 (19845) SS BOND : bond 0.00682 / 0.34 ( 5) SS BOND : angle 1.91943 / 0.83 ( 10) hydrogen bonds : bond 0.04831 / 3.26 ( 675) hydrogen bonds : angle 4.58219 / 3.15 ( 2385) link_NAG-ASN : bond 0.00121 / 0.08 ( 5) link_NAG-ASN : angle 1.07124 / 0.58 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 498 time to evaluate : 0.610 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 77 GLU cc_start: 0.8002 (pm20) cc_final: 0.7773 (pm20) REVERT: A 81 ASP cc_start: 0.7624 (p0) cc_final: 0.7368 (p0) REVERT: A 104 ASP cc_start: 0.8856 (p0) cc_final: 0.8370 (p0) REVERT: A 114 LEU cc_start: 0.8688 (mt) cc_final: 0.8021 (tp) REVERT: A 119 LYS cc_start: 0.9065 (mtmm) cc_final: 0.8312 (mtmt) REVERT: A 138 ASP cc_start: 0.8171 (p0) cc_final: 0.7438 (p0) REVERT: A 140 LYS cc_start: 0.8877 (mttp) cc_final: 0.8301 (mtmm) REVERT: A 187 MET cc_start: 0.8237 (mmp) cc_final: 0.8009 (mmm) REVERT: A 190 LEU cc_start: 0.8940 (tp) cc_final: 0.8342 (tp) REVERT: A 193 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7728 (mm-30) REVERT: A 214 LYS cc_start: 0.8739 (mmtp) cc_final: 0.8452 (mmmm) REVERT: A 235 GLU cc_start: 0.7758 (tt0) cc_final: 0.7558 (tt0) REVERT: A 237 ARG cc_start: 0.7908 (mtt-85) cc_final: 0.7460 (mtt-85) REVERT: A 241 GLU cc_start: 0.7164 (mp0) cc_final: 0.6501 (mp0) REVERT: A 256 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9130 (mp) REVERT: A 270 MET cc_start: 0.7686 (ppp) cc_final: 0.7422 (ppp) REVERT: A 287 MET cc_start: 0.8655 (tpp) cc_final: 0.8444 (ttt) REVERT: A 291 SER cc_start: 0.9378 (t) cc_final: 0.9036 (p) REVERT: A 317 PHE cc_start: 0.8422 (m-80) cc_final: 0.8131 (m-80) REVERT: A 322 LEU cc_start: 0.9351 (mt) cc_final: 0.9105 (mp) REVERT: A 406 ARG cc_start: 0.7825 (ttm170) cc_final: 0.7457 (mmt180) REVERT: A 431 ILE cc_start: 0.8387 (mm) cc_final: 0.8116 (pt) REVERT: B 32 MET cc_start: 0.5265 (tpp) cc_final: 0.4848 (tpt) REVERT: B 81 ASP cc_start: 0.7838 (p0) cc_final: 0.7481 (p0) REVERT: B 104 ASP cc_start: 0.8766 (p0) cc_final: 0.8230 (p0) REVERT: B 105 ASP cc_start: 0.8509 (p0) cc_final: 0.8250 (p0) REVERT: B 174 GLN cc_start: 0.8290 (mm-40) cc_final: 0.7790 (mm-40) REVERT: B 177 ILE cc_start: 0.9048 (mm) cc_final: 0.8708 (mt) REVERT: B 179 GLN cc_start: 0.8628 (mt0) cc_final: 0.8304 (mt0) REVERT: B 181 GLU cc_start: 0.6962 (pm20) cc_final: 0.6318 (pm20) REVERT: B 190 LEU cc_start: 0.9046 (tp) cc_final: 0.8507 (tp) REVERT: B 193 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7639 (mm-30) REVERT: B 197 LYS cc_start: 0.8580 (mmtt) cc_final: 0.8204 (ptpp) REVERT: B 214 LYS cc_start: 0.8700 (mmtp) cc_final: 0.8405 (mmmm) REVERT: B 287 MET cc_start: 0.8624 (tpp) cc_final: 0.8410 (tpp) REVERT: B 322 LEU cc_start: 0.9331 (mt) cc_final: 0.9096 (mp) REVERT: B 325 TYR cc_start: 0.8914 (t80) cc_final: 0.8670 (t80) REVERT: B 431 ILE cc_start: 0.8298 (mm) cc_final: 0.7965 (pt) REVERT: C 104 ASP cc_start: 0.8885 (p0) cc_final: 0.8590 (p0) REVERT: C 114 LEU cc_start: 0.8511 (mt) cc_final: 0.7864 (tp) REVERT: C 119 LYS cc_start: 0.9019 (mtmm) cc_final: 0.8509 (mttm) REVERT: C 127 GLU cc_start: 0.6783 (tm-30) cc_final: 0.6390 (tm-30) REVERT: C 134 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7954 (mm-30) REVERT: C 140 LYS cc_start: 0.8797 (mttp) cc_final: 0.8210 (mtmm) REVERT: C 142 LEU cc_start: 0.8853 (tp) cc_final: 0.8497 (tt) REVERT: C 181 GLU cc_start: 0.6865 (pm20) cc_final: 0.6406 (pm20) REVERT: C 190 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8386 (tp) REVERT: C 197 LYS cc_start: 0.8708 (mmtm) cc_final: 0.8499 (ptpp) REVERT: C 235 GLU cc_start: 0.7475 (tt0) cc_final: 0.6967 (tt0) REVERT: C 237 ARG cc_start: 0.8017 (mtt-85) cc_final: 0.7406 (mtt-85) REVERT: C 241 GLU cc_start: 0.7379 (mp0) cc_final: 0.6822 (mp0) REVERT: C 291 SER cc_start: 0.9255 (t) cc_final: 0.8915 (p) REVERT: C 406 ARG cc_start: 0.7925 (ttm170) cc_final: 0.7452 (mmp-170) REVERT: C 410 ILE cc_start: 0.8783 (mm) cc_final: 0.8483 (mm) REVERT: C 431 ILE cc_start: 0.8462 (mm) cc_final: 0.8067 (pt) REVERT: D 32 MET cc_start: 0.5186 (tpt) cc_final: 0.4432 (tpp) REVERT: D 41 LEU cc_start: 0.9227 (tp) cc_final: 0.8938 (tp) REVERT: D 49 ASP cc_start: 0.8958 (t0) cc_final: 0.8678 (t0) REVERT: D 81 ASP cc_start: 0.7994 (p0) cc_final: 0.7711 (p0) REVERT: D 104 ASP cc_start: 0.8739 (p0) cc_final: 0.8382 (p0) REVERT: D 113 MET cc_start: 0.8471 (pmm) cc_final: 0.8006 (pmm) REVERT: D 131 ASN cc_start: 0.9017 (p0) cc_final: 0.8802 (p0) REVERT: D 138 ASP cc_start: 0.7872 (p0) cc_final: 0.7630 (p0) REVERT: D 190 LEU cc_start: 0.8990 (tp) cc_final: 0.8595 (tp) REVERT: D 193 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7649 (mm-30) REVERT: D 210 GLN cc_start: 0.7972 (mp10) cc_final: 0.7702 (mp10) REVERT: D 214 LYS cc_start: 0.8775 (mmtp) cc_final: 0.8550 (mmmm) REVERT: D 235 GLU cc_start: 0.7685 (tt0) cc_final: 0.7365 (tt0) REVERT: D 237 ARG cc_start: 0.8072 (mtt-85) cc_final: 0.7578 (mtt-85) REVERT: D 241 GLU cc_start: 0.7253 (mp0) cc_final: 0.6618 (mp0) REVERT: D 248 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.9003 (pp) REVERT: D 291 SER cc_start: 0.9253 (t) cc_final: 0.8873 (p) REVERT: D 399 MET cc_start: 0.6189 (mpp) cc_final: 0.5310 (mpp) REVERT: D 403 PHE cc_start: 0.7117 (m-80) cc_final: 0.6622 (m-80) REVERT: D 406 ARG cc_start: 0.7765 (ttm170) cc_final: 0.7525 (mmp-170) REVERT: D 429 TYR cc_start: 0.9117 (t80) cc_final: 0.8799 (t80) REVERT: E 32 MET cc_start: 0.5253 (tpp) cc_final: 0.4352 (tpp) REVERT: E 89 ARG cc_start: 0.8512 (mtt90) cc_final: 0.8129 (mtt-85) REVERT: E 119 LYS cc_start: 0.9172 (mtmt) cc_final: 0.8869 (mtmm) REVERT: E 144 ILE cc_start: 0.9324 (mt) cc_final: 0.9020 (mm) REVERT: E 149 ASN cc_start: 0.8932 (m-40) cc_final: 0.8688 (m-40) REVERT: E 181 GLU cc_start: 0.6873 (pm20) cc_final: 0.6285 (pm20) REVERT: E 190 LEU cc_start: 0.8921 (tp) cc_final: 0.8602 (tp) REVERT: E 193 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7512 (mm-30) REVERT: E 214 LYS cc_start: 0.8734 (mmtp) cc_final: 0.8515 (mmmm) REVERT: E 235 GLU cc_start: 0.7698 (tt0) cc_final: 0.7330 (tt0) REVERT: E 237 ARG cc_start: 0.8002 (mtt-85) cc_final: 0.7742 (mtt-85) REVERT: E 241 GLU cc_start: 0.7139 (mp0) cc_final: 0.6448 (mp0) REVERT: E 263 TRP cc_start: 0.7366 (m-10) cc_final: 0.6857 (m-10) REVERT: E 311 MET cc_start: 0.8460 (mmm) cc_final: 0.8133 (mmm) REVERT: E 322 LEU cc_start: 0.9320 (mt) cc_final: 0.9062 (mp) REVERT: E 422 PHE cc_start: 0.8481 (t80) cc_final: 0.8260 (t80) outliers start: 48 outliers final: 29 residues processed: 518 average time/residue: 0.1084 time to fit residues: 83.5968 Evaluate side-chains 503 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 471 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 233 CYS Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 418 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 160 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 155 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN B 133 HIS D 290 GLN E 55 ASN E 66 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.099722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.081610 restraints weight = 32978.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.084812 restraints weight = 15060.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.086761 restraints weight = 8392.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.087984 restraints weight = 5369.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.088763 restraints weight = 3849.315| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14655 Z= 0.153 Angle : 0.715 9.503 19870 Z= 0.366 Chirality : 0.046 0.243 2230 Planarity : 0.004 0.043 2485 Dihedral : 4.901 44.801 1914 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.06 % Allowed : 17.26 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.20), residues: 1730 helix: 2.21 (0.20), residues: 630 sheet: 0.87 (0.25), residues: 365 loop : -1.72 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 276 TYR 0.020 0.002 TYR A 99 PHE 0.013 0.001 PHE C 169 TRP 0.016 0.001 TRP C 263 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (14645) covalent geometry : angle 0.71327 / 0.37 (19845) SS BOND : bond 0.01174 / 0.62 ( 5) SS BOND : angle 2.24151 / 1.08 ( 10) hydrogen bonds : bond 0.04480 / 3.01 ( 675) hydrogen bonds : angle 4.39409 / 3.01 ( 2385) link_NAG-ASN : bond 0.00051 / 0.04 ( 5) link_NAG-ASN : angle 1.09404 / 0.59 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 483 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.4781 (tpt) cc_final: 0.4486 (tpt) REVERT: A 77 GLU cc_start: 0.8053 (pm20) cc_final: 0.7764 (pm20) REVERT: A 81 ASP cc_start: 0.7679 (p0) cc_final: 0.7440 (p0) REVERT: A 104 ASP cc_start: 0.8944 (p0) cc_final: 0.8639 (p0) REVERT: A 114 LEU cc_start: 0.8779 (mt) cc_final: 0.8127 (tp) REVERT: A 119 LYS cc_start: 0.9072 (mtmm) cc_final: 0.8431 (mtmt) REVERT: A 138 ASP cc_start: 0.8017 (p0) cc_final: 0.7661 (p0) REVERT: A 140 LYS cc_start: 0.8880 (mttp) cc_final: 0.8248 (mtmm) REVERT: A 190 LEU cc_start: 0.9064 (tp) cc_final: 0.8544 (tp) REVERT: A 193 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7716 (mm-30) REVERT: A 214 LYS cc_start: 0.8763 (mmtp) cc_final: 0.8449 (mmmm) REVERT: A 235 GLU cc_start: 0.7793 (tt0) cc_final: 0.7523 (tt0) REVERT: A 237 ARG cc_start: 0.7874 (mtt-85) cc_final: 0.7413 (mtt-85) REVERT: A 241 GLU cc_start: 0.7211 (mp0) cc_final: 0.6484 (mp0) REVERT: A 256 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9101 (mt) REVERT: A 270 MET cc_start: 0.7846 (ppp) cc_final: 0.7523 (ppp) REVERT: A 291 SER cc_start: 0.9367 (t) cc_final: 0.8997 (p) REVERT: A 317 PHE cc_start: 0.8536 (m-80) cc_final: 0.8123 (m-80) REVERT: A 322 LEU cc_start: 0.9359 (mt) cc_final: 0.9090 (mp) REVERT: A 406 ARG cc_start: 0.7817 (ttm170) cc_final: 0.7440 (mmt180) REVERT: B 81 ASP cc_start: 0.7899 (p0) cc_final: 0.7581 (p0) REVERT: B 105 ASP cc_start: 0.8621 (p0) cc_final: 0.8345 (p0) REVERT: B 140 LYS cc_start: 0.8831 (mttp) cc_final: 0.8282 (mtmm) REVERT: B 144 ILE cc_start: 0.9205 (mt) cc_final: 0.8974 (mm) REVERT: B 177 ILE cc_start: 0.9047 (mm) cc_final: 0.8781 (mt) REVERT: B 181 GLU cc_start: 0.6992 (pm20) cc_final: 0.6302 (pm20) REVERT: B 190 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8506 (tp) REVERT: B 193 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7593 (mm-30) REVERT: B 214 LYS cc_start: 0.8728 (mmtp) cc_final: 0.8408 (mmmm) REVERT: B 287 MET cc_start: 0.8714 (tpp) cc_final: 0.8455 (tpp) REVERT: B 322 LEU cc_start: 0.9313 (mt) cc_final: 0.9078 (mp) REVERT: C 114 LEU cc_start: 0.8603 (mt) cc_final: 0.7903 (tp) REVERT: C 119 LYS cc_start: 0.9048 (mtmm) cc_final: 0.8496 (mttm) REVERT: C 127 GLU cc_start: 0.6815 (tm-30) cc_final: 0.6394 (tm-30) REVERT: C 134 GLU cc_start: 0.8283 (mm-30) cc_final: 0.8045 (mm-30) REVERT: C 140 LYS cc_start: 0.8784 (mttp) cc_final: 0.8154 (mtmm) REVERT: C 142 LEU cc_start: 0.8837 (tp) cc_final: 0.8455 (tt) REVERT: C 190 LEU cc_start: 0.9097 (tp) cc_final: 0.8464 (tp) REVERT: C 241 GLU cc_start: 0.7479 (mp0) cc_final: 0.6837 (mp0) REVERT: C 291 SER cc_start: 0.9227 (t) cc_final: 0.8901 (p) REVERT: C 406 ARG cc_start: 0.7930 (ttm170) cc_final: 0.7421 (mmp-170) REVERT: C 410 ILE cc_start: 0.8726 (mm) cc_final: 0.8416 (mm) REVERT: C 431 ILE cc_start: 0.8443 (mm) cc_final: 0.8058 (pt) REVERT: D 41 LEU cc_start: 0.9275 (tp) cc_final: 0.9034 (tp) REVERT: D 49 ASP cc_start: 0.9058 (t0) cc_final: 0.8696 (t0) REVERT: D 81 ASP cc_start: 0.8067 (p0) cc_final: 0.7811 (p0) REVERT: D 113 MET cc_start: 0.8532 (pmm) cc_final: 0.8090 (pmm) REVERT: D 138 ASP cc_start: 0.8001 (p0) cc_final: 0.7433 (p0) REVERT: D 140 LYS cc_start: 0.8815 (mttp) cc_final: 0.8529 (mttp) REVERT: D 177 ILE cc_start: 0.9012 (mm) cc_final: 0.8705 (tp) REVERT: D 190 LEU cc_start: 0.9084 (tp) cc_final: 0.8677 (tp) REVERT: D 193 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7611 (mm-30) REVERT: D 210 GLN cc_start: 0.8016 (mp10) cc_final: 0.7769 (mp10) REVERT: D 214 LYS cc_start: 0.8811 (mmtp) cc_final: 0.8556 (mmmm) REVERT: D 241 GLU cc_start: 0.7325 (mp0) cc_final: 0.6669 (mp0) REVERT: D 248 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8972 (pp) REVERT: D 399 MET cc_start: 0.6083 (mpp) cc_final: 0.5394 (mpp) REVERT: D 403 PHE cc_start: 0.7166 (m-80) cc_final: 0.6660 (m-80) REVERT: D 406 ARG cc_start: 0.7831 (ttm170) cc_final: 0.7535 (mmp-170) REVERT: D 429 TYR cc_start: 0.9149 (t80) cc_final: 0.8847 (t80) REVERT: D 431 ILE cc_start: 0.8427 (mm) cc_final: 0.8053 (pt) REVERT: E 89 ARG cc_start: 0.8601 (mtt90) cc_final: 0.8182 (mtt90) REVERT: E 144 ILE cc_start: 0.9302 (mt) cc_final: 0.8991 (mm) REVERT: E 149 ASN cc_start: 0.8981 (m-40) cc_final: 0.8715 (m-40) REVERT: E 181 GLU cc_start: 0.6923 (pm20) cc_final: 0.6207 (pm20) REVERT: E 190 LEU cc_start: 0.9016 (tp) cc_final: 0.8663 (tp) REVERT: E 193 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7536 (mm-30) REVERT: E 235 GLU cc_start: 0.7778 (tt0) cc_final: 0.7372 (tt0) REVERT: E 237 ARG cc_start: 0.8027 (mtt-85) cc_final: 0.7669 (mtt-85) REVERT: E 241 GLU cc_start: 0.7235 (mp0) cc_final: 0.6642 (mp0) REVERT: E 263 TRP cc_start: 0.7651 (m-10) cc_final: 0.7148 (m-10) REVERT: E 287 MET cc_start: 0.8951 (tpp) cc_final: 0.8736 (tpt) REVERT: E 322 LEU cc_start: 0.9375 (mt) cc_final: 0.9100 (mp) REVERT: E 422 PHE cc_start: 0.8567 (t80) cc_final: 0.8357 (t80) outliers start: 48 outliers final: 34 residues processed: 500 average time/residue: 0.0972 time to fit residues: 72.7250 Evaluate side-chains 496 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 459 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 233 CYS Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 418 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 173 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 6 optimal weight: 0.1980 chunk 101 optimal weight: 6.9990 chunk 59 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 158 optimal weight: 0.3980 chunk 90 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 90 GLN C 290 GLN E 55 ASN E 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.102114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.084323 restraints weight = 32811.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.087537 restraints weight = 14999.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.089495 restraints weight = 8342.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.090707 restraints weight = 5319.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.091440 restraints weight = 3810.616| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 14655 Z= 0.139 Angle : 0.745 13.452 19870 Z= 0.377 Chirality : 0.047 0.231 2230 Planarity : 0.004 0.046 2485 Dihedral : 4.868 47.504 1910 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.69 % Allowed : 17.71 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.20), residues: 1730 helix: 2.11 (0.20), residues: 630 sheet: 0.83 (0.25), residues: 365 loop : -1.69 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 237 TYR 0.017 0.001 TYR B 325 PHE 0.016 0.001 PHE C 123 TRP 0.010 0.001 TRP E 310 HIS 0.007 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (14645) covalent geometry : angle 0.73672 / 0.37 (19845) SS BOND : bond 0.00812 / 0.40 ( 5) SS BOND : angle 4.97145 / 2.88 ( 10) hydrogen bonds : bond 0.04195 / 2.84 ( 675) hydrogen bonds : angle 4.23941 / 2.90 ( 2385) link_NAG-ASN : bond 0.00123 / 0.08 ( 5) link_NAG-ASN : angle 0.83190 / 0.46 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 472 time to evaluate : 0.594 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: A 77 GLU cc_start: 0.8148 (pm20) cc_final: 0.7767 (pm20) REVERT: A 81 ASP cc_start: 0.7796 (p0) cc_final: 0.7490 (p0) REVERT: A 104 ASP cc_start: 0.8922 (p0) cc_final: 0.8652 (p0) REVERT: A 114 LEU cc_start: 0.8787 (mt) cc_final: 0.8100 (tp) REVERT: A 119 LYS cc_start: 0.9065 (mtmm) cc_final: 0.8379 (mtmt) REVERT: A 138 ASP cc_start: 0.7889 (p0) cc_final: 0.7505 (p0) REVERT: A 140 LYS cc_start: 0.8877 (mttp) cc_final: 0.8224 (mtmm) REVERT: A 190 LEU cc_start: 0.9020 (tp) cc_final: 0.8216 (tt) REVERT: A 193 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7702 (mm-30) REVERT: A 214 LYS cc_start: 0.8775 (mmtp) cc_final: 0.8435 (mmmm) REVERT: A 235 GLU cc_start: 0.7887 (tt0) cc_final: 0.7660 (tt0) REVERT: A 241 GLU cc_start: 0.7274 (mp0) cc_final: 0.6521 (mp0) REVERT: A 251 MET cc_start: 0.8034 (mpp) cc_final: 0.7741 (mpp) REVERT: A 270 MET cc_start: 0.7914 (ppp) cc_final: 0.7580 (ppp) REVERT: A 287 MET cc_start: 0.8894 (tpp) cc_final: 0.8610 (tpp) REVERT: A 291 SER cc_start: 0.9249 (t) cc_final: 0.8906 (p) REVERT: A 317 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.8094 (m-80) REVERT: A 322 LEU cc_start: 0.9368 (mt) cc_final: 0.9102 (mp) REVERT: A 403 PHE cc_start: 0.7238 (m-80) cc_final: 0.6681 (m-80) REVERT: A 406 ARG cc_start: 0.7815 (ttm170) cc_final: 0.7418 (mmt180) REVERT: B 81 ASP cc_start: 0.7859 (p0) cc_final: 0.7493 (p0) REVERT: B 105 ASP cc_start: 0.8835 (p0) cc_final: 0.8404 (p0) REVERT: B 144 ILE cc_start: 0.9199 (mt) cc_final: 0.8948 (mm) REVERT: B 179 GLN cc_start: 0.8666 (mt0) cc_final: 0.8340 (mt0) REVERT: B 181 GLU cc_start: 0.6971 (pm20) cc_final: 0.6213 (pm20) REVERT: B 190 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8494 (tp) REVERT: B 193 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7569 (mm-30) REVERT: B 214 LYS cc_start: 0.8757 (mmtp) cc_final: 0.8163 (mmmm) REVERT: B 241 GLU cc_start: 0.7101 (mp0) cc_final: 0.6116 (mp0) REVERT: B 287 MET cc_start: 0.8764 (tpp) cc_final: 0.8493 (tpp) REVERT: B 322 LEU cc_start: 0.9353 (mt) cc_final: 0.9119 (mp) REVERT: C 94 ASP cc_start: 0.8634 (t70) cc_final: 0.8400 (t0) REVERT: C 104 ASP cc_start: 0.8913 (p0) cc_final: 0.8624 (p0) REVERT: C 114 LEU cc_start: 0.8564 (mt) cc_final: 0.8160 (mp) REVERT: C 119 LYS cc_start: 0.9034 (mtmm) cc_final: 0.8716 (mttm) REVERT: C 127 GLU cc_start: 0.6841 (tm-30) cc_final: 0.6435 (tm-30) REVERT: C 134 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8066 (mm-30) REVERT: C 140 LYS cc_start: 0.8676 (mttp) cc_final: 0.8034 (mtmm) REVERT: C 142 LEU cc_start: 0.8718 (tp) cc_final: 0.8336 (tt) REVERT: C 181 GLU cc_start: 0.6934 (pm20) cc_final: 0.6524 (pm20) REVERT: C 190 LEU cc_start: 0.9091 (tp) cc_final: 0.8453 (tp) REVERT: C 197 LYS cc_start: 0.8657 (mmtt) cc_final: 0.8300 (ptpp) REVERT: C 235 GLU cc_start: 0.7696 (tt0) cc_final: 0.7486 (tt0) REVERT: C 241 GLU cc_start: 0.7507 (mp0) cc_final: 0.6821 (mp0) REVERT: C 270 MET cc_start: 0.7298 (ppp) cc_final: 0.6920 (ppp) REVERT: C 287 MET cc_start: 0.8918 (tpp) cc_final: 0.8651 (tpp) REVERT: C 291 SER cc_start: 0.9183 (t) cc_final: 0.8803 (p) REVERT: C 309 ILE cc_start: 0.8942 (mt) cc_final: 0.8693 (mt) REVERT: C 406 ARG cc_start: 0.7940 (ttm170) cc_final: 0.7357 (mmp-170) REVERT: C 410 ILE cc_start: 0.8697 (mm) cc_final: 0.8416 (mm) REVERT: D 41 LEU cc_start: 0.9272 (tp) cc_final: 0.9013 (tp) REVERT: D 49 ASP cc_start: 0.9048 (t0) cc_final: 0.8630 (t0) REVERT: D 138 ASP cc_start: 0.7953 (p0) cc_final: 0.7510 (p0) REVERT: D 190 LEU cc_start: 0.9117 (tp) cc_final: 0.8711 (tp) REVERT: D 193 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7612 (mm-30) REVERT: D 210 GLN cc_start: 0.8044 (mp10) cc_final: 0.7776 (mp10) REVERT: D 214 LYS cc_start: 0.8806 (mmtp) cc_final: 0.8547 (mmmm) REVERT: D 241 GLU cc_start: 0.7325 (mp0) cc_final: 0.6668 (mp0) REVERT: D 270 MET cc_start: 0.7568 (ppp) cc_final: 0.6775 (ppp) REVERT: D 291 SER cc_start: 0.9185 (t) cc_final: 0.8782 (p) REVERT: D 399 MET cc_start: 0.5917 (mpp) cc_final: 0.5305 (mpp) REVERT: D 403 PHE cc_start: 0.7230 (m-80) cc_final: 0.6732 (m-80) REVERT: D 406 ARG cc_start: 0.7884 (ttm170) cc_final: 0.7483 (mmp-170) REVERT: D 431 ILE cc_start: 0.8357 (mm) cc_final: 0.7985 (pt) REVERT: E 89 ARG cc_start: 0.8534 (mtt90) cc_final: 0.8108 (mtt-85) REVERT: E 144 ILE cc_start: 0.9282 (mt) cc_final: 0.9009 (mm) REVERT: E 149 ASN cc_start: 0.8986 (m-40) cc_final: 0.8720 (m-40) REVERT: E 181 GLU cc_start: 0.6952 (pm20) cc_final: 0.6153 (pm20) REVERT: E 190 LEU cc_start: 0.9015 (tp) cc_final: 0.8658 (tp) REVERT: E 193 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7620 (mm-30) REVERT: E 214 LYS cc_start: 0.8903 (mmmm) cc_final: 0.8445 (mmmm) REVERT: E 235 GLU cc_start: 0.7794 (tt0) cc_final: 0.7182 (tt0) REVERT: E 237 ARG cc_start: 0.8026 (mtt-85) cc_final: 0.7392 (mtt-85) REVERT: E 241 GLU cc_start: 0.7263 (mp0) cc_final: 0.6361 (mp0) REVERT: E 263 TRP cc_start: 0.7670 (m-10) cc_final: 0.7162 (m-10) REVERT: E 322 LEU cc_start: 0.9376 (mt) cc_final: 0.9085 (mp) REVERT: E 422 PHE cc_start: 0.8578 (t80) cc_final: 0.8371 (t80) outliers start: 58 outliers final: 37 residues processed: 496 average time/residue: 0.1116 time to fit residues: 83.3295 Evaluate side-chains 487 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 448 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 233 CYS Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 418 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 149 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 122 optimal weight: 0.0050 chunk 86 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 overall best weight: 1.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.099029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.081551 restraints weight = 32986.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.084593 restraints weight = 15389.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.086455 restraints weight = 8692.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.087611 restraints weight = 5603.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.088299 restraints weight = 4042.555| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14655 Z= 0.212 Angle : 0.750 8.651 19870 Z= 0.385 Chirality : 0.047 0.231 2230 Planarity : 0.005 0.050 2485 Dihedral : 4.982 51.205 1910 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.76 % Allowed : 18.22 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.20), residues: 1730 helix: 2.11 (0.20), residues: 620 sheet: 0.56 (0.24), residues: 385 loop : -1.80 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 237 TYR 0.019 0.002 TYR E 429 PHE 0.017 0.002 PHE A 169 TRP 0.013 0.002 TRP A 263 HIS 0.008 0.002 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 (14645) covalent geometry : angle 0.74512 / 0.38 (19845) SS BOND : bond 0.01577 / 0.82 ( 5) SS BOND : angle 3.39715 / 1.69 ( 10) hydrogen bonds : bond 0.04427 / 3.01 ( 675) hydrogen bonds : angle 4.31012 / 2.96 ( 2385) link_NAG-ASN : bond 0.00277 / 0.15 ( 5) link_NAG-ASN : angle 1.51128 / 0.84 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 465 time to evaluate : 0.557 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: A 49 ASP cc_start: 0.8971 (t0) cc_final: 0.8770 (t0) REVERT: A 77 GLU cc_start: 0.8133 (pm20) cc_final: 0.7919 (pm20) REVERT: A 81 ASP cc_start: 0.7964 (p0) cc_final: 0.7683 (p0) REVERT: A 104 ASP cc_start: 0.8862 (p0) cc_final: 0.8596 (p0) REVERT: A 114 LEU cc_start: 0.8910 (mt) cc_final: 0.8414 (tp) REVERT: A 119 LYS cc_start: 0.9069 (mtmm) cc_final: 0.8548 (mtmt) REVERT: A 140 LYS cc_start: 0.8890 (mttp) cc_final: 0.8299 (mtmm) REVERT: A 190 LEU cc_start: 0.9109 (tp) cc_final: 0.8407 (tt) REVERT: A 193 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7646 (mm-30) REVERT: A 214 LYS cc_start: 0.8852 (mmtp) cc_final: 0.8524 (mmmm) REVERT: A 235 GLU cc_start: 0.7709 (tt0) cc_final: 0.7497 (tt0) REVERT: A 241 GLU cc_start: 0.7340 (mp0) cc_final: 0.6589 (mp0) REVERT: A 270 MET cc_start: 0.7988 (ppp) cc_final: 0.7584 (ppp) REVERT: A 287 MET cc_start: 0.8820 (tpp) cc_final: 0.8545 (tpp) REVERT: A 317 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.8160 (m-10) REVERT: A 322 LEU cc_start: 0.9364 (mt) cc_final: 0.9091 (mp) REVERT: A 403 PHE cc_start: 0.7243 (m-80) cc_final: 0.6704 (m-80) REVERT: A 406 ARG cc_start: 0.7825 (ttm170) cc_final: 0.7344 (mmp-170) REVERT: B 81 ASP cc_start: 0.8001 (p0) cc_final: 0.7610 (p0) REVERT: B 102 TYR cc_start: 0.8695 (OUTLIER) cc_final: 0.8216 (m-80) REVERT: B 105 ASP cc_start: 0.8861 (p0) cc_final: 0.8473 (p0) REVERT: B 113 MET cc_start: 0.8432 (pmm) cc_final: 0.7595 (pmm) REVERT: B 144 ILE cc_start: 0.9264 (mt) cc_final: 0.9040 (mm) REVERT: B 153 SER cc_start: 0.9183 (t) cc_final: 0.8978 (t) REVERT: B 174 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7664 (mm-40) REVERT: B 179 GLN cc_start: 0.8721 (mt0) cc_final: 0.8277 (mt0) REVERT: B 181 GLU cc_start: 0.7223 (pm20) cc_final: 0.6414 (pm20) REVERT: B 190 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8714 (tp) REVERT: B 193 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7499 (mm-30) REVERT: B 214 LYS cc_start: 0.8858 (mmtp) cc_final: 0.8331 (mmmm) REVERT: B 235 GLU cc_start: 0.7988 (tt0) cc_final: 0.7569 (tt0) REVERT: B 237 ARG cc_start: 0.8449 (mtt180) cc_final: 0.7862 (mtt180) REVERT: B 241 GLU cc_start: 0.7242 (mp0) cc_final: 0.6276 (mp0) REVERT: B 287 MET cc_start: 0.8699 (tpp) cc_final: 0.8246 (tpp) REVERT: B 322 LEU cc_start: 0.9324 (mt) cc_final: 0.9082 (mp) REVERT: C 104 ASP cc_start: 0.8871 (p0) cc_final: 0.8618 (p0) REVERT: C 114 LEU cc_start: 0.8709 (mt) cc_final: 0.8349 (mp) REVERT: C 119 LYS cc_start: 0.9052 (mtmm) cc_final: 0.8729 (mttt) REVERT: C 127 GLU cc_start: 0.7143 (tm-30) cc_final: 0.6838 (tm-30) REVERT: C 134 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7938 (mm-30) REVERT: C 140 LYS cc_start: 0.8710 (mttp) cc_final: 0.8098 (mtmm) REVERT: C 142 LEU cc_start: 0.8835 (tp) cc_final: 0.8501 (tt) REVERT: C 181 GLU cc_start: 0.6945 (pm20) cc_final: 0.6538 (pm20) REVERT: C 190 LEU cc_start: 0.9165 (tp) cc_final: 0.8604 (tp) REVERT: C 235 GLU cc_start: 0.7650 (tt0) cc_final: 0.7370 (tt0) REVERT: C 241 GLU cc_start: 0.7563 (mp0) cc_final: 0.6952 (mp0) REVERT: C 270 MET cc_start: 0.7383 (ppp) cc_final: 0.6926 (ppp) REVERT: C 287 MET cc_start: 0.8833 (tpp) cc_final: 0.8621 (tpp) REVERT: C 291 SER cc_start: 0.9196 (t) cc_final: 0.8954 (p) REVERT: C 406 ARG cc_start: 0.7942 (ttm170) cc_final: 0.7372 (mmp-170) REVERT: C 410 ILE cc_start: 0.8777 (mm) cc_final: 0.8465 (mm) REVERT: D 49 ASP cc_start: 0.9073 (t0) cc_final: 0.8822 (t0) REVERT: D 138 ASP cc_start: 0.7986 (p0) cc_final: 0.7526 (p0) REVERT: D 140 LYS cc_start: 0.8733 (mttp) cc_final: 0.8306 (mtmm) REVERT: D 177 ILE cc_start: 0.8833 (mt) cc_final: 0.8626 (mm) REVERT: D 190 LEU cc_start: 0.9129 (tp) cc_final: 0.8744 (tp) REVERT: D 193 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7535 (mm-30) REVERT: D 210 GLN cc_start: 0.8011 (mp10) cc_final: 0.7735 (mp10) REVERT: D 214 LYS cc_start: 0.8853 (mmtp) cc_final: 0.8631 (mmmm) REVERT: D 235 GLU cc_start: 0.7871 (tt0) cc_final: 0.7636 (tt0) REVERT: D 241 GLU cc_start: 0.7375 (mp0) cc_final: 0.6749 (mp0) REVERT: D 270 MET cc_start: 0.7500 (ppp) cc_final: 0.6879 (ppp) REVERT: D 406 ARG cc_start: 0.7823 (ttm170) cc_final: 0.7501 (mmp-170) REVERT: E 144 ILE cc_start: 0.9335 (mt) cc_final: 0.9052 (mm) REVERT: E 181 GLU cc_start: 0.7171 (pm20) cc_final: 0.6315 (pm20) REVERT: E 187 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8084 (mmm) REVERT: E 190 LEU cc_start: 0.9084 (tp) cc_final: 0.8743 (tp) REVERT: E 193 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7520 (mm-30) REVERT: E 214 LYS cc_start: 0.8937 (mmmm) cc_final: 0.8469 (mmmm) REVERT: E 235 GLU cc_start: 0.7680 (tt0) cc_final: 0.7410 (tt0) REVERT: E 237 ARG cc_start: 0.8052 (mtt-85) cc_final: 0.7634 (mtt-85) REVERT: E 241 GLU cc_start: 0.7305 (mp0) cc_final: 0.6420 (mp0) REVERT: E 263 TRP cc_start: 0.7756 (m-10) cc_final: 0.7299 (m-10) REVERT: E 322 LEU cc_start: 0.9386 (mt) cc_final: 0.9099 (mp) outliers start: 59 outliers final: 51 residues processed: 488 average time/residue: 0.1091 time to fit residues: 80.5162 Evaluate side-chains 487 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 432 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 233 CYS Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 418 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 133 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 148 optimal weight: 0.0010 chunk 92 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 HIS D 290 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.099219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.081115 restraints weight = 32414.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.084311 restraints weight = 14904.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.086302 restraints weight = 8309.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.087526 restraints weight = 5279.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.088298 restraints weight = 3773.328| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14655 Z= 0.146 Angle : 0.752 7.953 19870 Z= 0.380 Chirality : 0.047 0.239 2230 Planarity : 0.004 0.051 2485 Dihedral : 4.899 50.206 1910 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.38 % Allowed : 20.64 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.20), residues: 1730 helix: 2.12 (0.20), residues: 620 sheet: 0.64 (0.25), residues: 365 loop : -1.75 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 437 TYR 0.016 0.001 TYR E 429 PHE 0.013 0.001 PHE A 169 TRP 0.015 0.001 TRP A 263 HIS 0.008 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (14645) covalent geometry : angle 0.74892 / 0.38 (19845) SS BOND : bond 0.00668 / 0.42 ( 5) SS BOND : angle 3.18999 / 1.47 ( 10) hydrogen bonds : bond 0.04152 / 2.81 ( 675) hydrogen bonds : angle 4.13701 / 2.85 ( 2385) link_NAG-ASN : bond 0.00106 / 0.07 ( 5) link_NAG-ASN : angle 0.83823 / 0.46 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 444 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8160 (pm20) cc_final: 0.7893 (pm20) REVERT: A 81 ASP cc_start: 0.7960 (p0) cc_final: 0.7679 (p0) REVERT: A 114 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8578 (tp) REVERT: A 140 LYS cc_start: 0.8870 (mttp) cc_final: 0.8268 (mtmm) REVERT: A 190 LEU cc_start: 0.9069 (tp) cc_final: 0.8350 (tt) REVERT: A 193 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7640 (mm-30) REVERT: A 214 LYS cc_start: 0.8841 (mmtp) cc_final: 0.8495 (mmmm) REVERT: A 235 GLU cc_start: 0.7713 (tt0) cc_final: 0.7459 (tt0) REVERT: A 241 GLU cc_start: 0.7344 (mp0) cc_final: 0.6582 (mp0) REVERT: A 270 MET cc_start: 0.8015 (ppp) cc_final: 0.7655 (ppp) REVERT: A 287 MET cc_start: 0.8765 (tpp) cc_final: 0.8520 (tpp) REVERT: A 317 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.8127 (m-10) REVERT: A 322 LEU cc_start: 0.9382 (mt) cc_final: 0.9112 (mp) REVERT: A 403 PHE cc_start: 0.7258 (m-80) cc_final: 0.6721 (m-80) REVERT: A 406 ARG cc_start: 0.7841 (ttm170) cc_final: 0.7425 (mmt180) REVERT: B 81 ASP cc_start: 0.7991 (p0) cc_final: 0.7628 (p0) REVERT: B 102 TYR cc_start: 0.8815 (OUTLIER) cc_final: 0.8379 (m-80) REVERT: B 113 MET cc_start: 0.8451 (pmm) cc_final: 0.7764 (pmm) REVERT: B 144 ILE cc_start: 0.9229 (mt) cc_final: 0.8998 (mm) REVERT: B 153 SER cc_start: 0.9169 (t) cc_final: 0.8968 (t) REVERT: B 174 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7638 (mm-40) REVERT: B 179 GLN cc_start: 0.8703 (mt0) cc_final: 0.8254 (mt0) REVERT: B 181 GLU cc_start: 0.7239 (pm20) cc_final: 0.6367 (pm20) REVERT: B 190 LEU cc_start: 0.9183 (tp) cc_final: 0.8591 (tp) REVERT: B 193 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7425 (mm-30) REVERT: B 197 LYS cc_start: 0.8726 (mmtt) cc_final: 0.8337 (ptpp) REVERT: B 214 LYS cc_start: 0.8892 (mmtp) cc_final: 0.8549 (mmmm) REVERT: B 235 GLU cc_start: 0.8019 (tt0) cc_final: 0.7636 (tt0) REVERT: B 287 MET cc_start: 0.8723 (tpp) cc_final: 0.8193 (tpp) REVERT: B 322 LEU cc_start: 0.9328 (mt) cc_final: 0.9088 (mp) REVERT: C 114 LEU cc_start: 0.8726 (mt) cc_final: 0.8430 (mp) REVERT: C 119 LYS cc_start: 0.9045 (mtmm) cc_final: 0.8738 (mtmt) REVERT: C 127 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6762 (tm-30) REVERT: C 134 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8023 (mm-30) REVERT: C 140 LYS cc_start: 0.8676 (mttp) cc_final: 0.8048 (mtmm) REVERT: C 142 LEU cc_start: 0.8761 (tp) cc_final: 0.8433 (tt) REVERT: C 181 GLU cc_start: 0.6955 (pm20) cc_final: 0.6556 (pm20) REVERT: C 190 LEU cc_start: 0.9149 (tp) cc_final: 0.8561 (tp) REVERT: C 197 LYS cc_start: 0.8699 (mmtt) cc_final: 0.8288 (ptpp) REVERT: C 235 GLU cc_start: 0.7615 (tt0) cc_final: 0.7375 (tt0) REVERT: C 241 GLU cc_start: 0.7501 (mp0) cc_final: 0.6819 (mp0) REVERT: C 270 MET cc_start: 0.7453 (ppp) cc_final: 0.7058 (ppp) REVERT: C 287 MET cc_start: 0.8858 (tpp) cc_final: 0.8579 (tpp) REVERT: C 291 SER cc_start: 0.9190 (t) cc_final: 0.8836 (p) REVERT: C 406 ARG cc_start: 0.7977 (ttm170) cc_final: 0.7371 (mmp-170) REVERT: C 410 ILE cc_start: 0.8761 (mm) cc_final: 0.8459 (mm) REVERT: D 140 LYS cc_start: 0.8692 (mttp) cc_final: 0.8271 (mtmm) REVERT: D 147 ASN cc_start: 0.8924 (p0) cc_final: 0.8505 (p0) REVERT: D 149 ASN cc_start: 0.9002 (m-40) cc_final: 0.8679 (m-40) REVERT: D 190 LEU cc_start: 0.9093 (tp) cc_final: 0.8346 (tt) REVERT: D 193 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7517 (mm-30) REVERT: D 214 LYS cc_start: 0.8844 (mmtp) cc_final: 0.8575 (mmmm) REVERT: D 241 GLU cc_start: 0.7353 (mp0) cc_final: 0.6690 (mp0) REVERT: D 270 MET cc_start: 0.7434 (ppp) cc_final: 0.6874 (ppp) REVERT: D 291 SER cc_start: 0.9178 (t) cc_final: 0.8758 (p) REVERT: D 406 ARG cc_start: 0.7761 (ttm170) cc_final: 0.7505 (mmp-170) REVERT: E 102 TYR cc_start: 0.9027 (OUTLIER) cc_final: 0.8763 (m-80) REVERT: E 144 ILE cc_start: 0.9312 (mt) cc_final: 0.9034 (mm) REVERT: E 181 GLU cc_start: 0.7240 (pm20) cc_final: 0.6406 (pm20) REVERT: E 187 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7972 (mmm) REVERT: E 190 LEU cc_start: 0.9025 (tp) cc_final: 0.8685 (tp) REVERT: E 193 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7519 (mm-30) REVERT: E 214 LYS cc_start: 0.8934 (mmmm) cc_final: 0.8492 (mmmm) REVERT: E 235 GLU cc_start: 0.7748 (tt0) cc_final: 0.7324 (tt0) REVERT: E 237 ARG cc_start: 0.7952 (mtt-85) cc_final: 0.7463 (mtt-85) REVERT: E 241 GLU cc_start: 0.7314 (mp0) cc_final: 0.6425 (mp0) REVERT: E 247 TYR cc_start: 0.8720 (m-80) cc_final: 0.8500 (m-80) REVERT: E 263 TRP cc_start: 0.7876 (m-10) cc_final: 0.7417 (m-10) REVERT: E 322 LEU cc_start: 0.9371 (mt) cc_final: 0.9083 (mp) outliers start: 53 outliers final: 38 residues processed: 469 average time/residue: 0.1063 time to fit residues: 75.9920 Evaluate side-chains 493 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 450 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 233 CYS Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 162 CYS Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 418 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 142 optimal weight: 0.3980 chunk 95 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 153 optimal weight: 0.0270 chunk 22 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 243 GLN ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.099360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.081127 restraints weight = 32675.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.084348 restraints weight = 15030.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.086344 restraints weight = 8399.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.087580 restraints weight = 5352.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.088365 restraints weight = 3828.433| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14655 Z= 0.145 Angle : 0.763 10.810 19870 Z= 0.385 Chirality : 0.047 0.238 2230 Planarity : 0.004 0.053 2485 Dihedral : 4.877 49.412 1910 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.31 % Allowed : 21.21 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.20), residues: 1730 helix: 2.11 (0.20), residues: 620 sheet: 0.57 (0.25), residues: 375 loop : -1.82 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 276 TYR 0.019 0.001 TYR E 429 PHE 0.018 0.001 PHE E 422 TRP 0.038 0.002 TRP B 263 HIS 0.009 0.001 HIS E 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (14645) covalent geometry : angle 0.75713 / 0.38 (19845) SS BOND : bond 0.00576 / 0.30 ( 5) SS BOND : angle 4.26373 / 2.05 ( 10) hydrogen bonds : bond 0.04026 / 2.74 ( 675) hydrogen bonds : angle 4.09131 / 2.81 ( 2385) link_NAG-ASN : bond 0.00043 / 0.04 ( 5) link_NAG-ASN : angle 0.92991 / 0.52 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 456 time to evaluate : 0.499 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: A 49 ASP cc_start: 0.8933 (t0) cc_final: 0.8710 (t0) REVERT: A 77 GLU cc_start: 0.8177 (pm20) cc_final: 0.7966 (pm20) REVERT: A 81 ASP cc_start: 0.8012 (p0) cc_final: 0.7741 (p0) REVERT: A 104 ASP cc_start: 0.8890 (p0) cc_final: 0.8652 (p0) REVERT: A 140 LYS cc_start: 0.8866 (mttp) cc_final: 0.8334 (mtmm) REVERT: A 187 MET cc_start: 0.8602 (mmm) cc_final: 0.8108 (tpp) REVERT: A 190 LEU cc_start: 0.9092 (tp) cc_final: 0.8388 (tt) REVERT: A 193 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7630 (mm-30) REVERT: A 214 LYS cc_start: 0.8861 (mmtp) cc_final: 0.8473 (mmmm) REVERT: A 240 LEU cc_start: 0.8819 (mp) cc_final: 0.8529 (mt) REVERT: A 241 GLU cc_start: 0.7364 (mp0) cc_final: 0.6583 (mp0) REVERT: A 270 MET cc_start: 0.8037 (ppp) cc_final: 0.7673 (ppp) REVERT: A 287 MET cc_start: 0.8761 (tpp) cc_final: 0.8537 (tpp) REVERT: A 317 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.8122 (m-10) REVERT: A 403 PHE cc_start: 0.7242 (m-80) cc_final: 0.6711 (m-80) REVERT: A 406 ARG cc_start: 0.7838 (ttm170) cc_final: 0.7417 (mmt180) REVERT: B 81 ASP cc_start: 0.8008 (p0) cc_final: 0.7633 (p0) REVERT: B 102 TYR cc_start: 0.8873 (OUTLIER) cc_final: 0.8421 (m-80) REVERT: B 105 ASP cc_start: 0.8952 (p0) cc_final: 0.8536 (p0) REVERT: B 113 MET cc_start: 0.8398 (pmm) cc_final: 0.7799 (pmm) REVERT: B 140 LYS cc_start: 0.8784 (mttp) cc_final: 0.8297 (mtmm) REVERT: B 144 ILE cc_start: 0.9230 (mt) cc_final: 0.9022 (mm) REVERT: B 153 SER cc_start: 0.9227 (t) cc_final: 0.8991 (t) REVERT: B 174 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7639 (mm-40) REVERT: B 177 ILE cc_start: 0.8664 (mt) cc_final: 0.8194 (tt) REVERT: B 179 GLN cc_start: 0.8661 (mt0) cc_final: 0.8232 (mt0) REVERT: B 181 GLU cc_start: 0.7231 (pm20) cc_final: 0.6376 (pm20) REVERT: B 190 LEU cc_start: 0.9185 (tp) cc_final: 0.8655 (tp) REVERT: B 193 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7421 (mm-30) REVERT: B 214 LYS cc_start: 0.8912 (mmtp) cc_final: 0.8560 (mmmm) REVERT: B 235 GLU cc_start: 0.8007 (tt0) cc_final: 0.7268 (tt0) REVERT: B 287 MET cc_start: 0.8680 (tpp) cc_final: 0.8278 (tpp) REVERT: B 322 LEU cc_start: 0.9327 (mt) cc_final: 0.9086 (mp) REVERT: C 104 ASP cc_start: 0.8857 (p0) cc_final: 0.8629 (p0) REVERT: C 119 LYS cc_start: 0.9043 (mtmm) cc_final: 0.8733 (mtmt) REVERT: C 127 GLU cc_start: 0.7154 (tm-30) cc_final: 0.6754 (tm-30) REVERT: C 134 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8030 (mm-30) REVERT: C 140 LYS cc_start: 0.8677 (mttp) cc_final: 0.8125 (mtmm) REVERT: C 142 LEU cc_start: 0.8758 (tp) cc_final: 0.8430 (tt) REVERT: C 181 GLU cc_start: 0.7003 (pm20) cc_final: 0.6590 (pm20) REVERT: C 190 LEU cc_start: 0.9162 (tp) cc_final: 0.8606 (tp) REVERT: C 197 LYS cc_start: 0.8672 (mmtt) cc_final: 0.8257 (ptpp) REVERT: C 235 GLU cc_start: 0.7616 (tt0) cc_final: 0.7384 (tt0) REVERT: C 241 GLU cc_start: 0.7507 (mp0) cc_final: 0.6841 (mp0) REVERT: C 270 MET cc_start: 0.7482 (ppp) cc_final: 0.7139 (ppp) REVERT: C 287 MET cc_start: 0.8861 (tpp) cc_final: 0.8587 (tpp) REVERT: C 291 SER cc_start: 0.9196 (t) cc_final: 0.8838 (p) REVERT: C 406 ARG cc_start: 0.7898 (ttm170) cc_final: 0.7297 (mmp-170) REVERT: C 410 ILE cc_start: 0.8699 (mm) cc_final: 0.8416 (mm) REVERT: D 49 ASP cc_start: 0.8984 (t0) cc_final: 0.8721 (t0) REVERT: D 134 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8206 (mm-30) REVERT: D 140 LYS cc_start: 0.8742 (mttp) cc_final: 0.8203 (mtmm) REVERT: D 190 LEU cc_start: 0.9107 (tp) cc_final: 0.8391 (tt) REVERT: D 193 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7499 (mm-30) REVERT: D 214 LYS cc_start: 0.8864 (mmtp) cc_final: 0.8582 (mmmm) REVERT: D 241 GLU cc_start: 0.7384 (mp0) cc_final: 0.6678 (mp0) REVERT: D 270 MET cc_start: 0.7426 (ppp) cc_final: 0.6952 (ppp) REVERT: D 291 SER cc_start: 0.9175 (t) cc_final: 0.8727 (p) REVERT: D 406 ARG cc_start: 0.7741 (ttm170) cc_final: 0.7492 (mmp-170) REVERT: D 431 ILE cc_start: 0.8399 (mm) cc_final: 0.8016 (pt) REVERT: E 102 TYR cc_start: 0.9023 (OUTLIER) cc_final: 0.8631 (m-80) REVERT: E 104 ASP cc_start: 0.8902 (p0) cc_final: 0.8691 (p0) REVERT: E 144 ILE cc_start: 0.9302 (mt) cc_final: 0.9013 (mm) REVERT: E 181 GLU cc_start: 0.7223 (pm20) cc_final: 0.6373 (pm20) REVERT: E 187 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7991 (mmm) REVERT: E 190 LEU cc_start: 0.9029 (tp) cc_final: 0.8694 (tp) REVERT: E 193 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7524 (mm-30) REVERT: E 214 LYS cc_start: 0.8945 (mmmm) cc_final: 0.8526 (mmmm) REVERT: E 235 GLU cc_start: 0.7736 (tt0) cc_final: 0.7348 (tt0) REVERT: E 237 ARG cc_start: 0.7973 (mtt-85) cc_final: 0.7493 (mtt-85) REVERT: E 241 GLU cc_start: 0.7321 (mp0) cc_final: 0.6448 (mp0) REVERT: E 263 TRP cc_start: 0.7927 (m-10) cc_final: 0.7466 (m-10) REVERT: E 322 LEU cc_start: 0.9352 (mt) cc_final: 0.9061 (mp) outliers start: 52 outliers final: 37 residues processed: 481 average time/residue: 0.1070 time to fit residues: 78.7149 Evaluate side-chains 469 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 428 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 233 CYS Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 418 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 135 optimal weight: 0.6980 chunk 51 optimal weight: 0.2980 chunk 27 optimal weight: 0.0270 chunk 130 optimal weight: 0.7980 chunk 83 optimal weight: 0.0060 chunk 53 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 155 optimal weight: 0.5980 chunk 157 optimal weight: 0.0030 chunk 87 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 overall best weight: 0.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 290 GLN C 243 GLN D 243 GLN D 290 GLN E 239 HIS E 290 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.102706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.085158 restraints weight = 32591.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.088361 restraints weight = 15014.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.090311 restraints weight = 8368.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.091529 restraints weight = 5337.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.092232 restraints weight = 3811.258| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14655 Z= 0.140 Angle : 0.774 9.960 19870 Z= 0.387 Chirality : 0.047 0.270 2230 Planarity : 0.004 0.050 2485 Dihedral : 4.779 47.483 1910 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.61 % Allowed : 22.80 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.20), residues: 1730 helix: 1.96 (0.21), residues: 620 sheet: 0.67 (0.26), residues: 365 loop : -1.75 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 53 TYR 0.022 0.001 TYR E 429 PHE 0.016 0.001 PHE E 422 TRP 0.057 0.002 TRP B 263 HIS 0.010 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (14645) covalent geometry : angle 0.77107 / 0.39 (19845) SS BOND : bond 0.00463 / 0.26 ( 5) SS BOND : angle 2.95086 / 1.29 ( 10) hydrogen bonds : bond 0.03887 / 2.61 ( 675) hydrogen bonds : angle 4.05076 / 2.78 ( 2385) link_NAG-ASN : bond 0.00251 / 0.15 ( 5) link_NAG-ASN : angle 0.45918 / 0.27 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 434 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7957 (p0) cc_final: 0.7701 (p0) REVERT: A 104 ASP cc_start: 0.8932 (p0) cc_final: 0.8722 (p0) REVERT: A 133 HIS cc_start: 0.8875 (OUTLIER) cc_final: 0.8609 (m-70) REVERT: A 140 LYS cc_start: 0.8824 (mttp) cc_final: 0.8248 (mtmm) REVERT: A 190 LEU cc_start: 0.8988 (tp) cc_final: 0.8313 (tt) REVERT: A 193 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7628 (mm-30) REVERT: A 214 LYS cc_start: 0.8906 (mmtp) cc_final: 0.8445 (mmmm) REVERT: A 237 ARG cc_start: 0.8152 (mtt-85) cc_final: 0.7725 (mtt180) REVERT: A 240 LEU cc_start: 0.8771 (mp) cc_final: 0.8513 (mt) REVERT: A 241 GLU cc_start: 0.7380 (mp0) cc_final: 0.6529 (mp0) REVERT: A 270 MET cc_start: 0.8091 (ppp) cc_final: 0.7740 (ppp) REVERT: A 287 MET cc_start: 0.8785 (tpp) cc_final: 0.8528 (tpp) REVERT: A 317 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.8050 (m-10) REVERT: A 403 PHE cc_start: 0.7289 (m-80) cc_final: 0.6736 (m-80) REVERT: A 406 ARG cc_start: 0.7777 (ttm170) cc_final: 0.7360 (mmt180) REVERT: B 81 ASP cc_start: 0.7959 (p0) cc_final: 0.7581 (p0) REVERT: B 105 ASP cc_start: 0.8982 (p0) cc_final: 0.8511 (p0) REVERT: B 113 MET cc_start: 0.8377 (pmm) cc_final: 0.7888 (pmm) REVERT: B 140 LYS cc_start: 0.8767 (mttp) cc_final: 0.8183 (mtmm) REVERT: B 144 ILE cc_start: 0.9195 (mt) cc_final: 0.8985 (mm) REVERT: B 153 SER cc_start: 0.9180 (t) cc_final: 0.8961 (t) REVERT: B 174 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7611 (mm-40) REVERT: B 177 ILE cc_start: 0.8536 (mt) cc_final: 0.8177 (tt) REVERT: B 179 GLN cc_start: 0.8611 (mt0) cc_final: 0.8078 (mt0) REVERT: B 190 LEU cc_start: 0.9143 (tp) cc_final: 0.8542 (tp) REVERT: B 193 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7436 (mm-30) REVERT: B 214 LYS cc_start: 0.8925 (mmtp) cc_final: 0.8539 (mmmm) REVERT: B 235 GLU cc_start: 0.7976 (tt0) cc_final: 0.7290 (tt0) REVERT: B 287 MET cc_start: 0.8750 (tpp) cc_final: 0.8415 (tpp) REVERT: B 291 SER cc_start: 0.9138 (t) cc_final: 0.8846 (p) REVERT: B 322 LEU cc_start: 0.9337 (mt) cc_final: 0.9109 (mp) REVERT: C 114 LEU cc_start: 0.8734 (mm) cc_final: 0.8384 (mp) REVERT: C 119 LYS cc_start: 0.9004 (mtmm) cc_final: 0.8684 (mtmt) REVERT: C 134 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8033 (mm-30) REVERT: C 140 LYS cc_start: 0.8668 (mttp) cc_final: 0.8004 (mtmm) REVERT: C 181 GLU cc_start: 0.6980 (pm20) cc_final: 0.6588 (pm20) REVERT: C 190 LEU cc_start: 0.9111 (tp) cc_final: 0.8429 (tp) REVERT: C 197 LYS cc_start: 0.8603 (mmtt) cc_final: 0.8181 (ptpp) REVERT: C 235 GLU cc_start: 0.7636 (tt0) cc_final: 0.7368 (tt0) REVERT: C 241 GLU cc_start: 0.7490 (mp0) cc_final: 0.6795 (mp0) REVERT: C 270 MET cc_start: 0.7432 (ppp) cc_final: 0.7078 (ppp) REVERT: C 287 MET cc_start: 0.8888 (tpp) cc_final: 0.8583 (tpp) REVERT: C 291 SER cc_start: 0.9167 (t) cc_final: 0.8803 (p) REVERT: C 309 ILE cc_start: 0.8966 (mt) cc_final: 0.8755 (mt) REVERT: C 406 ARG cc_start: 0.7956 (ttm170) cc_final: 0.7342 (mmp-170) REVERT: C 410 ILE cc_start: 0.8773 (mm) cc_final: 0.8500 (mm) REVERT: D 49 ASP cc_start: 0.8949 (t0) cc_final: 0.8523 (t0) REVERT: D 126 ASN cc_start: 0.8346 (p0) cc_final: 0.7505 (p0) REVERT: D 134 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8280 (mm-30) REVERT: D 140 LYS cc_start: 0.8663 (mttp) cc_final: 0.8228 (mtmm) REVERT: D 190 LEU cc_start: 0.9053 (tp) cc_final: 0.8671 (tp) REVERT: D 193 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7536 (mm-30) REVERT: D 214 LYS cc_start: 0.8865 (mmtp) cc_final: 0.8564 (mmmm) REVERT: D 241 GLU cc_start: 0.7374 (mp0) cc_final: 0.6726 (mp0) REVERT: D 406 ARG cc_start: 0.7760 (ttm170) cc_final: 0.7483 (mmp-170) REVERT: D 431 ILE cc_start: 0.8383 (mm) cc_final: 0.8015 (pt) REVERT: E 102 TYR cc_start: 0.9027 (OUTLIER) cc_final: 0.8599 (m-80) REVERT: E 104 ASP cc_start: 0.8933 (p0) cc_final: 0.8722 (p0) REVERT: E 144 ILE cc_start: 0.9272 (mt) cc_final: 0.8985 (mm) REVERT: E 181 GLU cc_start: 0.7147 (pm20) cc_final: 0.6234 (pm20) REVERT: E 190 LEU cc_start: 0.8993 (tp) cc_final: 0.8657 (tp) REVERT: E 193 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7518 (mm-30) REVERT: E 214 LYS cc_start: 0.8960 (mmmm) cc_final: 0.8516 (mmmm) REVERT: E 235 GLU cc_start: 0.7696 (tt0) cc_final: 0.7224 (tt0) REVERT: E 237 ARG cc_start: 0.7948 (mtt-85) cc_final: 0.7300 (mtt-85) REVERT: E 241 GLU cc_start: 0.7333 (mp0) cc_final: 0.6415 (mp0) REVERT: E 263 TRP cc_start: 0.7818 (m-10) cc_final: 0.7385 (m-10) REVERT: E 322 LEU cc_start: 0.9348 (mt) cc_final: 0.9070 (mp) outliers start: 41 outliers final: 33 residues processed: 450 average time/residue: 0.1080 time to fit residues: 74.3680 Evaluate side-chains 459 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 423 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 233 CYS Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 418 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 31 optimal weight: 0.0270 chunk 85 optimal weight: 0.0770 chunk 33 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 0.2980 chunk 122 optimal weight: 0.0770 overall best weight: 0.1754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.103814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.086080 restraints weight = 32712.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.089310 restraints weight = 15157.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.091301 restraints weight = 8481.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.092530 restraints weight = 5397.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.093277 restraints weight = 3860.788| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 14655 Z= 0.142 Angle : 0.774 8.847 19870 Z= 0.390 Chirality : 0.048 0.267 2230 Planarity : 0.004 0.050 2485 Dihedral : 4.666 46.395 1910 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.23 % Allowed : 23.25 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.20), residues: 1730 helix: 1.83 (0.20), residues: 615 sheet: 0.59 (0.26), residues: 375 loop : -1.72 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 333 TYR 0.025 0.001 TYR E 429 PHE 0.022 0.001 PHE A 418 TRP 0.061 0.001 TRP B 263 HIS 0.009 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (14645) covalent geometry : angle 0.77145 / 0.39 (19845) SS BOND : bond 0.00475 / 0.25 ( 5) SS BOND : angle 2.76489 / 1.24 ( 10) hydrogen bonds : bond 0.03844 / 2.58 ( 675) hydrogen bonds : angle 4.13681 / 2.88 ( 2385) link_NAG-ASN : bond 0.00160 / 0.10 ( 5) link_NAG-ASN : angle 0.63472 / 0.38 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 439 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7985 (p0) cc_final: 0.7703 (p0) REVERT: A 119 LYS cc_start: 0.9019 (mtmm) cc_final: 0.8451 (mtmt) REVERT: A 140 LYS cc_start: 0.8819 (mttp) cc_final: 0.8225 (mtmm) REVERT: A 187 MET cc_start: 0.8639 (mmm) cc_final: 0.8153 (tpp) REVERT: A 190 LEU cc_start: 0.9011 (tp) cc_final: 0.8470 (tp) REVERT: A 193 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7638 (mm-30) REVERT: A 214 LYS cc_start: 0.8931 (mmtp) cc_final: 0.8452 (mmmm) REVERT: A 237 ARG cc_start: 0.8145 (mtt-85) cc_final: 0.7831 (mmt180) REVERT: A 240 LEU cc_start: 0.8735 (mp) cc_final: 0.8484 (mt) REVERT: A 241 GLU cc_start: 0.7389 (mp0) cc_final: 0.6537 (mp0) REVERT: A 287 MET cc_start: 0.8776 (tpp) cc_final: 0.8521 (tpp) REVERT: A 317 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.8012 (m-80) REVERT: A 403 PHE cc_start: 0.7267 (m-80) cc_final: 0.6798 (m-80) REVERT: A 406 ARG cc_start: 0.7766 (ttm170) cc_final: 0.7357 (mmt180) REVERT: B 81 ASP cc_start: 0.7969 (p0) cc_final: 0.7588 (p0) REVERT: B 105 ASP cc_start: 0.9007 (p0) cc_final: 0.8553 (p0) REVERT: B 113 MET cc_start: 0.8469 (pmm) cc_final: 0.7918 (pmm) REVERT: B 140 LYS cc_start: 0.8732 (mttp) cc_final: 0.8161 (mtmm) REVERT: B 144 ILE cc_start: 0.9200 (mt) cc_final: 0.8987 (mm) REVERT: B 153 SER cc_start: 0.9186 (t) cc_final: 0.8962 (t) REVERT: B 174 GLN cc_start: 0.7980 (mm-40) cc_final: 0.7634 (mm-40) REVERT: B 177 ILE cc_start: 0.8417 (mt) cc_final: 0.8042 (tt) REVERT: B 190 LEU cc_start: 0.9142 (tp) cc_final: 0.8536 (tp) REVERT: B 193 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7452 (mm-30) REVERT: B 214 LYS cc_start: 0.8924 (mmtp) cc_final: 0.8499 (mmmm) REVERT: B 287 MET cc_start: 0.8891 (tpp) cc_final: 0.8443 (tpp) REVERT: B 322 LEU cc_start: 0.9332 (mt) cc_final: 0.9101 (mp) REVERT: C 114 LEU cc_start: 0.8785 (mm) cc_final: 0.8346 (mp) REVERT: C 119 LYS cc_start: 0.9016 (mtmm) cc_final: 0.8688 (mtmt) REVERT: C 134 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8060 (mm-30) REVERT: C 140 LYS cc_start: 0.8675 (mttp) cc_final: 0.7992 (mtmm) REVERT: C 181 GLU cc_start: 0.6953 (pm20) cc_final: 0.6541 (pm20) REVERT: C 190 LEU cc_start: 0.9090 (tp) cc_final: 0.8443 (tp) REVERT: C 235 GLU cc_start: 0.7523 (tt0) cc_final: 0.7295 (tt0) REVERT: C 241 GLU cc_start: 0.7496 (mp0) cc_final: 0.6804 (mp0) REVERT: C 270 MET cc_start: 0.7544 (ppp) cc_final: 0.7205 (ppp) REVERT: C 287 MET cc_start: 0.8901 (tpp) cc_final: 0.8596 (tpp) REVERT: C 291 SER cc_start: 0.9182 (t) cc_final: 0.8829 (p) REVERT: C 300 LYS cc_start: 0.9114 (mptt) cc_final: 0.8542 (mmtp) REVERT: C 309 ILE cc_start: 0.8943 (mt) cc_final: 0.8731 (mt) REVERT: C 406 ARG cc_start: 0.7933 (ttm170) cc_final: 0.7340 (mmp-170) REVERT: C 410 ILE cc_start: 0.8699 (mm) cc_final: 0.8431 (mm) REVERT: C 423 LEU cc_start: 0.8614 (mt) cc_final: 0.8388 (pp) REVERT: D 49 ASP cc_start: 0.8916 (t0) cc_final: 0.8483 (t0) REVERT: D 114 LEU cc_start: 0.8755 (pt) cc_final: 0.8489 (pt) REVERT: D 126 ASN cc_start: 0.8304 (p0) cc_final: 0.7492 (p0) REVERT: D 134 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8295 (mm-30) REVERT: D 140 LYS cc_start: 0.8733 (mttp) cc_final: 0.8147 (mtmm) REVERT: D 190 LEU cc_start: 0.9068 (tp) cc_final: 0.8702 (tp) REVERT: D 193 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7547 (mm-30) REVERT: D 196 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8353 (mt-10) REVERT: D 197 LYS cc_start: 0.8410 (mmtm) cc_final: 0.8181 (mmtt) REVERT: D 214 LYS cc_start: 0.8880 (mmtp) cc_final: 0.8573 (mmmm) REVERT: D 241 GLU cc_start: 0.7383 (mp0) cc_final: 0.6646 (mp0) REVERT: D 406 ARG cc_start: 0.7796 (ttm170) cc_final: 0.7508 (mmp-170) REVERT: D 431 ILE cc_start: 0.8350 (mm) cc_final: 0.7985 (pt) REVERT: E 81 ASP cc_start: 0.8146 (p0) cc_final: 0.7869 (p0) REVERT: E 102 TYR cc_start: 0.9027 (OUTLIER) cc_final: 0.8599 (m-80) REVERT: E 104 ASP cc_start: 0.8934 (p0) cc_final: 0.8731 (p0) REVERT: E 144 ILE cc_start: 0.9277 (mt) cc_final: 0.8982 (mm) REVERT: E 169 PHE cc_start: 0.8941 (t80) cc_final: 0.8723 (t80) REVERT: E 181 GLU cc_start: 0.7154 (pm20) cc_final: 0.6412 (pm20) REVERT: E 190 LEU cc_start: 0.8997 (tp) cc_final: 0.8673 (tp) REVERT: E 193 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7517 (mm-30) REVERT: E 214 LYS cc_start: 0.8953 (mmmm) cc_final: 0.8511 (mmmm) REVERT: E 237 ARG cc_start: 0.8020 (mtt-85) cc_final: 0.7763 (mtt-85) REVERT: E 241 GLU cc_start: 0.7312 (mp0) cc_final: 0.6413 (mp0) REVERT: E 263 TRP cc_start: 0.7772 (m-10) cc_final: 0.7348 (m-10) outliers start: 35 outliers final: 29 residues processed: 454 average time/residue: 0.1081 time to fit residues: 74.9715 Evaluate side-chains 461 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 430 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 233 CYS Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 418 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 46 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 94 optimal weight: 0.0770 chunk 84 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 8 optimal weight: 0.0020 chunk 81 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 121 optimal weight: 0.0770 chunk 10 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 243 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.103409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.085580 restraints weight = 32667.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.088856 restraints weight = 15105.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.090881 restraints weight = 8448.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.092114 restraints weight = 5376.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.092903 restraints weight = 3848.049| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14655 Z= 0.137 Angle : 0.778 14.961 19870 Z= 0.389 Chirality : 0.047 0.328 2230 Planarity : 0.004 0.051 2485 Dihedral : 4.634 45.532 1910 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.04 % Allowed : 24.01 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.20), residues: 1730 helix: 1.83 (0.21), residues: 615 sheet: 0.59 (0.26), residues: 375 loop : -1.75 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 53 TYR 0.020 0.001 TYR E 429 PHE 0.032 0.001 PHE A 418 TRP 0.041 0.001 TRP B 263 HIS 0.009 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (14645) covalent geometry : angle 0.77623 / 0.39 (19845) SS BOND : bond 0.00437 / 0.22 ( 5) SS BOND : angle 2.77307 / 1.25 ( 10) hydrogen bonds : bond 0.03754 / 2.54 ( 675) hydrogen bonds : angle 4.11433 / 2.86 ( 2385) link_NAG-ASN : bond 0.00129 / 0.08 ( 5) link_NAG-ASN : angle 0.70575 / 0.42 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2577.19 seconds wall clock time: 45 minutes 24.54 seconds (2724.54 seconds total)