Starting phenix.real_space_refine on Wed Mar 4 15:13:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m6r_23705/03_2026/7m6r_23705.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m6r_23705/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7m6r_23705/03_2026/7m6r_23705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m6r_23705/03_2026/7m6r_23705.map" model { file = "/net/cci-nas-00/data/ceres_data/7m6r_23705/03_2026/7m6r_23705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m6r_23705/03_2026/7m6r_23705.cif" } 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-5986/lib/python3.9/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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.99, per 1000 atoms: 0.21 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: 1.22 Conformation dependent library (CDL) restraints added in 553.1 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: 0.48 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: 2.27 Time building geometry restraints manager: 1.65 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: 8150 16.58 - 33.16: 539 33.16 - 49.74: 116 49.74 - 66.33: 15 66.33 - 82.91: 10 Dihedral angle restraints: 8830 sinusoidal: 3655 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 8827 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: 1.780 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.000 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 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 : 12.245 82.907 5455 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 covalent geometry : bond 0.00759 (14645) covalent geometry : angle 1.20416 (19845) SS BOND : bond 0.00918 ( 5) SS BOND : angle 1.10106 ( 10) hydrogen bonds : bond 0.19192 ( 675) hydrogen bonds : angle 6.89472 ( 2385) link_NAG-ASN : bond 0.00174 ( 5) link_NAG-ASN : angle 2.60278 ( 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 : 0.399 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: 0.1138 time to fit residues: 105.4514 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 : 0.367 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3551 r_free = 0.3551 target = 0.101904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.083303 restraints weight = 32530.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.086551 restraints weight = 14876.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.088554 restraints weight = 8328.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.089798 restraints weight = 5351.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.090590 restraints weight = 3870.430| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 14655 Z= 0.173 Angle : 0.787 11.825 19870 Z= 0.410 Chirality : 0.049 0.194 2230 Planarity : 0.005 0.056 2485 Dihedral : 5.503 37.576 2029 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.06 % Allowed : 12.61 % Favored : 84.33 % 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: 0.52 (0.20), residues: 1730 helix: 2.36 (0.20), residues: 630 sheet: 0.77 (0.28), residues: 360 loop : -1.80 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 409 TYR 0.022 0.002 TYR B 429 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 covalent geometry : bond 0.00396 (14645) covalent geometry : angle 0.76827 (19845) SS BOND : bond 0.00737 ( 5) SS BOND : angle 7.53556 ( 10) hydrogen bonds : bond 0.05557 ( 675) hydrogen bonds : angle 5.03389 ( 2385) link_NAG-ASN : bond 0.00039 ( 5) link_NAG-ASN : angle 1.34132 ( 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 550 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 502 time to evaluate : 0.384 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: 0.8060 (pm20) cc_final: 0.7775 (pm20) REVERT: A 81 ASP cc_start: 0.7654 (p0) cc_final: 0.7429 (p0) REVERT: A 114 LEU cc_start: 0.8714 (mt) cc_final: 0.8362 (tp) REVERT: A 119 LYS cc_start: 0.9076 (mtmm) cc_final: 0.8811 (mtmt) REVERT: A 138 ASP cc_start: 0.8349 (p0) cc_final: 0.7975 (p0) REVERT: A 140 LYS cc_start: 0.8900 (mttp) cc_final: 0.8344 (mtmm) REVERT: A 142 LEU cc_start: 0.8719 (tp) cc_final: 0.8509 (tt) REVERT: A 146 LYS cc_start: 0.8921 (ttmm) cc_final: 0.8693 (tppp) REVERT: A 190 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8066 (tp) REVERT: A 193 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7826 (mm-30) REVERT: A 197 LYS cc_start: 0.8641 (mmtp) cc_final: 0.8323 (mmtt) REVERT: A 214 LYS cc_start: 0.8688 (mmtp) cc_final: 0.8425 (mmmm) REVERT: A 235 GLU cc_start: 0.7837 (tt0) cc_final: 0.7546 (tt0) REVERT: A 237 ARG cc_start: 0.7850 (mtt-85) cc_final: 0.7393 (mtt-85) REVERT: A 241 GLU cc_start: 0.7181 (mp0) cc_final: 0.6523 (mp0) REVERT: A 270 MET cc_start: 0.7835 (ppp) cc_final: 0.7266 (ppp) REVERT: A 287 MET cc_start: 0.8804 (tpp) cc_final: 0.8419 (tpp) REVERT: A 291 SER cc_start: 0.9369 (t) cc_final: 0.9151 (p) REVERT: A 322 LEU cc_start: 0.9376 (mt) cc_final: 0.9141 (mp) REVERT: A 329 ASN cc_start: 0.8684 (t0) cc_final: 0.8455 (t0) REVERT: A 406 ARG cc_start: 0.7847 (ttm170) cc_final: 0.7454 (mmt180) REVERT: A 428 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.8618 (t80) REVERT: A 431 ILE cc_start: 0.8411 (mm) cc_final: 0.8117 (pt) REVERT: B 42 MET cc_start: 0.8627 (pmm) cc_final: 0.8351 (pmm) REVERT: B 81 ASP cc_start: 0.7837 (p0) cc_final: 0.7509 (p0) REVERT: B 113 MET cc_start: 0.8369 (pmm) cc_final: 0.7656 (pmm) REVERT: B 140 LYS cc_start: 0.8867 (mttp) cc_final: 0.8264 (mtmm) REVERT: B 146 LYS cc_start: 0.8873 (ttmm) cc_final: 0.8575 (tppp) REVERT: B 177 ILE cc_start: 0.8977 (mm) cc_final: 0.8538 (mt) REVERT: B 179 GLN cc_start: 0.8635 (mt0) cc_final: 0.8260 (mt0) REVERT: B 181 GLU cc_start: 0.6700 (pm20) cc_final: 0.5892 (pm20) REVERT: B 190 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8358 (tp) REVERT: B 193 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7682 (mm-30) REVERT: B 214 LYS cc_start: 0.8661 (mmtp) cc_final: 0.8363 (mmmm) REVERT: B 287 MET cc_start: 0.8714 (tpp) cc_final: 0.8374 (tpp) REVERT: B 322 LEU cc_start: 0.9362 (mt) cc_final: 0.9133 (mp) REVERT: B 324 GLU cc_start: 0.8361 (pp20) cc_final: 0.8136 (mm-30) REVERT: B 325 TYR cc_start: 0.9015 (t80) cc_final: 0.8757 (t80) REVERT: C 81 ASP cc_start: 0.7459 (p0) cc_final: 0.7244 (p0) REVERT: C 104 ASP cc_start: 0.8859 (p0) cc_final: 0.8412 (p0) REVERT: C 114 LEU cc_start: 0.8506 (mt) cc_final: 0.7900 (tp) REVERT: C 119 LYS cc_start: 0.9026 (mtmm) cc_final: 0.8500 (mttm) REVERT: C 127 GLU cc_start: 0.6552 (tm-30) cc_final: 0.6351 (tm-30) REVERT: C 140 LYS cc_start: 0.8794 (mttp) cc_final: 0.8195 (mtmm) REVERT: C 142 LEU cc_start: 0.8702 (tp) cc_final: 0.8403 (tt) REVERT: C 190 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8257 (tp) REVERT: C 195 ASP cc_start: 0.8363 (t0) cc_final: 0.8155 (t0) REVERT: C 197 LYS cc_start: 0.8755 (mmtm) cc_final: 0.8420 (ptpp) REVERT: C 235 GLU cc_start: 0.7653 (tt0) cc_final: 0.6930 (tt0) REVERT: C 237 ARG cc_start: 0.8062 (mtt-85) cc_final: 0.7406 (mtt-85) REVERT: C 241 GLU cc_start: 0.7318 (mp0) cc_final: 0.6730 (mp0) REVERT: C 263 TRP cc_start: 0.6524 (t60) cc_final: 0.6291 (t60) REVERT: C 287 MET cc_start: 0.8938 (tpp) cc_final: 0.8562 (tpp) REVERT: C 291 SER cc_start: 0.9259 (t) cc_final: 0.8984 (p) REVERT: C 406 ARG cc_start: 0.7988 (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: 0.8502 (mm) cc_final: 0.8157 (pt) REVERT: D 41 LEU cc_start: 0.9276 (tp) cc_final: 0.8998 (tp) REVERT: D 81 ASP cc_start: 0.7944 (p0) cc_final: 0.7656 (p0) REVERT: D 113 MET cc_start: 0.8378 (pmm) cc_final: 0.7615 (pmm) REVERT: D 114 LEU cc_start: 0.8592 (mt) cc_final: 0.8307 (mt) REVERT: D 138 ASP cc_start: 0.8064 (p0) cc_final: 0.7070 (p0) REVERT: D 140 LYS cc_start: 0.8826 (mttp) cc_final: 0.8010 (mtmm) REVERT: D 190 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8514 (tp) REVERT: D 193 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7695 (mm-30) REVERT: D 210 GLN cc_start: 0.7966 (mp10) cc_final: 0.7666 (mp10) REVERT: D 214 LYS cc_start: 0.8724 (mmtp) cc_final: 0.8469 (mmmm) REVERT: D 235 GLU cc_start: 0.7870 (tt0) cc_final: 0.7458 (tt0) REVERT: D 237 ARG cc_start: 0.8105 (mtt-85) cc_final: 0.7674 (mtt-85) REVERT: D 241 GLU cc_start: 0.7218 (mp0) cc_final: 0.6569 (mp0) REVERT: D 260 ILE cc_start: 0.8933 (mt) cc_final: 0.8641 (tp) REVERT: D 287 MET cc_start: 0.8682 (tpp) cc_final: 0.8413 (tpp) REVERT: D 291 SER cc_start: 0.9258 (t) cc_final: 0.8954 (p) REVERT: D 399 MET cc_start: 0.6090 (mpp) cc_final: 0.4869 (mpp) REVERT: D 403 PHE cc_start: 0.7185 (m-80) cc_final: 0.6644 (m-80) REVERT: D 406 ARG cc_start: 0.7778 (ttm170) cc_final: 0.7495 (mmp-170) REVERT: E 101 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7573 (mm-30) REVERT: E 102 TYR cc_start: 0.8724 (m-80) cc_final: 0.8172 (m-80) REVERT: E 144 ILE cc_start: 0.9285 (mt) cc_final: 0.9021 (mm) REVERT: E 169 PHE cc_start: 0.8621 (t80) cc_final: 0.8309 (t80) REVERT: E 190 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8549 (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: 0.8492 (mmmm) REVERT: E 241 GLU cc_start: 0.7106 (mp0) cc_final: 0.6310 (mp0) REVERT: E 287 MET cc_start: 0.8933 (tpp) cc_final: 0.8614 (tmm) REVERT: E 300 LYS cc_start: 0.8908 (mttp) cc_final: 0.8545 (mttp) REVERT: E 315 LEU cc_start: 0.9353 (mt) cc_final: 0.9063 (tp) REVERT: E 322 LEU cc_start: 0.9430 (mt) cc_final: 0.9204 (mp) REVERT: E 422 PHE cc_start: 0.8657 (t80) cc_final: 0.8328 (t80) outliers start: 48 outliers final: 24 residues processed: 521 average time/residue: 0.1094 time to fit residues: 83.5849 Evaluate side-chains 521 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 491 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 64 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 132 optimal weight: 0.0670 chunk 108 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 HIS C 250 GLN E 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.100331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.081856 restraints weight = 32721.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.084997 restraints weight = 15398.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.086955 restraints weight = 8700.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.088137 restraints weight = 5607.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.088934 restraints weight = 4093.455| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14655 Z= 0.150 Angle : 0.707 8.267 19870 Z= 0.365 Chirality : 0.047 0.207 2230 Planarity : 0.004 0.050 2485 Dihedral : 5.140 43.131 2027 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.38 % Allowed : 15.29 % Favored : 81.34 % 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: 0.56 (0.20), residues: 1730 helix: 2.33 (0.20), residues: 630 sheet: 0.90 (0.27), residues: 360 loop : -1.77 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 409 TYR 0.017 0.002 TYR D 429 PHE 0.020 0.002 PHE A 169 TRP 0.009 0.001 TRP D 310 HIS 0.005 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00327 (14645) covalent geometry : angle 0.70576 (19845) SS BOND : bond 0.00372 ( 5) SS BOND : angle 1.94773 ( 10) hydrogen bonds : bond 0.04879 ( 675) hydrogen bonds : angle 4.60169 ( 2385) link_NAG-ASN : bond 0.00066 ( 5) link_NAG-ASN : angle 1.18996 ( 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 552 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 499 time to evaluate : 0.545 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 32 MET cc_start: 0.5078 (tpt) cc_final: 0.4657 (tpt) REVERT: A 77 GLU cc_start: 0.8014 (pm20) cc_final: 0.7776 (pm20) REVERT: A 81 ASP cc_start: 0.7638 (p0) cc_final: 0.7369 (p0) REVERT: A 104 ASP cc_start: 0.8869 (p0) cc_final: 0.8392 (p0) REVERT: A 114 LEU cc_start: 0.8701 (mt) cc_final: 0.8037 (tp) REVERT: A 119 LYS cc_start: 0.9070 (mtmm) cc_final: 0.8311 (mtmt) REVERT: A 138 ASP cc_start: 0.8171 (p0) cc_final: 0.7420 (p0) REVERT: A 140 LYS cc_start: 0.8885 (mttp) cc_final: 0.8304 (mtmm) REVERT: A 190 LEU cc_start: 0.8953 (tp) cc_final: 0.8367 (tp) REVERT: A 193 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7731 (mm-30) REVERT: A 214 LYS cc_start: 0.8738 (mmtp) cc_final: 0.8491 (mmmm) REVERT: A 235 GLU cc_start: 0.7729 (tt0) cc_final: 0.7327 (tt0) REVERT: A 237 ARG cc_start: 0.7850 (mtt-85) cc_final: 0.7264 (mtt-85) REVERT: A 241 GLU cc_start: 0.7167 (mp0) cc_final: 0.6521 (mp0) REVERT: A 256 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9115 (mp) REVERT: A 270 MET cc_start: 0.7740 (ppp) cc_final: 0.7462 (ppp) REVERT: A 287 MET cc_start: 0.8664 (tpp) cc_final: 0.8281 (tpp) REVERT: A 291 SER cc_start: 0.9373 (t) cc_final: 0.9032 (p) REVERT: A 317 PHE cc_start: 0.8435 (m-80) cc_final: 0.8141 (m-80) REVERT: A 322 LEU cc_start: 0.9354 (mt) cc_final: 0.9113 (mp) REVERT: A 406 ARG cc_start: 0.7828 (ttm170) cc_final: 0.7457 (mmt180) REVERT: A 431 ILE cc_start: 0.8389 (mm) cc_final: 0.8115 (pt) REVERT: B 81 ASP cc_start: 0.7843 (p0) cc_final: 0.7485 (p0) REVERT: B 104 ASP cc_start: 0.8774 (p0) cc_final: 0.8216 (p0) REVERT: B 105 ASP cc_start: 0.8519 (p0) cc_final: 0.8260 (p0) REVERT: B 174 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7786 (mm-40) REVERT: B 177 ILE cc_start: 0.9046 (mm) cc_final: 0.8712 (mt) REVERT: B 179 GLN cc_start: 0.8633 (mt0) cc_final: 0.8294 (mt0) REVERT: B 181 GLU cc_start: 0.6963 (pm20) cc_final: 0.6313 (pm20) REVERT: B 190 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8492 (tp) REVERT: B 193 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7643 (mm-30) REVERT: B 197 LYS cc_start: 0.8579 (mmtt) cc_final: 0.8202 (ptpp) REVERT: B 214 LYS cc_start: 0.8704 (mmtp) cc_final: 0.8406 (mmmm) REVERT: B 287 MET cc_start: 0.8628 (tpp) cc_final: 0.8413 (tpp) REVERT: B 322 LEU cc_start: 0.9334 (mt) cc_final: 0.9099 (mp) REVERT: B 325 TYR cc_start: 0.8925 (t80) cc_final: 0.8683 (t80) REVERT: B 431 ILE cc_start: 0.8302 (mm) cc_final: 0.7969 (pt) REVERT: C 81 ASP cc_start: 0.7458 (p0) cc_final: 0.7256 (p0) REVERT: C 104 ASP cc_start: 0.8890 (p0) cc_final: 0.8597 (p0) REVERT: C 114 LEU cc_start: 0.8533 (mt) cc_final: 0.7900 (tp) REVERT: C 119 LYS cc_start: 0.9027 (mtmm) cc_final: 0.8507 (mttm) REVERT: C 127 GLU cc_start: 0.6754 (tm-30) cc_final: 0.6388 (tm-30) REVERT: C 134 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7979 (mm-30) REVERT: C 140 LYS cc_start: 0.8802 (mttp) cc_final: 0.8207 (mtmm) REVERT: C 142 LEU cc_start: 0.8852 (tp) cc_final: 0.8483 (tt) REVERT: C 154 ILE cc_start: 0.8695 (mm) cc_final: 0.8494 (mm) REVERT: C 181 GLU cc_start: 0.6785 (pm20) cc_final: 0.6203 (pm20) REVERT: C 190 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8378 (tp) REVERT: C 197 LYS cc_start: 0.8726 (mmtm) cc_final: 0.8520 (ptpp) REVERT: C 235 GLU cc_start: 0.7494 (tt0) cc_final: 0.6949 (tt0) REVERT: C 237 ARG cc_start: 0.8027 (mtt-85) cc_final: 0.7397 (mtt-85) REVERT: C 241 GLU cc_start: 0.7396 (mp0) cc_final: 0.6823 (mp0) REVERT: C 291 SER cc_start: 0.9256 (t) cc_final: 0.8982 (p) REVERT: C 406 ARG cc_start: 0.7932 (ttm170) cc_final: 0.7455 (mmp-170) REVERT: C 410 ILE cc_start: 0.8786 (mm) cc_final: 0.8485 (mm) REVERT: C 431 ILE cc_start: 0.8467 (mm) cc_final: 0.8069 (pt) REVERT: D 32 MET cc_start: 0.5175 (tpt) cc_final: 0.4508 (tpp) REVERT: D 41 LEU cc_start: 0.9237 (tp) cc_final: 0.8941 (tp) REVERT: D 49 ASP cc_start: 0.8959 (t0) cc_final: 0.8667 (t0) REVERT: D 104 ASP cc_start: 0.8740 (p0) cc_final: 0.8347 (p0) REVERT: D 113 MET cc_start: 0.8484 (pmm) cc_final: 0.7971 (pmm) REVERT: D 131 ASN cc_start: 0.9021 (p0) cc_final: 0.8820 (p0) REVERT: D 138 ASP cc_start: 0.7875 (p0) cc_final: 0.7625 (p0) REVERT: D 190 LEU cc_start: 0.8997 (tp) cc_final: 0.8597 (tp) REVERT: D 193 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7624 (mm-30) REVERT: D 210 GLN cc_start: 0.7967 (mp10) cc_final: 0.7678 (mp10) REVERT: D 214 LYS cc_start: 0.8776 (mmtp) cc_final: 0.8546 (mmmm) REVERT: D 235 GLU cc_start: 0.7698 (tt0) cc_final: 0.7327 (tt0) REVERT: D 237 ARG cc_start: 0.8073 (mtt-85) cc_final: 0.7559 (mtt-85) REVERT: D 241 GLU cc_start: 0.7255 (mp0) cc_final: 0.6617 (mp0) REVERT: D 248 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8996 (pp) REVERT: D 291 SER cc_start: 0.9251 (t) cc_final: 0.8876 (p) REVERT: D 399 MET cc_start: 0.6173 (mpp) cc_final: 0.5339 (mpp) REVERT: D 403 PHE cc_start: 0.7112 (m-80) cc_final: 0.6618 (m-80) REVERT: D 406 ARG cc_start: 0.7796 (ttm170) cc_final: 0.7548 (mmp-170) REVERT: E 89 ARG cc_start: 0.8517 (mtt90) cc_final: 0.8053 (mtt-85) REVERT: E 104 ASP cc_start: 0.8876 (p0) cc_final: 0.8668 (p0) REVERT: E 119 LYS cc_start: 0.9191 (mtmt) cc_final: 0.8889 (mtmm) REVERT: E 144 ILE cc_start: 0.9320 (mt) cc_final: 0.9019 (mm) REVERT: E 181 GLU cc_start: 0.6870 (pm20) cc_final: 0.6262 (pm20) REVERT: E 190 LEU cc_start: 0.8935 (tp) cc_final: 0.8602 (tp) REVERT: E 193 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7507 (mm-30) REVERT: E 214 LYS cc_start: 0.8742 (mmtp) cc_final: 0.8516 (mmmm) REVERT: E 235 GLU cc_start: 0.7682 (tt0) cc_final: 0.7439 (tt0) REVERT: E 241 GLU cc_start: 0.7142 (mp0) cc_final: 0.6446 (mp0) REVERT: E 263 TRP cc_start: 0.7361 (m-10) cc_final: 0.6832 (m-10) REVERT: E 311 MET cc_start: 0.8470 (mmm) cc_final: 0.8156 (mmm) REVERT: E 322 LEU cc_start: 0.9370 (mt) cc_final: 0.9109 (mp) REVERT: E 399 MET cc_start: 0.5108 (mpp) cc_final: 0.4906 (mpp) REVERT: E 422 PHE cc_start: 0.8498 (t80) cc_final: 0.8236 (t80) outliers start: 53 outliers final: 32 residues processed: 521 average time/residue: 0.1084 time to fit residues: 83.6646 Evaluate side-chains 511 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 475 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 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 324 GLU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 90 GLN 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 428 PHE Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 190 LEU 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 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 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: 2.9990 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN B 133 HIS D 290 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.099494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.081191 restraints weight = 33004.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.084421 restraints weight = 15131.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.086393 restraints weight = 8440.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.087630 restraints weight = 5390.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.088372 restraints weight = 3865.145| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14655 Z= 0.157 Angle : 0.716 9.669 19870 Z= 0.367 Chirality : 0.046 0.235 2230 Planarity : 0.004 0.050 2485 Dihedral : 4.915 43.751 2021 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.99 % Allowed : 17.32 % 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: 0.52 (0.20), residues: 1730 helix: 2.23 (0.20), residues: 630 sheet: 0.86 (0.25), residues: 365 loop : -1.73 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 83 TYR 0.022 0.002 TYR A 99 PHE 0.014 0.002 PHE E 169 TRP 0.014 0.001 TRP C 263 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00348 (14645) covalent geometry : angle 0.71362 (19845) SS BOND : bond 0.00688 ( 5) SS BOND : angle 2.54904 ( 10) hydrogen bonds : bond 0.04524 ( 675) hydrogen bonds : angle 4.40289 ( 2385) link_NAG-ASN : bond 0.00042 ( 5) link_NAG-ASN : angle 1.21127 ( 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 527 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 480 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8044 (pm20) cc_final: 0.7772 (pm20) REVERT: A 81 ASP cc_start: 0.7697 (p0) cc_final: 0.7468 (p0) REVERT: A 101 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7301 (mm-30) REVERT: A 102 TYR cc_start: 0.8906 (m-10) cc_final: 0.8308 (m-80) REVERT: A 104 ASP cc_start: 0.8923 (p0) cc_final: 0.8625 (p0) REVERT: A 114 LEU cc_start: 0.8782 (mt) cc_final: 0.8123 (tp) REVERT: A 119 LYS cc_start: 0.9072 (mtmm) cc_final: 0.8423 (mtmt) REVERT: A 138 ASP cc_start: 0.8015 (p0) cc_final: 0.7640 (p0) REVERT: A 140 LYS cc_start: 0.8881 (mttp) cc_final: 0.8255 (mtmm) REVERT: A 190 LEU cc_start: 0.9066 (tp) cc_final: 0.8564 (tp) REVERT: A 193 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7713 (mm-30) REVERT: A 214 LYS cc_start: 0.8756 (mmtp) cc_final: 0.8456 (mmmm) REVERT: A 235 GLU cc_start: 0.7799 (tt0) cc_final: 0.7495 (tt0) REVERT: A 237 ARG cc_start: 0.7921 (mtt-85) cc_final: 0.7430 (mtt-85) REVERT: A 241 GLU cc_start: 0.7204 (mp0) cc_final: 0.6495 (mp0) REVERT: A 251 MET cc_start: 0.7993 (mpp) cc_final: 0.7765 (mpp) REVERT: A 256 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9125 (mp) REVERT: A 270 MET cc_start: 0.7857 (ppp) cc_final: 0.7519 (ppp) REVERT: A 287 MET cc_start: 0.8710 (tpp) cc_final: 0.8394 (tpp) REVERT: A 291 SER cc_start: 0.9358 (t) cc_final: 0.8993 (p) REVERT: A 317 PHE cc_start: 0.8546 (m-80) cc_final: 0.8135 (m-80) REVERT: A 322 LEU cc_start: 0.9361 (mt) cc_final: 0.9094 (mp) REVERT: A 406 ARG cc_start: 0.7746 (ttm170) cc_final: 0.7400 (mmt180) REVERT: B 81 ASP cc_start: 0.7904 (p0) cc_final: 0.7589 (p0) REVERT: B 105 ASP cc_start: 0.8610 (p0) cc_final: 0.8350 (p0) REVERT: B 140 LYS cc_start: 0.8820 (mttp) cc_final: 0.8275 (mtmm) REVERT: B 144 ILE cc_start: 0.9213 (mt) cc_final: 0.9005 (mm) REVERT: B 177 ILE cc_start: 0.9052 (mm) cc_final: 0.8797 (mt) REVERT: B 179 GLN cc_start: 0.8648 (mt0) cc_final: 0.8445 (mt0) REVERT: B 181 GLU cc_start: 0.7029 (pm20) cc_final: 0.6331 (pm20) REVERT: B 190 LEU cc_start: 0.9118 (tp) cc_final: 0.8532 (tp) REVERT: B 193 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7588 (mm-30) REVERT: B 214 LYS cc_start: 0.8736 (mmtp) cc_final: 0.8416 (mmmm) REVERT: B 287 MET cc_start: 0.8717 (tpp) cc_final: 0.8441 (tpp) REVERT: B 322 LEU cc_start: 0.9316 (mt) cc_final: 0.9076 (mp) REVERT: C 81 ASP cc_start: 0.7536 (p0) cc_final: 0.7321 (p0) REVERT: C 105 ASP cc_start: 0.8406 (p0) cc_final: 0.8194 (p0) REVERT: C 114 LEU cc_start: 0.8605 (mt) cc_final: 0.7937 (tp) REVERT: C 119 LYS cc_start: 0.9035 (mtmm) cc_final: 0.8499 (mttm) REVERT: C 127 GLU cc_start: 0.6837 (tm-30) cc_final: 0.6423 (tm-30) REVERT: C 134 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8045 (mm-30) REVERT: C 140 LYS cc_start: 0.8801 (mttp) cc_final: 0.8168 (mtmm) REVERT: C 142 LEU cc_start: 0.8856 (tp) cc_final: 0.8467 (tt) REVERT: C 154 ILE cc_start: 0.8683 (mm) cc_final: 0.8459 (mm) REVERT: C 190 LEU cc_start: 0.9097 (tp) cc_final: 0.8480 (tp) REVERT: C 241 GLU cc_start: 0.7467 (mp0) cc_final: 0.6837 (mp0) REVERT: C 291 SER cc_start: 0.9225 (t) cc_final: 0.8893 (p) REVERT: C 317 PHE cc_start: 0.8245 (m-80) cc_final: 0.7982 (m-80) REVERT: C 406 ARG cc_start: 0.7942 (ttm170) cc_final: 0.7424 (mmp-170) REVERT: C 410 ILE cc_start: 0.8729 (mm) cc_final: 0.8418 (mm) REVERT: C 431 ILE cc_start: 0.8433 (mm) cc_final: 0.8058 (pt) REVERT: D 41 LEU cc_start: 0.9272 (tp) cc_final: 0.9029 (tp) REVERT: D 81 ASP cc_start: 0.8079 (p0) cc_final: 0.7824 (p0) REVERT: D 113 MET cc_start: 0.8602 (pmm) cc_final: 0.8224 (pmm) REVERT: D 138 ASP cc_start: 0.8001 (p0) cc_final: 0.7058 (p0) REVERT: D 140 LYS cc_start: 0.8795 (mttp) cc_final: 0.7879 (mtmm) REVERT: D 142 LEU cc_start: 0.8877 (tp) cc_final: 0.8601 (tt) REVERT: D 190 LEU cc_start: 0.9085 (tp) cc_final: 0.8691 (tp) REVERT: D 193 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7605 (mm-30) REVERT: D 210 GLN cc_start: 0.8012 (mp10) cc_final: 0.7764 (mp10) REVERT: D 214 LYS cc_start: 0.8806 (mmtp) cc_final: 0.8567 (mmmm) REVERT: D 235 GLU cc_start: 0.7896 (tt0) cc_final: 0.7567 (tt0) REVERT: D 241 GLU cc_start: 0.7327 (mp0) cc_final: 0.6695 (mp0) REVERT: D 248 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8975 (pp) REVERT: D 399 MET cc_start: 0.6088 (mpp) cc_final: 0.5394 (mpp) REVERT: D 403 PHE cc_start: 0.7176 (m-80) cc_final: 0.6668 (m-80) REVERT: D 406 ARG cc_start: 0.7839 (ttm170) cc_final: 0.7535 (mmp-170) REVERT: D 429 TYR cc_start: 0.9150 (t80) cc_final: 0.8879 (t80) REVERT: D 431 ILE cc_start: 0.8430 (mm) cc_final: 0.8061 (pt) REVERT: E 32 MET cc_start: 0.5091 (tpp) cc_final: 0.4366 (tpp) REVERT: E 81 ASP cc_start: 0.8221 (p0) cc_final: 0.7949 (p0) REVERT: E 89 ARG cc_start: 0.8506 (mtt90) cc_final: 0.8150 (mtt90) REVERT: E 144 ILE cc_start: 0.9314 (mt) cc_final: 0.8997 (mm) REVERT: E 149 ASN cc_start: 0.8965 (m-40) cc_final: 0.8716 (m-40) REVERT: E 181 GLU cc_start: 0.6940 (pm20) cc_final: 0.6235 (pm20) REVERT: E 190 LEU cc_start: 0.9010 (tp) cc_final: 0.8678 (tp) REVERT: E 193 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7528 (mm-30) REVERT: E 235 GLU cc_start: 0.7737 (tt0) cc_final: 0.7445 (tt0) REVERT: E 241 GLU cc_start: 0.7231 (mp0) cc_final: 0.6654 (mp0) REVERT: E 263 TRP cc_start: 0.7528 (m-10) cc_final: 0.7039 (m-10) REVERT: E 287 MET cc_start: 0.8948 (tpp) cc_final: 0.8739 (tpt) REVERT: E 322 LEU cc_start: 0.9374 (mt) cc_final: 0.9101 (mp) outliers start: 47 outliers final: 33 residues processed: 498 average time/residue: 0.1072 time to fit residues: 79.8166 Evaluate side-chains 497 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 462 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP 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 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 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 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 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: 1.9990 chunk 61 optimal weight: 5.9990 chunk 6 optimal weight: 0.0980 chunk 101 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 chunk 23 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 HIS B 90 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 = 0.3538 r_free = 0.3538 target = 0.100363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.082693 restraints weight = 32938.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.085875 restraints weight = 15027.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.087806 restraints weight = 8354.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.089004 restraints weight = 5324.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.089701 restraints weight = 3806.817| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 14655 Z= 0.166 Angle : 0.751 14.585 19870 Z= 0.382 Chirality : 0.047 0.248 2230 Planarity : 0.004 0.053 2485 Dihedral : 4.873 47.846 2015 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.82 % Allowed : 17.77 % Favored : 78.41 % 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: 0.43 (0.20), residues: 1730 helix: 2.19 (0.20), residues: 630 sheet: 0.76 (0.25), residues: 375 loop : -1.81 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 276 TYR 0.016 0.002 TYR E 429 PHE 0.014 0.002 PHE C 123 TRP 0.010 0.001 TRP E 310 HIS 0.006 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00371 (14645) covalent geometry : angle 0.74598 (19845) SS BOND : bond 0.01110 ( 5) SS BOND : angle 3.92175 ( 10) hydrogen bonds : bond 0.04358 ( 675) hydrogen bonds : angle 4.28297 ( 2385) link_NAG-ASN : bond 0.00071 ( 5) link_NAG-ASN : angle 1.21488 ( 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 528 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 468 time to evaluate : 0.425 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 77 GLU cc_start: 0.8144 (pm20) cc_final: 0.7770 (pm20) REVERT: A 81 ASP cc_start: 0.7851 (p0) cc_final: 0.7552 (p0) REVERT: A 104 ASP cc_start: 0.8944 (p0) cc_final: 0.8689 (p0) REVERT: A 114 LEU cc_start: 0.8814 (mt) cc_final: 0.8152 (tp) REVERT: A 119 LYS cc_start: 0.9080 (mtmm) cc_final: 0.8368 (mtmt) REVERT: A 138 ASP cc_start: 0.8041 (p0) cc_final: 0.7308 (p0) REVERT: A 140 LYS cc_start: 0.8891 (mttp) cc_final: 0.8277 (mtmm) REVERT: A 190 LEU cc_start: 0.9100 (tp) cc_final: 0.8297 (tt) REVERT: A 193 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7709 (mm-30) REVERT: A 214 LYS cc_start: 0.8803 (mmtp) cc_final: 0.8455 (mmmm) REVERT: A 235 GLU cc_start: 0.7879 (tt0) cc_final: 0.7635 (tt0) REVERT: A 241 GLU cc_start: 0.7285 (mp0) cc_final: 0.6521 (mp0) REVERT: A 270 MET cc_start: 0.7909 (ppp) cc_final: 0.7533 (ppp) REVERT: A 287 MET cc_start: 0.8737 (tpp) cc_final: 0.8411 (tpp) REVERT: A 291 SER cc_start: 0.9357 (t) cc_final: 0.8982 (p) REVERT: A 317 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.8158 (m-80) REVERT: A 322 LEU cc_start: 0.9376 (mt) cc_final: 0.9115 (mp) REVERT: A 403 PHE cc_start: 0.7232 (m-80) cc_final: 0.6664 (m-80) REVERT: A 406 ARG cc_start: 0.7778 (ttm170) cc_final: 0.7393 (mmt180) REVERT: B 81 ASP cc_start: 0.7910 (p0) cc_final: 0.7538 (p0) REVERT: B 105 ASP cc_start: 0.8825 (p0) cc_final: 0.8399 (p0) REVERT: B 144 ILE cc_start: 0.9217 (mt) cc_final: 0.8980 (mm) REVERT: B 177 ILE cc_start: 0.8872 (mm) cc_final: 0.8644 (mt) REVERT: B 179 GLN cc_start: 0.8678 (mt0) cc_final: 0.8257 (mt0) REVERT: B 181 GLU cc_start: 0.7033 (pm20) cc_final: 0.6283 (pm20) REVERT: B 190 LEU cc_start: 0.9181 (tp) cc_final: 0.8604 (tp) REVERT: B 193 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7573 (mm-30) REVERT: B 214 LYS cc_start: 0.8774 (mmtp) cc_final: 0.8151 (mmmm) REVERT: B 241 GLU cc_start: 0.7142 (mp0) cc_final: 0.6144 (mp0) REVERT: B 287 MET cc_start: 0.8768 (tpp) cc_final: 0.8517 (tpp) REVERT: B 305 LYS cc_start: 0.8385 (mtmt) cc_final: 0.8060 (mtpt) REVERT: B 322 LEU cc_start: 0.9364 (mt) cc_final: 0.9127 (mp) REVERT: C 94 ASP cc_start: 0.8657 (t70) cc_final: 0.8429 (t0) REVERT: C 104 ASP cc_start: 0.8943 (p0) cc_final: 0.8649 (p0) REVERT: C 114 LEU cc_start: 0.8622 (mt) cc_final: 0.8284 (mp) REVERT: C 119 LYS cc_start: 0.9038 (mtmm) cc_final: 0.8736 (mttt) REVERT: C 127 GLU cc_start: 0.6924 (tm-30) cc_final: 0.6542 (tm-30) REVERT: C 134 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8055 (mm-30) REVERT: C 140 LYS cc_start: 0.8736 (mttp) cc_final: 0.8093 (mtmm) REVERT: C 142 LEU cc_start: 0.8775 (tp) cc_final: 0.8394 (tt) REVERT: C 154 ILE cc_start: 0.8634 (mm) cc_final: 0.8423 (mm) REVERT: C 181 GLU cc_start: 0.6935 (pm20) cc_final: 0.6473 (pm20) REVERT: C 190 LEU cc_start: 0.9132 (tp) cc_final: 0.8487 (tp) REVERT: C 197 LYS cc_start: 0.8713 (mmtt) cc_final: 0.8358 (ptpp) REVERT: C 235 GLU cc_start: 0.7720 (tt0) cc_final: 0.7496 (tt0) REVERT: C 241 GLU cc_start: 0.7524 (mp0) cc_final: 0.6854 (mp0) REVERT: C 270 MET cc_start: 0.7403 (ppp) cc_final: 0.7019 (ppp) REVERT: C 287 MET cc_start: 0.8894 (tpp) cc_final: 0.8662 (tpp) REVERT: C 291 SER cc_start: 0.9193 (t) cc_final: 0.8834 (p) REVERT: C 406 ARG cc_start: 0.8028 (ttm170) cc_final: 0.7470 (mmp-170) REVERT: C 410 ILE cc_start: 0.8773 (mm) cc_final: 0.8499 (mm) REVERT: D 41 LEU cc_start: 0.9301 (tp) cc_final: 0.9051 (tp) REVERT: D 49 ASP cc_start: 0.9037 (t0) cc_final: 0.8755 (t0) REVERT: D 138 ASP cc_start: 0.7984 (p0) cc_final: 0.7018 (p0) REVERT: D 140 LYS cc_start: 0.8701 (mttp) cc_final: 0.7982 (mtmm) REVERT: D 190 LEU cc_start: 0.9145 (tp) cc_final: 0.8753 (tp) REVERT: D 193 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7596 (mm-30) REVERT: D 210 GLN cc_start: 0.8046 (mp10) cc_final: 0.7775 (mp10) REVERT: D 214 LYS cc_start: 0.8821 (mmtp) cc_final: 0.8569 (mmmm) REVERT: D 235 GLU cc_start: 0.7853 (tt0) cc_final: 0.7624 (tt0) REVERT: D 241 GLU cc_start: 0.7365 (mp0) cc_final: 0.6719 (mp0) REVERT: D 270 MET cc_start: 0.7590 (ppp) cc_final: 0.6646 (ppp) REVERT: D 291 SER cc_start: 0.9208 (t) cc_final: 0.8798 (p) REVERT: D 406 ARG cc_start: 0.7892 (ttm170) cc_final: 0.7552 (mmp-170) REVERT: E 89 ARG cc_start: 0.8545 (mtt90) cc_final: 0.8157 (mtt90) REVERT: E 144 ILE cc_start: 0.9297 (mt) cc_final: 0.9015 (mm) REVERT: E 181 GLU cc_start: 0.6971 (pm20) cc_final: 0.6187 (pm20) REVERT: E 190 LEU cc_start: 0.9068 (tp) cc_final: 0.8721 (tp) REVERT: E 193 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7616 (mm-30) REVERT: E 214 LYS cc_start: 0.8910 (mmmm) cc_final: 0.8451 (mmmm) REVERT: E 235 GLU cc_start: 0.7786 (tt0) cc_final: 0.7463 (tt0) REVERT: E 241 GLU cc_start: 0.7275 (mp0) cc_final: 0.6400 (mp0) REVERT: E 263 TRP cc_start: 0.7615 (m-10) cc_final: 0.7122 (m-10) REVERT: E 287 MET cc_start: 0.8984 (tpp) cc_final: 0.8771 (tpt) REVERT: E 300 LYS cc_start: 0.8956 (mttp) cc_final: 0.8574 (mttp) REVERT: E 322 LEU cc_start: 0.9371 (mt) cc_final: 0.9089 (mp) REVERT: E 422 PHE cc_start: 0.8557 (t80) cc_final: 0.8316 (t80) outliers start: 60 outliers final: 37 residues processed: 494 average time/residue: 0.1033 time to fit residues: 76.9367 Evaluate side-chains 491 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 453 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 210 GLN 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 157 THR Chi-restraints excluded: chain B residue 164 MET 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 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 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 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 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: 2.9990 chunk 53 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 122 optimal weight: 0.7980 chunk 86 optimal weight: 0.3980 chunk 82 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.099063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.080650 restraints weight = 32687.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.083757 restraints weight = 15487.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.085694 restraints weight = 8812.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.086902 restraints weight = 5702.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.087672 restraints weight = 4126.683| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14655 Z= 0.139 Angle : 0.721 8.778 19870 Z= 0.364 Chirality : 0.046 0.228 2230 Planarity : 0.004 0.047 2485 Dihedral : 4.744 48.590 2015 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.68 % Allowed : 19.55 % Favored : 77.77 % 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: 0.44 (0.20), residues: 1730 helix: 2.24 (0.20), residues: 620 sheet: 0.70 (0.25), residues: 385 loop : -1.78 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 237 TYR 0.015 0.001 TYR E 429 PHE 0.014 0.001 PHE E 169 TRP 0.010 0.001 TRP A 310 HIS 0.008 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00312 (14645) covalent geometry : angle 0.71783 (19845) SS BOND : bond 0.00706 ( 5) SS BOND : angle 2.78051 ( 10) hydrogen bonds : bond 0.04064 ( 675) hydrogen bonds : angle 4.15189 ( 2385) link_NAG-ASN : bond 0.00059 ( 5) link_NAG-ASN : angle 0.96040 ( 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 513 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 471 time to evaluate : 0.522 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 81 ASP cc_start: 0.7853 (p0) cc_final: 0.7582 (p0) REVERT: A 102 TYR cc_start: 0.8874 (OUTLIER) cc_final: 0.8558 (m-80) REVERT: A 104 ASP cc_start: 0.8877 (p0) cc_final: 0.8590 (p0) REVERT: A 114 LEU cc_start: 0.8813 (mt) cc_final: 0.8023 (tp) REVERT: A 119 LYS cc_start: 0.9046 (mtmm) cc_final: 0.8268 (mtmt) REVERT: A 140 LYS cc_start: 0.8884 (mttp) cc_final: 0.8251 (mtmm) REVERT: A 190 LEU cc_start: 0.9048 (tp) cc_final: 0.8339 (tt) REVERT: A 193 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7620 (mm-30) REVERT: A 214 LYS cc_start: 0.8823 (mmtp) cc_final: 0.8500 (mmmm) REVERT: A 241 GLU cc_start: 0.7256 (mp0) cc_final: 0.6534 (mp0) REVERT: A 270 MET cc_start: 0.7969 (ppp) cc_final: 0.7617 (ppp) REVERT: A 291 SER cc_start: 0.9363 (t) cc_final: 0.8974 (p) REVERT: A 317 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.8104 (m-10) REVERT: A 322 LEU cc_start: 0.9402 (mt) cc_final: 0.9134 (mp) REVERT: A 403 PHE cc_start: 0.7255 (m-80) cc_final: 0.6710 (m-80) REVERT: A 406 ARG cc_start: 0.7824 (ttm170) cc_final: 0.7431 (mmt180) REVERT: B 81 ASP cc_start: 0.7914 (p0) cc_final: 0.7598 (p0) REVERT: B 101 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7785 (tm-30) REVERT: B 102 TYR cc_start: 0.8669 (OUTLIER) cc_final: 0.8122 (m-10) REVERT: B 105 ASP cc_start: 0.8798 (p0) cc_final: 0.8419 (p0) REVERT: B 144 ILE cc_start: 0.9247 (mt) cc_final: 0.9007 (mm) REVERT: B 153 SER cc_start: 0.9165 (t) cc_final: 0.8955 (t) REVERT: B 174 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7572 (mm-40) REVERT: B 179 GLN cc_start: 0.8631 (mt0) cc_final: 0.8384 (mt0) REVERT: B 181 GLU cc_start: 0.7230 (pm20) cc_final: 0.6436 (pm20) REVERT: B 190 LEU cc_start: 0.9164 (tp) cc_final: 0.8620 (tp) REVERT: B 193 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7450 (mm-30) REVERT: B 214 LYS cc_start: 0.8838 (mmtp) cc_final: 0.8520 (mmmm) REVERT: B 237 ARG cc_start: 0.8400 (mtt180) cc_final: 0.7865 (mtt180) REVERT: B 287 MET cc_start: 0.8678 (tpp) cc_final: 0.8179 (tpp) REVERT: B 322 LEU cc_start: 0.9354 (mt) cc_final: 0.9113 (mp) REVERT: C 114 LEU cc_start: 0.8604 (mt) cc_final: 0.8258 (mp) REVERT: C 119 LYS cc_start: 0.9018 (mtmm) cc_final: 0.8721 (mttt) REVERT: C 127 GLU cc_start: 0.7020 (tm-30) cc_final: 0.6658 (tm-30) REVERT: C 134 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7981 (mm-30) REVERT: C 140 LYS cc_start: 0.8670 (mttp) cc_final: 0.8128 (mtmm) REVERT: C 142 LEU cc_start: 0.8808 (tp) cc_final: 0.8457 (tt) REVERT: C 181 GLU cc_start: 0.6981 (pm20) cc_final: 0.6637 (pm20) REVERT: C 190 LEU cc_start: 0.9111 (tp) cc_final: 0.8537 (tp) REVERT: C 197 LYS cc_start: 0.8693 (mmtt) cc_final: 0.8314 (ptpp) REVERT: C 241 GLU cc_start: 0.7495 (mp0) cc_final: 0.6906 (mp0) REVERT: C 270 MET cc_start: 0.7391 (ppp) cc_final: 0.6941 (ppp) REVERT: C 287 MET cc_start: 0.8808 (tpp) cc_final: 0.8588 (tpp) REVERT: C 291 SER cc_start: 0.9193 (t) cc_final: 0.8810 (p) REVERT: C 406 ARG cc_start: 0.7992 (ttm170) cc_final: 0.7393 (mmp-170) REVERT: C 410 ILE cc_start: 0.8732 (mm) cc_final: 0.8415 (mm) REVERT: D 41 LEU cc_start: 0.9259 (tp) cc_final: 0.9044 (tp) REVERT: D 49 ASP cc_start: 0.8972 (t0) cc_final: 0.8757 (t0) REVERT: D 93 ASN cc_start: 0.8924 (t0) cc_final: 0.8672 (t0) REVERT: D 138 ASP cc_start: 0.7896 (p0) cc_final: 0.7512 (p0) REVERT: D 147 ASN cc_start: 0.8866 (p0) cc_final: 0.8439 (p0) REVERT: D 149 ASN cc_start: 0.9000 (m-40) cc_final: 0.8653 (m-40) REVERT: D 190 LEU cc_start: 0.9086 (tp) cc_final: 0.8728 (tp) REVERT: D 193 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7559 (mm-30) REVERT: D 210 GLN cc_start: 0.7979 (mp10) cc_final: 0.7730 (mp10) REVERT: D 214 LYS cc_start: 0.8820 (mmtp) cc_final: 0.8605 (mmmm) REVERT: D 241 GLU cc_start: 0.7351 (mp0) cc_final: 0.6737 (mp0) REVERT: D 270 MET cc_start: 0.7401 (ppp) cc_final: 0.6708 (ppp) REVERT: D 291 SER cc_start: 0.9225 (t) cc_final: 0.8788 (p) REVERT: D 406 ARG cc_start: 0.7784 (ttm170) cc_final: 0.7523 (mmp-170) REVERT: E 89 ARG cc_start: 0.8533 (mtt90) cc_final: 0.8044 (mtt-85) REVERT: E 144 ILE cc_start: 0.9320 (mt) cc_final: 0.9044 (mm) REVERT: E 181 GLU cc_start: 0.7140 (pm20) cc_final: 0.6334 (pm20) REVERT: E 190 LEU cc_start: 0.8997 (tp) cc_final: 0.8676 (tp) REVERT: E 193 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7506 (mm-30) REVERT: E 214 LYS cc_start: 0.8904 (mmmm) cc_final: 0.8476 (mmmm) REVERT: E 235 GLU cc_start: 0.7622 (tt0) cc_final: 0.7391 (tt0) REVERT: E 241 GLU cc_start: 0.7231 (mp0) cc_final: 0.6404 (mp0) REVERT: E 247 TYR cc_start: 0.8761 (m-80) cc_final: 0.8551 (m-80) REVERT: E 263 TRP cc_start: 0.7792 (m-10) cc_final: 0.7280 (m-10) REVERT: E 287 MET cc_start: 0.8875 (tpp) cc_final: 0.8649 (tpt) REVERT: E 322 LEU cc_start: 0.9367 (mt) cc_final: 0.9082 (mp) REVERT: E 422 PHE cc_start: 0.8524 (t80) cc_final: 0.8307 (t80) outliers start: 42 outliers final: 33 residues processed: 488 average time/residue: 0.1048 time to fit residues: 77.5996 Evaluate side-chains 482 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 446 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 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 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 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 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 187 MET Chi-restraints excluded: chain E residue 233 CYS 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: 1.9990 chunk 3 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 92 optimal weight: 0.0970 chunk 38 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 chunk 153 optimal weight: 0.0270 chunk 16 optimal weight: 1.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 HIS B 243 GLN C 290 GLN D 243 GLN D 290 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.101047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.083667 restraints weight = 32684.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.086825 restraints weight = 14934.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.088737 restraints weight = 8310.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.089924 restraints weight = 5282.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.090654 restraints weight = 3777.815| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4271 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= 0.138 Angle : 0.735 8.018 19870 Z= 0.369 Chirality : 0.046 0.202 2230 Planarity : 0.004 0.048 2485 Dihedral : 4.673 45.884 2015 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.93 % Allowed : 20.45 % Favored : 76.62 % 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: 0.39 (0.20), residues: 1730 helix: 2.15 (0.20), residues: 620 sheet: 0.70 (0.25), residues: 385 loop : -1.78 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 276 TYR 0.019 0.001 TYR E 429 PHE 0.015 0.001 PHE A 169 TRP 0.013 0.001 TRP A 263 HIS 0.008 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00307 (14645) covalent geometry : angle 0.73315 (19845) SS BOND : bond 0.00559 ( 5) SS BOND : angle 2.57532 ( 10) hydrogen bonds : bond 0.03963 ( 675) hydrogen bonds : angle 4.06599 ( 2385) link_NAG-ASN : bond 0.00048 ( 5) link_NAG-ASN : angle 0.93276 ( 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 502 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 456 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7924 (p0) cc_final: 0.7604 (p0) REVERT: A 89 ARG cc_start: 0.8661 (mtt90) cc_final: 0.8402 (mtt-85) REVERT: A 114 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8004 (tp) REVERT: A 119 LYS cc_start: 0.9061 (mtmm) cc_final: 0.8234 (mtmt) REVERT: A 140 LYS cc_start: 0.8883 (mttp) cc_final: 0.8249 (mtmm) REVERT: A 190 LEU cc_start: 0.9099 (tp) cc_final: 0.8350 (tt) REVERT: A 193 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7669 (mm-30) REVERT: A 214 LYS cc_start: 0.8838 (mmtp) cc_final: 0.8439 (mmmm) REVERT: A 237 ARG cc_start: 0.8220 (mtt-85) cc_final: 0.7926 (mtt-85) REVERT: A 241 GLU cc_start: 0.7344 (mp0) cc_final: 0.6465 (mp0) REVERT: A 270 MET cc_start: 0.8095 (ppp) cc_final: 0.7777 (ppp) REVERT: A 287 MET cc_start: 0.8876 (tpp) cc_final: 0.8650 (tpp) REVERT: A 291 SER cc_start: 0.9300 (t) cc_final: 0.8945 (p) REVERT: A 317 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.8107 (m-10) REVERT: A 403 PHE cc_start: 0.7295 (m-80) cc_final: 0.6759 (m-80) REVERT: A 406 ARG cc_start: 0.7841 (ttm170) cc_final: 0.7412 (mmt180) REVERT: B 81 ASP cc_start: 0.7960 (p0) cc_final: 0.7634 (p0) REVERT: B 101 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7782 (tm-30) REVERT: B 102 TYR cc_start: 0.8757 (OUTLIER) cc_final: 0.8184 (m-10) REVERT: B 105 ASP cc_start: 0.8987 (p0) cc_final: 0.8564 (p0) REVERT: B 113 MET cc_start: 0.8386 (pmm) cc_final: 0.7502 (pmm) REVERT: B 140 LYS cc_start: 0.8768 (mttp) cc_final: 0.8267 (mtmm) REVERT: B 144 ILE cc_start: 0.9199 (mt) cc_final: 0.8953 (mm) REVERT: B 153 SER cc_start: 0.9168 (t) cc_final: 0.8960 (t) REVERT: B 174 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7552 (mm-40) REVERT: B 179 GLN cc_start: 0.8590 (mt0) cc_final: 0.8114 (mt0) REVERT: B 181 GLU cc_start: 0.7129 (pm20) cc_final: 0.6249 (pm20) REVERT: B 190 LEU cc_start: 0.9187 (tp) cc_final: 0.8595 (tp) REVERT: B 193 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7467 (mm-30) REVERT: B 214 LYS cc_start: 0.8891 (mmtp) cc_final: 0.8539 (mmmm) REVERT: B 287 MET cc_start: 0.8735 (tpp) cc_final: 0.8346 (tpp) REVERT: B 322 LEU cc_start: 0.9331 (mt) cc_final: 0.9086 (mp) REVERT: C 114 LEU cc_start: 0.8738 (mt) cc_final: 0.8444 (mp) REVERT: C 119 LYS cc_start: 0.9062 (mtmm) cc_final: 0.8772 (mtmt) REVERT: C 127 GLU cc_start: 0.6998 (tm-30) cc_final: 0.6618 (tm-30) REVERT: C 134 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8072 (mm-30) REVERT: C 140 LYS cc_start: 0.8657 (mttp) cc_final: 0.8007 (mtmm) REVERT: C 142 LEU cc_start: 0.8713 (tp) cc_final: 0.8366 (tt) REVERT: C 181 GLU cc_start: 0.6856 (pm20) cc_final: 0.6499 (pm20) REVERT: C 190 LEU cc_start: 0.9159 (tp) cc_final: 0.8537 (tp) REVERT: C 241 GLU cc_start: 0.7580 (mp0) cc_final: 0.6876 (mp0) REVERT: C 270 MET cc_start: 0.7426 (ppp) cc_final: 0.7047 (ppp) REVERT: C 287 MET cc_start: 0.8901 (tpp) cc_final: 0.8615 (tpp) REVERT: C 291 SER cc_start: 0.9156 (t) cc_final: 0.8774 (p) REVERT: C 300 LYS cc_start: 0.9109 (mptt) cc_final: 0.8533 (mmtp) REVERT: C 406 ARG cc_start: 0.7983 (ttm170) cc_final: 0.7352 (mmp-170) REVERT: C 410 ILE cc_start: 0.8729 (mm) cc_final: 0.8453 (mm) REVERT: D 41 LEU cc_start: 0.9306 (tp) cc_final: 0.9089 (tp) REVERT: D 49 ASP cc_start: 0.8994 (t0) cc_final: 0.8679 (t0) REVERT: D 93 ASN cc_start: 0.8967 (t0) cc_final: 0.8697 (t0) REVERT: D 140 LYS cc_start: 0.8707 (mttp) cc_final: 0.8236 (mtmm) REVERT: D 147 ASN cc_start: 0.8879 (p0) cc_final: 0.8474 (p0) REVERT: D 149 ASN cc_start: 0.9007 (m-40) cc_final: 0.8679 (m-40) REVERT: D 178 MET cc_start: 0.8044 (ttm) cc_final: 0.7754 (ttm) REVERT: D 190 LEU cc_start: 0.9138 (tp) cc_final: 0.8748 (tp) REVERT: D 193 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7552 (mm-30) REVERT: D 210 GLN cc_start: 0.8066 (mp10) cc_final: 0.7764 (mp10) REVERT: D 214 LYS cc_start: 0.8857 (mmtp) cc_final: 0.8546 (mmmm) REVERT: D 241 GLU cc_start: 0.7394 (mp0) cc_final: 0.6652 (mp0) REVERT: D 270 MET cc_start: 0.7433 (ppp) cc_final: 0.6832 (ppp) REVERT: D 291 SER cc_start: 0.9166 (t) cc_final: 0.8755 (p) REVERT: D 406 ARG cc_start: 0.7776 (ttm170) cc_final: 0.7500 (mmp-170) REVERT: D 431 ILE cc_start: 0.8380 (mm) cc_final: 0.8004 (pt) REVERT: E 89 ARG cc_start: 0.8549 (mtt90) cc_final: 0.8041 (mtt-85) REVERT: E 144 ILE cc_start: 0.9269 (mt) cc_final: 0.8987 (mm) REVERT: E 181 GLU cc_start: 0.7139 (pm20) cc_final: 0.6294 (pm20) REVERT: E 190 LEU cc_start: 0.9043 (tp) cc_final: 0.8684 (tp) REVERT: E 193 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7547 (mm-30) REVERT: E 214 LYS cc_start: 0.8909 (mmmm) cc_final: 0.8449 (mmmm) REVERT: E 235 GLU cc_start: 0.7758 (tt0) cc_final: 0.7444 (tt0) REVERT: E 241 GLU cc_start: 0.7298 (mp0) cc_final: 0.6343 (mp0) REVERT: E 247 TYR cc_start: 0.8789 (m-80) cc_final: 0.8588 (m-80) REVERT: E 263 TRP cc_start: 0.7845 (m-10) cc_final: 0.7384 (m-10) REVERT: E 287 MET cc_start: 0.8929 (tpp) cc_final: 0.8375 (tpp) REVERT: E 314 CYS cc_start: 0.7957 (p) cc_final: 0.7580 (p) REVERT: E 422 PHE cc_start: 0.8574 (t80) cc_final: 0.8361 (t80) outliers start: 46 outliers final: 33 residues processed: 476 average time/residue: 0.1057 time to fit residues: 76.2020 Evaluate side-chains 483 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 447 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 114 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 233 CYS 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 157 THR 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 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 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 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: 0.9990 chunk 77 optimal weight: 2.9990 chunk 142 optimal weight: 0.0970 chunk 95 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 153 optimal weight: 0.0370 chunk 22 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 GLN C 243 GLN D 243 GLN E 290 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.101677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.084040 restraints weight = 32863.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.087215 restraints weight = 15083.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.089162 restraints weight = 8418.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.090318 restraints weight = 5348.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.091110 restraints weight = 3856.691| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14655 Z= 0.137 Angle : 0.749 8.564 19870 Z= 0.376 Chirality : 0.046 0.280 2230 Planarity : 0.004 0.048 2485 Dihedral : 4.610 44.684 2015 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.80 % Allowed : 22.10 % Favored : 75.10 % 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: 0.37 (0.20), residues: 1730 helix: 2.11 (0.20), residues: 620 sheet: 0.73 (0.26), residues: 365 loop : -1.73 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 276 TYR 0.018 0.001 TYR E 429 PHE 0.016 0.001 PHE C 418 TRP 0.039 0.001 TRP B 263 HIS 0.004 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00309 (14645) covalent geometry : angle 0.74604 (19845) SS BOND : bond 0.00937 ( 5) SS BOND : angle 2.89843 ( 10) hydrogen bonds : bond 0.03854 ( 675) hydrogen bonds : angle 4.05201 ( 2385) link_NAG-ASN : bond 0.00085 ( 5) link_NAG-ASN : angle 0.82271 ( 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 494 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 450 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8928 (t0) cc_final: 0.8652 (t0) REVERT: A 81 ASP cc_start: 0.7956 (p0) cc_final: 0.7624 (p0) REVERT: A 104 ASP cc_start: 0.8960 (p0) cc_final: 0.8707 (p0) REVERT: A 114 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8292 (mm) REVERT: A 119 LYS cc_start: 0.9059 (mtmm) cc_final: 0.8415 (mtmt) REVERT: A 140 LYS cc_start: 0.8883 (mttp) cc_final: 0.8293 (mtmm) REVERT: A 190 LEU cc_start: 0.9040 (tp) cc_final: 0.8308 (tt) REVERT: A 193 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7655 (mm-30) REVERT: A 214 LYS cc_start: 0.8858 (mmtp) cc_final: 0.8439 (mmmm) REVERT: A 237 ARG cc_start: 0.8236 (mtt-85) cc_final: 0.7933 (mtt-85) REVERT: A 241 GLU cc_start: 0.7376 (mp0) cc_final: 0.6488 (mp0) REVERT: A 270 MET cc_start: 0.8112 (ppp) cc_final: 0.7832 (ppp) REVERT: A 287 MET cc_start: 0.8929 (tpp) cc_final: 0.8422 (tpp) REVERT: A 317 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.8094 (m-80) REVERT: A 403 PHE cc_start: 0.7273 (m-80) cc_final: 0.6744 (m-80) REVERT: A 406 ARG cc_start: 0.7828 (ttm170) cc_final: 0.7398 (mmt180) REVERT: B 81 ASP cc_start: 0.7956 (p0) cc_final: 0.7575 (p0) REVERT: B 101 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7774 (tm-30) REVERT: B 102 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.8278 (m-10) REVERT: B 113 MET cc_start: 0.8352 (pmm) cc_final: 0.7620 (pmm) REVERT: B 140 LYS cc_start: 0.8757 (mttp) cc_final: 0.8238 (mtmm) REVERT: B 144 ILE cc_start: 0.9190 (mt) cc_final: 0.8941 (mm) REVERT: B 153 SER cc_start: 0.9212 (t) cc_final: 0.8968 (t) REVERT: B 174 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7563 (mm-40) REVERT: B 179 GLN cc_start: 0.8552 (mt0) cc_final: 0.8081 (mt0) REVERT: B 181 GLU cc_start: 0.7154 (pm20) cc_final: 0.6259 (pm20) REVERT: B 190 LEU cc_start: 0.9166 (tp) cc_final: 0.8552 (tp) REVERT: B 193 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7460 (mm-30) REVERT: B 214 LYS cc_start: 0.8912 (mmtp) cc_final: 0.8534 (mmmm) REVERT: B 237 ARG cc_start: 0.8424 (mtt180) cc_final: 0.7741 (mtt90) REVERT: B 287 MET cc_start: 0.8786 (tpp) cc_final: 0.8279 (tpp) REVERT: B 291 SER cc_start: 0.9267 (t) cc_final: 0.9031 (p) REVERT: B 322 LEU cc_start: 0.9330 (mt) cc_final: 0.9085 (mp) REVERT: C 119 LYS cc_start: 0.9067 (mtmm) cc_final: 0.8771 (mtmt) REVERT: C 127 GLU cc_start: 0.7003 (tm-30) cc_final: 0.6640 (tm-30) REVERT: C 134 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8080 (mm-30) REVERT: C 140 LYS cc_start: 0.8657 (mttp) cc_final: 0.8091 (mtmm) REVERT: C 142 LEU cc_start: 0.8678 (tp) cc_final: 0.8340 (tt) REVERT: C 181 GLU cc_start: 0.6887 (pm20) cc_final: 0.6505 (pm20) REVERT: C 190 LEU cc_start: 0.9156 (tp) cc_final: 0.8541 (tp) REVERT: C 197 LYS cc_start: 0.8549 (mmtt) cc_final: 0.8139 (ptpp) REVERT: C 241 GLU cc_start: 0.7555 (mp0) cc_final: 0.6849 (mp0) REVERT: C 270 MET cc_start: 0.7503 (ppp) cc_final: 0.7155 (ppp) REVERT: C 287 MET cc_start: 0.8946 (tpp) cc_final: 0.8739 (tpp) REVERT: C 291 SER cc_start: 0.9121 (t) cc_final: 0.8760 (p) REVERT: C 300 LYS cc_start: 0.9110 (mptt) cc_final: 0.8527 (mmtp) REVERT: C 309 ILE cc_start: 0.8958 (mt) cc_final: 0.8740 (mt) REVERT: C 406 ARG cc_start: 0.7966 (ttm170) cc_final: 0.7328 (mmp-170) REVERT: C 410 ILE cc_start: 0.8668 (mm) cc_final: 0.8392 (mm) REVERT: D 41 LEU cc_start: 0.9302 (tp) cc_final: 0.9073 (tp) REVERT: D 49 ASP cc_start: 0.8979 (t0) cc_final: 0.8532 (t0) REVERT: D 134 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8257 (mm-30) REVERT: D 178 MET cc_start: 0.8041 (ttm) cc_final: 0.7733 (ttm) REVERT: D 190 LEU cc_start: 0.9158 (tp) cc_final: 0.8766 (tp) REVERT: D 193 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7532 (mm-30) REVERT: D 210 GLN cc_start: 0.8067 (mp10) cc_final: 0.7834 (mp10) REVERT: D 214 LYS cc_start: 0.8857 (mmtp) cc_final: 0.8542 (mmmm) REVERT: D 241 GLU cc_start: 0.7417 (mp0) cc_final: 0.6637 (mp0) REVERT: D 270 MET cc_start: 0.7436 (ppp) cc_final: 0.6907 (ppp) REVERT: D 406 ARG cc_start: 0.7780 (ttm170) cc_final: 0.7502 (mmp-170) REVERT: D 431 ILE cc_start: 0.8346 (mm) cc_final: 0.7977 (pt) REVERT: E 89 ARG cc_start: 0.8564 (mtt90) cc_final: 0.8062 (mtt-85) REVERT: E 144 ILE cc_start: 0.9258 (mt) cc_final: 0.8975 (mm) REVERT: E 181 GLU cc_start: 0.7048 (pm20) cc_final: 0.6174 (pm20) REVERT: E 190 LEU cc_start: 0.9030 (tp) cc_final: 0.8668 (tp) REVERT: E 193 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7543 (mm-30) REVERT: E 214 LYS cc_start: 0.8930 (mmmm) cc_final: 0.8489 (mmmm) REVERT: E 235 GLU cc_start: 0.7882 (tt0) cc_final: 0.7486 (tt0) REVERT: E 241 GLU cc_start: 0.7324 (mp0) cc_final: 0.6377 (mp0) REVERT: E 263 TRP cc_start: 0.7901 (m-10) cc_final: 0.7441 (m-10) REVERT: E 287 MET cc_start: 0.8923 (tpp) cc_final: 0.8279 (tpp) REVERT: E 314 CYS cc_start: 0.8001 (p) cc_final: 0.7587 (p) outliers start: 44 outliers final: 37 residues processed: 470 average time/residue: 0.1036 time to fit residues: 73.7434 Evaluate side-chains 480 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 440 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 114 LEU Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 235 GLU 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 79 THR Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 157 THR 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 135 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 157 optimal weight: 0.0050 chunk 87 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 GLN C 290 GLN ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN D 243 GLN D 290 GLN E 290 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.101248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.083822 restraints weight = 32816.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.086904 restraints weight = 15302.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.088792 restraints weight = 8608.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.089970 restraints weight = 5521.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.090695 restraints weight = 3965.776| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14655 Z= 0.147 Angle : 0.784 12.978 19870 Z= 0.393 Chirality : 0.047 0.290 2230 Planarity : 0.004 0.048 2485 Dihedral : 4.678 44.123 2015 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.87 % Allowed : 22.42 % Favored : 74.71 % 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: 0.24 (0.20), residues: 1730 helix: 2.01 (0.20), residues: 615 sheet: 0.66 (0.25), residues: 375 loop : -1.82 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 276 TYR 0.019 0.001 TYR E 429 PHE 0.019 0.001 PHE E 422 TRP 0.049 0.002 TRP B 263 HIS 0.010 0.001 HIS E 239 Details of bonding type rmsd covalent geometry : bond 0.00333 (14645) covalent geometry : angle 0.77749 (19845) SS BOND : bond 0.00526 ( 5) SS BOND : angle 4.44936 ( 10) hydrogen bonds : bond 0.03909 ( 675) hydrogen bonds : angle 4.06004 ( 2385) link_NAG-ASN : bond 0.00041 ( 5) link_NAG-ASN : angle 0.94734 ( 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 478 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 433 time to evaluate : 0.599 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 81 ASP cc_start: 0.7987 (p0) cc_final: 0.7668 (p0) REVERT: A 104 ASP cc_start: 0.8907 (p0) cc_final: 0.8683 (p0) REVERT: A 114 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8298 (mm) REVERT: A 119 LYS cc_start: 0.9059 (mtmm) cc_final: 0.8417 (mtmt) REVERT: A 140 LYS cc_start: 0.8882 (mttp) cc_final: 0.8300 (mtmm) REVERT: A 190 LEU cc_start: 0.9097 (tp) cc_final: 0.8382 (tt) REVERT: A 193 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7664 (mm-30) REVERT: A 214 LYS cc_start: 0.8855 (mmtp) cc_final: 0.8395 (mmmm) REVERT: A 237 ARG cc_start: 0.8255 (mtt-85) cc_final: 0.7942 (mtt-85) REVERT: A 241 GLU cc_start: 0.7392 (mp0) cc_final: 0.6515 (mp0) REVERT: A 270 MET cc_start: 0.8110 (ppp) cc_final: 0.7789 (ppp) REVERT: A 276 ARG cc_start: 0.7203 (mpt180) cc_final: 0.6583 (mmt-90) REVERT: A 287 MET cc_start: 0.8897 (tpp) cc_final: 0.8438 (tpp) REVERT: A 317 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.8086 (m-80) REVERT: A 403 PHE cc_start: 0.7332 (m-80) cc_final: 0.6779 (m-80) REVERT: A 406 ARG cc_start: 0.7831 (ttm170) cc_final: 0.7403 (mmt180) REVERT: B 81 ASP cc_start: 0.7973 (p0) cc_final: 0.7594 (p0) REVERT: B 101 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7881 (tm-30) REVERT: B 102 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.8270 (m-10) REVERT: B 113 MET cc_start: 0.8321 (pmm) cc_final: 0.7650 (pmm) REVERT: B 144 ILE cc_start: 0.9211 (mt) cc_final: 0.8994 (mm) REVERT: B 153 SER cc_start: 0.9222 (t) cc_final: 0.8991 (t) REVERT: B 174 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7592 (mm-40) REVERT: B 179 GLN cc_start: 0.8519 (mt0) cc_final: 0.8162 (mt0) REVERT: B 190 LEU cc_start: 0.9198 (tp) cc_final: 0.8622 (tp) REVERT: B 193 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7443 (mm-30) REVERT: B 214 LYS cc_start: 0.8928 (mmtp) cc_final: 0.8547 (mmmm) REVERT: B 237 ARG cc_start: 0.8433 (mtt180) cc_final: 0.7762 (mtt180) REVERT: B 287 MET cc_start: 0.8788 (tpp) cc_final: 0.8226 (tpp) REVERT: B 291 SER cc_start: 0.9251 (t) cc_final: 0.9018 (p) REVERT: B 322 LEU cc_start: 0.9333 (mt) cc_final: 0.9095 (mp) REVERT: C 114 LEU cc_start: 0.8757 (mm) cc_final: 0.8500 (mp) REVERT: C 119 LYS cc_start: 0.9034 (mtmm) cc_final: 0.8727 (mtmt) REVERT: C 127 GLU cc_start: 0.7086 (tm-30) cc_final: 0.6675 (tm-30) REVERT: C 134 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8014 (mm-30) REVERT: C 181 GLU cc_start: 0.6950 (pm20) cc_final: 0.6528 (pm20) REVERT: C 190 LEU cc_start: 0.9162 (tp) cc_final: 0.8573 (tp) REVERT: C 197 LYS cc_start: 0.8612 (mmtt) cc_final: 0.8233 (ptpp) REVERT: C 241 GLU cc_start: 0.7575 (mp0) cc_final: 0.6876 (mp0) REVERT: C 270 MET cc_start: 0.7519 (ppp) cc_final: 0.7191 (ppp) REVERT: C 291 SER cc_start: 0.9132 (t) cc_final: 0.8728 (p) REVERT: C 300 LYS cc_start: 0.9111 (mptt) cc_final: 0.8544 (mmtp) REVERT: C 406 ARG cc_start: 0.7972 (ttm170) cc_final: 0.7343 (mmp-170) REVERT: C 410 ILE cc_start: 0.8703 (mm) cc_final: 0.8426 (mm) REVERT: D 41 LEU cc_start: 0.9291 (tp) cc_final: 0.9071 (tp) REVERT: D 49 ASP cc_start: 0.8976 (t0) cc_final: 0.8656 (t0) REVERT: D 126 ASN cc_start: 0.8361 (p0) cc_final: 0.7497 (p0) REVERT: D 134 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8254 (mm-30) REVERT: D 140 LYS cc_start: 0.8727 (mttp) cc_final: 0.8278 (mtmm) REVERT: D 178 MET cc_start: 0.8040 (ttm) cc_final: 0.7787 (ttm) REVERT: D 190 LEU cc_start: 0.9158 (tp) cc_final: 0.8781 (tp) REVERT: D 193 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7513 (mm-30) REVERT: D 210 GLN cc_start: 0.8063 (mp10) cc_final: 0.7838 (mp10) REVERT: D 214 LYS cc_start: 0.8878 (mmtp) cc_final: 0.8567 (mmmm) REVERT: D 241 GLU cc_start: 0.7410 (mp0) cc_final: 0.6661 (mp0) REVERT: D 270 MET cc_start: 0.7429 (ppp) cc_final: 0.6968 (ppp) REVERT: D 406 ARG cc_start: 0.7817 (ttm170) cc_final: 0.7530 (mmp-170) REVERT: D 431 ILE cc_start: 0.8356 (mm) cc_final: 0.7984 (pt) REVERT: E 89 ARG cc_start: 0.8566 (mtt90) cc_final: 0.8078 (mtt-85) REVERT: E 144 ILE cc_start: 0.9283 (mt) cc_final: 0.9001 (mm) REVERT: E 181 GLU cc_start: 0.7147 (pm20) cc_final: 0.6424 (pm20) REVERT: E 190 LEU cc_start: 0.9039 (tp) cc_final: 0.8693 (tp) REVERT: E 193 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7525 (mm-30) REVERT: E 214 LYS cc_start: 0.8946 (mmmm) cc_final: 0.8505 (mmmm) REVERT: E 235 GLU cc_start: 0.7847 (tt0) cc_final: 0.7466 (tt0) REVERT: E 241 GLU cc_start: 0.7327 (mp0) cc_final: 0.6400 (mp0) REVERT: E 263 TRP cc_start: 0.7931 (m-10) cc_final: 0.7475 (m-10) REVERT: E 270 MET cc_start: 0.7995 (ppp) cc_final: 0.7252 (ppp) REVERT: E 287 MET cc_start: 0.8820 (tpp) cc_final: 0.8567 (tpt) outliers start: 45 outliers final: 39 residues processed: 452 average time/residue: 0.1038 time to fit residues: 71.1761 Evaluate side-chains 477 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 435 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 114 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 235 GLU 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 79 THR Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 157 THR 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 290 GLN Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 79 THR 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 290 GLN 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 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 178 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 31 optimal weight: 0.9980 chunk 85 optimal weight: 0.0370 chunk 33 optimal weight: 0.5980 chunk 99 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 GLN E 239 HIS E 290 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.101085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.083590 restraints weight = 32792.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.086675 restraints weight = 15338.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.088572 restraints weight = 8633.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.089757 restraints weight = 5535.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.090492 restraints weight = 3986.670| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4568 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= 0.152 Angle : 0.787 11.337 19870 Z= 0.397 Chirality : 0.047 0.289 2230 Planarity : 0.004 0.047 2485 Dihedral : 4.719 43.359 2015 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.68 % Allowed : 22.29 % Favored : 75.03 % 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: 0.18 (0.20), residues: 1730 helix: 1.95 (0.20), residues: 615 sheet: 0.65 (0.25), residues: 375 loop : -1.85 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 276 TYR 0.021 0.001 TYR E 429 PHE 0.018 0.001 PHE E 422 TRP 0.049 0.002 TRP B 263 HIS 0.006 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00345 (14645) covalent geometry : angle 0.78328 (19845) SS BOND : bond 0.00461 ( 5) SS BOND : angle 3.59797 ( 10) hydrogen bonds : bond 0.03962 ( 675) hydrogen bonds : angle 4.08895 ( 2385) link_NAG-ASN : bond 0.00045 ( 5) link_NAG-ASN : angle 0.94256 ( 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 477 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 435 time to evaluate : 0.388 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: 0.8923 (t0) cc_final: 0.8656 (t0) REVERT: A 77 GLU cc_start: 0.7991 (pm20) cc_final: 0.7698 (pm20) REVERT: A 81 ASP cc_start: 0.8007 (p0) cc_final: 0.7682 (p0) REVERT: A 102 TYR cc_start: 0.8981 (OUTLIER) cc_final: 0.8636 (m-80) REVERT: A 104 ASP cc_start: 0.8923 (p0) cc_final: 0.8689 (p0) REVERT: A 140 LYS cc_start: 0.8876 (mttp) cc_final: 0.8298 (mtmm) REVERT: A 147 ASN cc_start: 0.8812 (p0) cc_final: 0.8374 (p0) REVERT: A 187 MET cc_start: 0.8666 (mmm) cc_final: 0.8151 (tpp) REVERT: A 190 LEU cc_start: 0.9050 (tp) cc_final: 0.8346 (tt) REVERT: A 193 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7660 (mm-30) REVERT: A 214 LYS cc_start: 0.8884 (mmtp) cc_final: 0.8407 (mmmm) REVERT: A 237 ARG cc_start: 0.8257 (mtt-85) cc_final: 0.7936 (mtt-85) REVERT: A 241 GLU cc_start: 0.7393 (mp0) cc_final: 0.6495 (mp0) REVERT: A 270 MET cc_start: 0.7935 (ppp) cc_final: 0.7609 (ppp) REVERT: A 287 MET cc_start: 0.8906 (tpp) cc_final: 0.8432 (tpp) REVERT: A 403 PHE cc_start: 0.7328 (m-80) cc_final: 0.6779 (m-80) REVERT: A 406 ARG cc_start: 0.7828 (ttm170) cc_final: 0.7398 (mmt180) REVERT: B 81 ASP cc_start: 0.7989 (p0) cc_final: 0.7608 (p0) REVERT: B 101 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7874 (tm-30) REVERT: B 102 TYR cc_start: 0.8798 (OUTLIER) cc_final: 0.8281 (m-10) REVERT: B 113 MET cc_start: 0.8288 (pmm) cc_final: 0.7668 (pmm) REVERT: B 140 LYS cc_start: 0.8770 (mttp) cc_final: 0.8239 (mtmm) REVERT: B 144 ILE cc_start: 0.9207 (mt) cc_final: 0.8989 (mm) REVERT: B 153 SER cc_start: 0.9226 (t) cc_final: 0.8996 (t) REVERT: B 174 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7585 (mm-40) REVERT: B 179 GLN cc_start: 0.8504 (mt0) cc_final: 0.8163 (mt0) REVERT: B 190 LEU cc_start: 0.9203 (tp) cc_final: 0.8618 (tp) REVERT: B 193 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7446 (mm-30) REVERT: B 214 LYS cc_start: 0.8938 (mmtp) cc_final: 0.8541 (mmmm) REVERT: B 237 ARG cc_start: 0.8441 (mtt180) cc_final: 0.8209 (mtt180) REVERT: B 287 MET cc_start: 0.8771 (tpp) cc_final: 0.8197 (tpp) REVERT: B 322 LEU cc_start: 0.9350 (mt) cc_final: 0.9115 (mp) REVERT: C 114 LEU cc_start: 0.8784 (mm) cc_final: 0.8506 (mp) REVERT: C 119 LYS cc_start: 0.9034 (mtmm) cc_final: 0.8723 (mtmt) REVERT: C 127 GLU cc_start: 0.7064 (tm-30) cc_final: 0.6670 (tm-30) REVERT: C 134 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8036 (mm-30) REVERT: C 181 GLU cc_start: 0.6961 (pm20) cc_final: 0.6493 (pm20) REVERT: C 190 LEU cc_start: 0.9169 (tp) cc_final: 0.8577 (tp) REVERT: C 197 LYS cc_start: 0.8641 (mmtt) cc_final: 0.8262 (ptpp) REVERT: C 241 GLU cc_start: 0.7574 (mp0) cc_final: 0.6848 (mp0) REVERT: C 270 MET cc_start: 0.7610 (ppp) cc_final: 0.7298 (ppp) REVERT: C 291 SER cc_start: 0.9134 (t) cc_final: 0.8782 (p) REVERT: C 300 LYS cc_start: 0.9119 (mptt) cc_final: 0.8538 (mmtp) REVERT: C 406 ARG cc_start: 0.7950 (ttm170) cc_final: 0.7336 (mmp-170) REVERT: C 410 ILE cc_start: 0.8739 (mm) cc_final: 0.8460 (mm) REVERT: D 41 LEU cc_start: 0.9297 (tp) cc_final: 0.9070 (tp) REVERT: D 49 ASP cc_start: 0.8979 (t0) cc_final: 0.8649 (t0) REVERT: D 114 LEU cc_start: 0.8750 (mt) cc_final: 0.8467 (mp) REVERT: D 126 ASN cc_start: 0.8360 (p0) cc_final: 0.7503 (p0) REVERT: D 134 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8295 (mm-30) REVERT: D 140 LYS cc_start: 0.8735 (mttp) cc_final: 0.8177 (mtmm) REVERT: D 190 LEU cc_start: 0.9148 (tp) cc_final: 0.8772 (tp) REVERT: D 193 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7513 (mm-30) REVERT: D 197 LYS cc_start: 0.8632 (mmtm) cc_final: 0.8397 (mmtt) REVERT: D 210 GLN cc_start: 0.8060 (mp10) cc_final: 0.7836 (mp10) REVERT: D 214 LYS cc_start: 0.8881 (mmtp) cc_final: 0.8556 (mmmm) REVERT: D 241 GLU cc_start: 0.7434 (mp0) cc_final: 0.6625 (mp0) REVERT: D 314 CYS cc_start: 0.7855 (p) cc_final: 0.7508 (p) REVERT: D 406 ARG cc_start: 0.7788 (ttm170) cc_final: 0.7479 (mmp-170) REVERT: E 89 ARG cc_start: 0.8570 (mtt90) cc_final: 0.8080 (mtt-85) REVERT: E 144 ILE cc_start: 0.9273 (mt) cc_final: 0.8995 (mm) REVERT: E 181 GLU cc_start: 0.7157 (pm20) cc_final: 0.6427 (pm20) REVERT: E 190 LEU cc_start: 0.9040 (tp) cc_final: 0.8697 (tp) REVERT: E 193 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7535 (mm-30) REVERT: E 214 LYS cc_start: 0.8957 (mmmm) cc_final: 0.8494 (mmmm) REVERT: E 235 GLU cc_start: 0.7870 (tt0) cc_final: 0.7525 (tt0) REVERT: E 241 GLU cc_start: 0.7344 (mp0) cc_final: 0.6411 (mp0) REVERT: E 263 TRP cc_start: 0.7933 (m-10) cc_final: 0.7489 (m-10) REVERT: E 270 MET cc_start: 0.8118 (ppp) cc_final: 0.7420 (ppp) outliers start: 42 outliers final: 36 residues processed: 453 average time/residue: 0.1009 time to fit residues: 69.4942 Evaluate side-chains 465 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 427 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 235 GLU Chi-restraints excluded: chain A residue 268 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 79 THR Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 157 THR 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 79 THR Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 248 LEU 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 46 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 161 optimal weight: 0.4980 chunk 8 optimal weight: 0.0020 chunk 81 optimal weight: 0.3980 chunk 118 optimal weight: 0.2980 chunk 121 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 overall best weight: 0.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 GLN C 290 GLN D 243 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.102514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.084838 restraints weight = 32652.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.087944 restraints weight = 15345.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.089861 restraints weight = 8691.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.091058 restraints weight = 5581.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.091806 restraints weight = 4014.819| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14655 Z= 0.141 Angle : 0.793 12.968 19870 Z= 0.396 Chirality : 0.048 0.339 2230 Planarity : 0.004 0.048 2485 Dihedral : 4.634 41.733 2015 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.42 % Allowed : 22.93 % Favored : 74.65 % 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: 1.82 (0.20), residues: 615 sheet: 0.70 (0.26), residues: 365 loop : -1.79 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 437 TYR 0.017 0.001 TYR E 429 PHE 0.020 0.001 PHE A 418 TRP 0.054 0.001 TRP B 263 HIS 0.006 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00314 (14645) covalent geometry : angle 0.79076 (19845) SS BOND : bond 0.00440 ( 5) SS BOND : angle 2.87935 ( 10) hydrogen bonds : bond 0.03883 ( 675) hydrogen bonds : angle 4.13014 ( 2385) link_NAG-ASN : bond 0.00151 ( 5) link_NAG-ASN : angle 0.69466 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2446.67 seconds wall clock time: 42 minutes 57.76 seconds (2577.76 seconds total)