Starting phenix.real_space_refine on Sat Mar 16 09:41:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6r_23705/03_2024/7m6r_23705.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6r_23705/03_2024/7m6r_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6r_23705/03_2024/7m6r_23705.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6r_23705/03_2024/7m6r_23705.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6r_23705/03_2024/7m6r_23705.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6r_23705/03_2024/7m6r_23705.pdb" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14300 Number of models: 1 Model: "" Number of chains: 10 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: 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: "C" 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: "D" 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: "E" 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 Time building chain proxies: 8.29, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 5.42 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 1.62 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: 5.19 Time building geometry restraints manager: 5.95 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: 97.44 - 104.82: 280 104.82 - 112.20: 6845 112.20 - 119.58: 5341 119.58 - 126.96: 7201 126.96 - 134.34: 178 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 2.440 nonbonded pdb=" OG1 THR B 186 " pdb=" OD1 ASN B 188 " model vdw 2.333 2.440 nonbonded pdb=" OG1 THR E 186 " pdb=" OD1 ASN E 188 " model vdw 2.333 2.440 nonbonded pdb=" OG1 THR C 186 " pdb=" OD1 ASN C 188 " model vdw 2.333 2.440 nonbonded pdb=" OG1 THR A 186 " pdb=" OD1 ASN A 188 " model vdw 2.333 2.440 ... (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 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: 1.690 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: 6.160 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 40.070 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.070 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.290 ------------------------------------------------------------------------------- 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 14645 Z= 0.494 Angle : 1.204 10.687 19845 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.040 0.004 TRP B 430 HIS 0.008 0.002 HIS B 225 PHE 0.023 0.004 PHE C 192 TYR 0.021 0.004 TYR D 325 ARG 0.024 0.002 ARG D 276 *********************** 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 fitting. rotamer outliers: 10 poor density : 627 time to evaluate : 1.767 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: 0.7297 (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: 0.6560 (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: 0.7734 (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: 0.7994 (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: 0.8219 (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: 0.7991 (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: 0.8814 (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: 0.7578 (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: 0.8519 (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: 0.8686 (t80) REVERT: B 328 VAL cc_start: 0.9020 (p) cc_final: 0.8734 (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: 0.7291 (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: 0.8067 (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: 0.7102 (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: 0.8458 (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: 0.7163 (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: 0.8706 (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: 0.8594 (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: 0.2653 time to fit residues: 242.8644 Evaluate side-chains 517 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 510 time to evaluate : 1.690 ------------------------------------------------------------------------------- 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 147 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 158 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 14645 Z= 0.254 Angle : 0.742 9.209 19845 Z= 0.393 Chirality : 0.048 0.194 2230 Planarity : 0.005 0.060 2485 Dihedral : 5.544 38.158 2029 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.93 % Allowed : 13.38 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.20), residues: 1730 helix: 2.37 (0.20), residues: 630 sheet: 0.75 (0.27), residues: 365 loop : -1.79 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 310 HIS 0.004 0.001 HIS A 133 PHE 0.022 0.002 PHE E 56 TYR 0.024 0.002 TYR D 99 ARG 0.009 0.001 ARG E 409 *********************** 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 546 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 500 time to evaluate : 1.620 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: 0.8128 (pm20) cc_final: 0.7806 (pm20) REVERT: A 81 ASP cc_start: 0.7610 (p0) cc_final: 0.7382 (p0) REVERT: A 104 ASP cc_start: 0.8915 (p0) cc_final: 0.8241 (p0) REVERT: A 114 LEU cc_start: 0.8668 (mt) cc_final: 0.8351 (tp) REVERT: A 119 LYS cc_start: 0.8990 (mtmm) cc_final: 0.8735 (mtmt) REVERT: A 138 ASP cc_start: 0.8461 (p0) cc_final: 0.7960 (p0) REVERT: A 140 LYS cc_start: 0.8909 (mttp) cc_final: 0.8276 (mtmm) REVERT: A 142 LEU cc_start: 0.8710 (tp) cc_final: 0.8497 (tt) REVERT: A 146 LYS cc_start: 0.8868 (ttmm) cc_final: 0.8588 (tppp) REVERT: A 190 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8054 (tp) REVERT: A 193 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7878 (mm-30) REVERT: A 195 ASP cc_start: 0.8359 (t0) cc_final: 0.8128 (t0) REVERT: A 197 LYS cc_start: 0.8646 (mmtp) cc_final: 0.8308 (mmtt) REVERT: A 214 LYS cc_start: 0.8674 (mmtp) cc_final: 0.8408 (mmmm) REVERT: A 235 GLU cc_start: 0.7789 (tt0) cc_final: 0.7533 (tt0) REVERT: A 237 ARG cc_start: 0.7845 (mtt-85) cc_final: 0.7449 (mtt-85) REVERT: A 241 GLU cc_start: 0.7193 (mp0) cc_final: 0.6527 (mp0) REVERT: A 270 MET cc_start: 0.7817 (ppp) cc_final: 0.7535 (ppp) REVERT: A 322 LEU cc_start: 0.9394 (mt) cc_final: 0.9166 (mp) REVERT: A 329 ASN cc_start: 0.8746 (t0) cc_final: 0.8517 (t0) REVERT: A 406 ARG cc_start: 0.7894 (ttm170) cc_final: 0.7448 (mmt180) REVERT: A 428 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.8602 (t80) REVERT: A 431 ILE cc_start: 0.8442 (mm) cc_final: 0.8155 (pt) REVERT: B 81 ASP cc_start: 0.7875 (p0) cc_final: 0.7550 (p0) REVERT: B 140 LYS cc_start: 0.8885 (mttp) cc_final: 0.8296 (mtmm) REVERT: B 177 ILE cc_start: 0.8935 (mm) cc_final: 0.8528 (mt) REVERT: B 179 GLN cc_start: 0.8635 (mt0) cc_final: 0.8290 (mt0) REVERT: B 181 GLU cc_start: 0.6692 (pm20) cc_final: 0.5832 (pm20) REVERT: B 190 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8285 (tp) REVERT: B 193 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7714 (mm-30) REVERT: B 214 LYS cc_start: 0.8563 (mmtp) cc_final: 0.7994 (mmmm) REVERT: B 241 GLU cc_start: 0.6976 (mp0) cc_final: 0.6086 (mp0) REVERT: B 287 MET cc_start: 0.8829 (tpp) cc_final: 0.8553 (tpp) REVERT: B 322 LEU cc_start: 0.9387 (mt) cc_final: 0.9182 (mp) REVERT: B 324 GLU cc_start: 0.8364 (pp20) cc_final: 0.8132 (mm-30) REVERT: B 325 TYR cc_start: 0.9095 (t80) cc_final: 0.8826 (t80) REVERT: C 81 ASP cc_start: 0.7365 (p0) cc_final: 0.7110 (p0) REVERT: C 102 TYR cc_start: 0.8827 (m-10) cc_final: 0.8620 (m-10) REVERT: C 104 ASP cc_start: 0.8870 (p0) cc_final: 0.8355 (p0) REVERT: C 114 LEU cc_start: 0.8499 (mt) cc_final: 0.7889 (tp) REVERT: C 119 LYS cc_start: 0.8954 (mtmm) cc_final: 0.8494 (mttm) REVERT: C 127 GLU cc_start: 0.6595 (tm-30) cc_final: 0.6390 (tm-30) REVERT: C 140 LYS cc_start: 0.8820 (mttp) cc_final: 0.8228 (mtmm) REVERT: C 142 LEU cc_start: 0.8718 (tp) cc_final: 0.8383 (tt) REVERT: C 190 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8247 (tp) REVERT: C 195 ASP cc_start: 0.8432 (t0) cc_final: 0.8200 (t0) REVERT: C 197 LYS cc_start: 0.8805 (mmtm) cc_final: 0.8406 (ptpp) REVERT: C 235 GLU cc_start: 0.7669 (tt0) cc_final: 0.7030 (tt0) REVERT: C 237 ARG cc_start: 0.8056 (mtt-85) cc_final: 0.7498 (mtt-85) REVERT: C 241 GLU cc_start: 0.7281 (mp0) cc_final: 0.6757 (mp0) REVERT: C 287 MET cc_start: 0.9042 (tpp) cc_final: 0.8689 (tpp) REVERT: C 291 SER cc_start: 0.9177 (t) cc_final: 0.8959 (p) REVERT: C 406 ARG cc_start: 0.8028 (ttm170) cc_final: 0.7488 (mmp-170) REVERT: C 410 ILE cc_start: 0.8694 (mm) cc_final: 0.8431 (mm) REVERT: C 426 ASN cc_start: 0.8181 (p0) cc_final: 0.7920 (p0) REVERT: C 431 ILE cc_start: 0.8494 (mm) cc_final: 0.8165 (pt) REVERT: D 41 LEU cc_start: 0.9264 (tp) cc_final: 0.8926 (tp) REVERT: D 42 MET cc_start: 0.8915 (pmm) cc_final: 0.8612 (pmm) REVERT: D 81 ASP cc_start: 0.7977 (p0) cc_final: 0.7670 (p0) REVERT: D 138 ASP cc_start: 0.8172 (p0) cc_final: 0.7125 (p0) REVERT: D 140 LYS cc_start: 0.8841 (mttp) cc_final: 0.8026 (mtmm) REVERT: D 190 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8511 (tp) REVERT: D 193 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7678 (mm-30) REVERT: D 210 GLN cc_start: 0.8010 (mp10) cc_final: 0.7736 (mp10) REVERT: D 214 LYS cc_start: 0.8678 (mmtp) cc_final: 0.8393 (mmmm) REVERT: D 235 GLU cc_start: 0.7893 (tt0) cc_final: 0.7453 (tt0) REVERT: D 237 ARG cc_start: 0.8120 (mtt-85) cc_final: 0.7646 (mtt-85) REVERT: D 241 GLU cc_start: 0.7202 (mp0) cc_final: 0.6565 (mp0) REVERT: D 260 ILE cc_start: 0.8940 (mt) cc_final: 0.8656 (tp) REVERT: D 403 PHE cc_start: 0.7337 (m-80) cc_final: 0.6762 (m-80) REVERT: D 406 ARG cc_start: 0.7835 (ttm170) cc_final: 0.7497 (mmp-170) REVERT: E 81 ASP cc_start: 0.8135 (p0) cc_final: 0.7829 (p0) REVERT: E 101 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7560 (mm-30) REVERT: E 102 TYR cc_start: 0.8847 (m-80) cc_final: 0.8268 (m-80) REVERT: E 138 ASP cc_start: 0.8355 (p0) cc_final: 0.7543 (p0) REVERT: E 140 LYS cc_start: 0.8944 (mttp) cc_final: 0.8294 (mtmm) REVERT: E 190 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8545 (tp) REVERT: E 193 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7617 (mm-30) REVERT: E 214 LYS cc_start: 0.8729 (mmtp) cc_final: 0.8475 (mmmm) REVERT: E 235 GLU cc_start: 0.7798 (tt0) cc_final: 0.7211 (tt0) REVERT: E 237 ARG cc_start: 0.7941 (mtt-85) cc_final: 0.7506 (mtt-85) REVERT: E 241 GLU cc_start: 0.7084 (mp0) cc_final: 0.6322 (mp0) REVERT: E 287 MET cc_start: 0.9028 (tpp) cc_final: 0.8730 (tmm) REVERT: E 300 LYS cc_start: 0.8906 (mttp) cc_final: 0.8547 (mttp) REVERT: E 315 LEU cc_start: 0.9359 (mt) cc_final: 0.9078 (tp) REVERT: E 322 LEU cc_start: 0.9454 (mt) cc_final: 0.9232 (mp) REVERT: E 422 PHE cc_start: 0.8710 (t80) cc_final: 0.8374 (t80) outliers start: 46 outliers final: 24 residues processed: 516 average time/residue: 0.2635 time to fit residues: 196.7499 Evaluate side-chains 508 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 478 time to evaluate : 1.633 ------------------------------------------------------------------------------- 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 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 138 ASP 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 C residue 39 ASP Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 138 ASP 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 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 132 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14645 Z= 0.228 Angle : 0.682 8.103 19845 Z= 0.353 Chirality : 0.046 0.201 2230 Planarity : 0.005 0.049 2485 Dihedral : 5.104 33.379 2027 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.44 % Allowed : 16.37 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.20), residues: 1730 helix: 2.27 (0.20), residues: 630 sheet: 0.94 (0.26), residues: 365 loop : -1.78 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 263 HIS 0.008 0.001 HIS B 133 PHE 0.013 0.002 PHE D 418 TYR 0.016 0.002 TYR D 429 ARG 0.005 0.001 ARG C 333 *********************** 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 537 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 483 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8119 (pm20) cc_final: 0.7828 (pm20) REVERT: A 114 LEU cc_start: 0.8674 (mt) cc_final: 0.8009 (tp) REVERT: A 119 LYS cc_start: 0.8974 (mtmm) cc_final: 0.8320 (mtmt) REVERT: A 138 ASP cc_start: 0.8404 (p0) cc_final: 0.7939 (p0) REVERT: A 140 LYS cc_start: 0.8905 (mttp) cc_final: 0.8344 (mtmm) REVERT: A 187 MET cc_start: 0.8469 (mmp) cc_final: 0.8232 (mmm) REVERT: A 190 LEU cc_start: 0.8985 (tp) cc_final: 0.8402 (tp) REVERT: A 193 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7773 (mm-30) REVERT: A 197 LYS cc_start: 0.8744 (mmtp) cc_final: 0.8538 (mmtt) REVERT: A 214 LYS cc_start: 0.8705 (mmtp) cc_final: 0.8429 (mmmm) REVERT: A 235 GLU cc_start: 0.7877 (tt0) cc_final: 0.7364 (tt0) REVERT: A 237 ARG cc_start: 0.7899 (mtt-85) cc_final: 0.7333 (mtt-85) REVERT: A 241 GLU cc_start: 0.7241 (mp0) cc_final: 0.6536 (mp0) REVERT: A 256 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9063 (mt) REVERT: A 270 MET cc_start: 0.7851 (ppp) cc_final: 0.7590 (ppp) REVERT: A 287 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8551 (tpp) REVERT: A 317 PHE cc_start: 0.8481 (m-80) cc_final: 0.8120 (m-80) REVERT: A 322 LEU cc_start: 0.9385 (mt) cc_final: 0.9147 (mp) REVERT: A 406 ARG cc_start: 0.7916 (ttm170) cc_final: 0.7456 (mmt180) REVERT: A 431 ILE cc_start: 0.8429 (mm) cc_final: 0.8171 (pt) REVERT: B 42 MET cc_start: 0.8658 (pmm) cc_final: 0.8279 (pmm) REVERT: B 81 ASP cc_start: 0.7911 (p0) cc_final: 0.7535 (p0) REVERT: B 138 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7737 (p0) REVERT: B 144 ILE cc_start: 0.9217 (mt) cc_final: 0.9005 (mm) REVERT: B 174 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7778 (mm-40) REVERT: B 177 ILE cc_start: 0.9031 (mm) cc_final: 0.8702 (mt) REVERT: B 181 GLU cc_start: 0.6877 (pm20) cc_final: 0.6148 (pm20) REVERT: B 190 LEU cc_start: 0.9091 (tp) cc_final: 0.8474 (tp) REVERT: B 193 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7677 (mm-30) REVERT: B 197 LYS cc_start: 0.8626 (mmtt) cc_final: 0.8254 (ptpp) REVERT: B 214 LYS cc_start: 0.8605 (mmtp) cc_final: 0.8331 (mmmm) REVERT: B 322 LEU cc_start: 0.9377 (mt) cc_final: 0.9138 (mp) REVERT: B 325 TYR cc_start: 0.9078 (t80) cc_final: 0.8834 (t80) REVERT: B 431 ILE cc_start: 0.8282 (mm) cc_final: 0.7971 (pt) REVERT: C 81 ASP cc_start: 0.7277 (p0) cc_final: 0.7004 (p0) REVERT: C 105 ASP cc_start: 0.8607 (p0) cc_final: 0.8372 (p0) REVERT: C 114 LEU cc_start: 0.8527 (mt) cc_final: 0.7878 (tp) REVERT: C 119 LYS cc_start: 0.8935 (mtmm) cc_final: 0.8459 (mttm) REVERT: C 127 GLU cc_start: 0.6690 (tm-30) cc_final: 0.6362 (tm-30) REVERT: C 134 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8053 (mm-30) REVERT: C 138 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.6929 (p0) REVERT: C 140 LYS cc_start: 0.8866 (mttp) cc_final: 0.8121 (mtmm) REVERT: C 142 LEU cc_start: 0.8811 (tp) cc_final: 0.8448 (tt) REVERT: C 190 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8376 (tp) REVERT: C 235 GLU cc_start: 0.7623 (tt0) cc_final: 0.6867 (tt0) REVERT: C 237 ARG cc_start: 0.8067 (mtt-85) cc_final: 0.7349 (mtt-85) REVERT: C 241 GLU cc_start: 0.7373 (mp0) cc_final: 0.6805 (mp0) REVERT: C 317 PHE cc_start: 0.8304 (m-80) cc_final: 0.8020 (m-80) REVERT: C 406 ARG cc_start: 0.7998 (ttm170) cc_final: 0.7435 (mmp-170) REVERT: C 410 ILE cc_start: 0.8746 (mm) cc_final: 0.8480 (mm) REVERT: C 431 ILE cc_start: 0.8439 (mm) cc_final: 0.8065 (pt) REVERT: D 32 MET cc_start: 0.5095 (tpt) cc_final: 0.4448 (tpp) REVERT: D 42 MET cc_start: 0.8903 (pmm) cc_final: 0.8685 (pmm) REVERT: D 49 ASP cc_start: 0.9059 (t0) cc_final: 0.8731 (t0) REVERT: D 104 ASP cc_start: 0.8943 (p0) cc_final: 0.8452 (p0) REVERT: D 113 MET cc_start: 0.8642 (pmm) cc_final: 0.7953 (pmm) REVERT: D 114 LEU cc_start: 0.8727 (mt) cc_final: 0.8409 (tp) REVERT: D 138 ASP cc_start: 0.8034 (p0) cc_final: 0.7732 (p0) REVERT: D 178 MET cc_start: 0.7953 (ttm) cc_final: 0.7737 (ttm) REVERT: D 190 LEU cc_start: 0.9052 (tp) cc_final: 0.8622 (tp) REVERT: D 193 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7653 (mm-30) REVERT: D 210 GLN cc_start: 0.8036 (mp10) cc_final: 0.7752 (mp10) REVERT: D 214 LYS cc_start: 0.8737 (mmtp) cc_final: 0.8416 (mmmm) REVERT: D 235 GLU cc_start: 0.7810 (tt0) cc_final: 0.7377 (tt0) REVERT: D 241 GLU cc_start: 0.7246 (mp0) cc_final: 0.6570 (mp0) REVERT: D 300 LYS cc_start: 0.9020 (mttt) cc_final: 0.8558 (mmtp) REVERT: D 399 MET cc_start: 0.6065 (mpp) cc_final: 0.5111 (mpp) REVERT: D 403 PHE cc_start: 0.7299 (m-80) cc_final: 0.6789 (m-80) REVERT: D 406 ARG cc_start: 0.7873 (ttm170) cc_final: 0.7485 (mmp-170) REVERT: E 81 ASP cc_start: 0.8174 (p0) cc_final: 0.7880 (p0) REVERT: E 144 ILE cc_start: 0.9316 (mt) cc_final: 0.9011 (mm) REVERT: E 181 GLU cc_start: 0.6767 (pm20) cc_final: 0.6143 (pm20) REVERT: E 190 LEU cc_start: 0.8975 (tp) cc_final: 0.8591 (tp) REVERT: E 193 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7566 (mm-30) REVERT: E 214 LYS cc_start: 0.8728 (mmtp) cc_final: 0.8464 (mmmm) REVERT: E 235 GLU cc_start: 0.7798 (tt0) cc_final: 0.7362 (tt0) REVERT: E 237 ARG cc_start: 0.8027 (mtt-85) cc_final: 0.7595 (mtt-85) REVERT: E 241 GLU cc_start: 0.7148 (mp0) cc_final: 0.6425 (mp0) REVERT: E 263 TRP cc_start: 0.7630 (m-10) cc_final: 0.7163 (m-10) REVERT: E 311 MET cc_start: 0.8502 (mmm) cc_final: 0.8204 (mmm) REVERT: E 322 LEU cc_start: 0.9356 (mt) cc_final: 0.9096 (mp) REVERT: E 422 PHE cc_start: 0.8609 (t80) cc_final: 0.8343 (t80) outliers start: 54 outliers final: 32 residues processed: 506 average time/residue: 0.2422 time to fit residues: 180.4556 Evaluate side-chains 508 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 471 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP 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 287 MET Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 138 ASP 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 268 ILE Chi-restraints excluded: chain D residue 291 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 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 157 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 159 optimal weight: 0.5980 chunk 169 optimal weight: 4.9990 chunk 83 optimal weight: 0.0770 chunk 151 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14645 Z= 0.192 Angle : 0.683 11.668 19845 Z= 0.351 Chirality : 0.045 0.258 2230 Planarity : 0.004 0.055 2485 Dihedral : 4.835 48.093 2019 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.18 % Allowed : 18.47 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.20), residues: 1730 helix: 2.24 (0.20), residues: 630 sheet: 0.93 (0.26), residues: 365 loop : -1.77 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 263 HIS 0.004 0.001 HIS B 133 PHE 0.017 0.001 PHE E 169 TYR 0.020 0.001 TYR A 99 ARG 0.003 0.000 ARG E 242 *********************** 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 532 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 482 time to evaluate : 1.635 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: 0.8146 (pm20) cc_final: 0.7813 (pm20) REVERT: A 104 ASP cc_start: 0.8978 (p0) cc_final: 0.8627 (p0) REVERT: A 114 LEU cc_start: 0.8686 (mt) cc_final: 0.8002 (tp) REVERT: A 119 LYS cc_start: 0.8948 (mtmm) cc_final: 0.8278 (mtmt) REVERT: A 140 LYS cc_start: 0.8904 (mttp) cc_final: 0.8239 (mtmm) REVERT: A 181 GLU cc_start: 0.6701 (pm20) cc_final: 0.6175 (pm20) REVERT: A 190 LEU cc_start: 0.9008 (tp) cc_final: 0.8229 (tt) REVERT: A 193 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7748 (mm-30) REVERT: A 214 LYS cc_start: 0.8718 (mmtp) cc_final: 0.8410 (mmmm) REVERT: A 235 GLU cc_start: 0.7803 (tt0) cc_final: 0.7370 (tt0) REVERT: A 237 ARG cc_start: 0.7843 (mtt-85) cc_final: 0.7357 (mtt-85) REVERT: A 241 GLU cc_start: 0.7215 (mp0) cc_final: 0.6458 (mp0) REVERT: A 251 MET cc_start: 0.8053 (mpp) cc_final: 0.7818 (mpp) REVERT: A 256 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9095 (mt) REVERT: A 270 MET cc_start: 0.7929 (ppp) cc_final: 0.7548 (ppp) REVERT: A 287 MET cc_start: 0.8781 (tpp) cc_final: 0.8572 (tpp) REVERT: A 317 PHE cc_start: 0.8526 (m-80) cc_final: 0.8112 (m-80) REVERT: A 322 LEU cc_start: 0.9375 (mt) cc_final: 0.9112 (mp) REVERT: A 406 ARG cc_start: 0.7846 (ttm170) cc_final: 0.7405 (mmt180) REVERT: B 42 MET cc_start: 0.8670 (pmm) cc_final: 0.8416 (pmm) REVERT: B 81 ASP cc_start: 0.7923 (p0) cc_final: 0.7611 (p0) REVERT: B 104 ASP cc_start: 0.8600 (p0) cc_final: 0.8287 (p0) REVERT: B 138 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7441 (p0) REVERT: B 140 LYS cc_start: 0.8836 (mttp) cc_final: 0.8174 (mtmm) REVERT: B 144 ILE cc_start: 0.9203 (mt) cc_final: 0.9001 (mm) REVERT: B 177 ILE cc_start: 0.8998 (mm) cc_final: 0.8755 (mt) REVERT: B 179 GLN cc_start: 0.8679 (mt0) cc_final: 0.8375 (mt0) REVERT: B 181 GLU cc_start: 0.7004 (pm20) cc_final: 0.6223 (pm20) REVERT: B 190 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8435 (tp) REVERT: B 193 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7628 (mm-30) REVERT: B 214 LYS cc_start: 0.8635 (mmtp) cc_final: 0.8040 (mmmm) REVERT: B 241 GLU cc_start: 0.7055 (mp0) cc_final: 0.6118 (mp0) REVERT: B 322 LEU cc_start: 0.9423 (mt) cc_final: 0.9205 (mp) REVERT: C 81 ASP cc_start: 0.7272 (p0) cc_final: 0.6999 (p0) REVERT: C 105 ASP cc_start: 0.8674 (p0) cc_final: 0.8400 (p0) REVERT: C 114 LEU cc_start: 0.8473 (mt) cc_final: 0.7775 (tp) REVERT: C 119 LYS cc_start: 0.8906 (mtmm) cc_final: 0.8419 (mttm) REVERT: C 127 GLU cc_start: 0.6686 (tm-30) cc_final: 0.6288 (tm-30) REVERT: C 138 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.6902 (p0) REVERT: C 140 LYS cc_start: 0.8807 (mttp) cc_final: 0.8111 (mtmm) REVERT: C 142 LEU cc_start: 0.8788 (tp) cc_final: 0.8399 (tt) REVERT: C 181 GLU cc_start: 0.6779 (pm20) cc_final: 0.6321 (pm20) REVERT: C 190 LEU cc_start: 0.9087 (tp) cc_final: 0.8435 (tp) REVERT: C 197 LYS cc_start: 0.8693 (mmtt) cc_final: 0.8365 (ptpp) REVERT: C 235 GLU cc_start: 0.7662 (tt0) cc_final: 0.7392 (tt0) REVERT: C 241 GLU cc_start: 0.7354 (mp0) cc_final: 0.6750 (mp0) REVERT: C 406 ARG cc_start: 0.7986 (ttm170) cc_final: 0.7398 (mmp-170) REVERT: C 410 ILE cc_start: 0.8688 (mm) cc_final: 0.8403 (mm) REVERT: C 431 ILE cc_start: 0.8432 (mm) cc_final: 0.8070 (pt) REVERT: D 113 MET cc_start: 0.8622 (pmm) cc_final: 0.8077 (pmm) REVERT: D 114 LEU cc_start: 0.8777 (mt) cc_final: 0.8526 (tp) REVERT: D 138 ASP cc_start: 0.8097 (p0) cc_final: 0.7720 (p0) REVERT: D 178 MET cc_start: 0.8015 (ttm) cc_final: 0.7785 (ttm) REVERT: D 190 LEU cc_start: 0.9097 (tp) cc_final: 0.8687 (tp) REVERT: D 193 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7624 (mm-30) REVERT: D 210 GLN cc_start: 0.8032 (mp10) cc_final: 0.7740 (mp10) REVERT: D 214 LYS cc_start: 0.8736 (mmtp) cc_final: 0.8434 (mmmm) REVERT: D 241 GLU cc_start: 0.7265 (mp0) cc_final: 0.6585 (mp0) REVERT: D 300 LYS cc_start: 0.9016 (mttt) cc_final: 0.8552 (mmtp) REVERT: D 399 MET cc_start: 0.5933 (mpp) cc_final: 0.5126 (mpp) REVERT: D 403 PHE cc_start: 0.7306 (m-80) cc_final: 0.6782 (m-80) REVERT: D 406 ARG cc_start: 0.7924 (ttm170) cc_final: 0.7548 (mmp-170) REVERT: D 429 TYR cc_start: 0.9116 (t80) cc_final: 0.8808 (t80) REVERT: D 431 ILE cc_start: 0.8367 (mm) cc_final: 0.8031 (pt) REVERT: E 32 MET cc_start: 0.5076 (tpp) cc_final: 0.4343 (tpp) REVERT: E 144 ILE cc_start: 0.9306 (mt) cc_final: 0.9007 (mm) REVERT: E 181 GLU cc_start: 0.6783 (pm20) cc_final: 0.6060 (pm20) REVERT: E 190 LEU cc_start: 0.9004 (tp) cc_final: 0.8648 (tp) REVERT: E 193 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7595 (mm-30) REVERT: E 235 GLU cc_start: 0.7762 (tt0) cc_final: 0.7191 (tt0) REVERT: E 237 ARG cc_start: 0.8006 (mtt-85) cc_final: 0.7412 (mtt-85) REVERT: E 241 GLU cc_start: 0.7147 (mp0) cc_final: 0.6614 (mp0) REVERT: E 263 TRP cc_start: 0.7677 (m-10) cc_final: 0.7195 (m-10) REVERT: E 287 MET cc_start: 0.8915 (tpp) cc_final: 0.8421 (tpp) REVERT: E 314 CYS cc_start: 0.7924 (p) cc_final: 0.7300 (p) REVERT: E 322 LEU cc_start: 0.9399 (mt) cc_final: 0.9132 (mp) outliers start: 50 outliers final: 33 residues processed: 503 average time/residue: 0.2433 time to fit residues: 180.0714 Evaluate side-chains 487 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 450 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 164 MET 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 138 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 138 ASP 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 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 291 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 140 optimal weight: 2.9990 chunk 96 optimal weight: 0.1980 chunk 2 optimal weight: 0.0040 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 151 optimal weight: 0.0970 chunk 42 optimal weight: 0.9980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN D 243 GLN E 55 ASN E 290 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 14645 Z= 0.182 Angle : 0.688 9.824 19845 Z= 0.350 Chirality : 0.045 0.223 2230 Planarity : 0.004 0.058 2485 Dihedral : 4.652 48.436 2015 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.93 % Allowed : 18.85 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.20), residues: 1730 helix: 2.23 (0.21), residues: 620 sheet: 0.94 (0.26), residues: 365 loop : -1.74 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 263 HIS 0.004 0.001 HIS B 239 PHE 0.015 0.001 PHE E 422 TYR 0.016 0.001 TYR E 429 ARG 0.002 0.000 ARG E 242 *********************** 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 507 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 461 time to evaluate : 1.605 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 101 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7395 (mm-30) REVERT: A 102 TYR cc_start: 0.8947 (OUTLIER) cc_final: 0.8431 (m-80) REVERT: A 114 LEU cc_start: 0.8664 (mt) cc_final: 0.7992 (tp) REVERT: A 119 LYS cc_start: 0.8937 (mtmm) cc_final: 0.8243 (mtmt) REVERT: A 140 LYS cc_start: 0.8906 (mttp) cc_final: 0.8282 (mtmm) REVERT: A 181 GLU cc_start: 0.6718 (pm20) cc_final: 0.6153 (pm20) REVERT: A 190 LEU cc_start: 0.9006 (tp) cc_final: 0.8301 (tt) REVERT: A 193 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7708 (mm-30) REVERT: A 214 LYS cc_start: 0.8763 (mmtp) cc_final: 0.8445 (mmmm) REVERT: A 235 GLU cc_start: 0.7752 (tt0) cc_final: 0.7334 (tt0) REVERT: A 237 ARG cc_start: 0.7761 (mtt-85) cc_final: 0.7357 (mtt-85) REVERT: A 241 GLU cc_start: 0.7231 (mp0) cc_final: 0.6522 (mp0) REVERT: A 287 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8544 (tpp) REVERT: A 317 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.8123 (m-10) REVERT: A 322 LEU cc_start: 0.9379 (mt) cc_final: 0.9119 (mp) REVERT: A 403 PHE cc_start: 0.7404 (m-80) cc_final: 0.6839 (m-80) REVERT: A 406 ARG cc_start: 0.7837 (ttm170) cc_final: 0.7411 (mmt180) REVERT: B 42 MET cc_start: 0.8659 (pmm) cc_final: 0.8398 (pmm) REVERT: B 81 ASP cc_start: 0.7911 (p0) cc_final: 0.7568 (p0) REVERT: B 138 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7612 (p0) REVERT: B 144 ILE cc_start: 0.9208 (mt) cc_final: 0.8972 (mm) REVERT: B 177 ILE cc_start: 0.8788 (mm) cc_final: 0.8553 (mt) REVERT: B 179 GLN cc_start: 0.8688 (mt0) cc_final: 0.8323 (mt0) REVERT: B 181 GLU cc_start: 0.7038 (pm20) cc_final: 0.6286 (pm20) REVERT: B 190 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8469 (tp) REVERT: B 193 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7610 (mm-30) REVERT: B 214 LYS cc_start: 0.8670 (mmtp) cc_final: 0.8370 (mmmm) REVERT: B 322 LEU cc_start: 0.9365 (mt) cc_final: 0.9136 (mp) REVERT: C 105 ASP cc_start: 0.8739 (p0) cc_final: 0.8454 (p0) REVERT: C 114 LEU cc_start: 0.8426 (mt) cc_final: 0.7696 (tp) REVERT: C 119 LYS cc_start: 0.8889 (mtmm) cc_final: 0.8404 (mttm) REVERT: C 127 GLU cc_start: 0.6683 (tm-30) cc_final: 0.6284 (tm-30) REVERT: C 138 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.6888 (p0) REVERT: C 140 LYS cc_start: 0.8817 (mttp) cc_final: 0.8097 (mtmm) REVERT: C 142 LEU cc_start: 0.8723 (tp) cc_final: 0.8388 (tt) REVERT: C 154 ILE cc_start: 0.8645 (mm) cc_final: 0.8386 (mm) REVERT: C 181 GLU cc_start: 0.6803 (pm20) cc_final: 0.6311 (pm20) REVERT: C 190 LEU cc_start: 0.9052 (tp) cc_final: 0.8409 (tp) REVERT: C 197 LYS cc_start: 0.8676 (mmtt) cc_final: 0.8284 (ptpp) REVERT: C 235 GLU cc_start: 0.7609 (tt0) cc_final: 0.7379 (tt0) REVERT: C 241 GLU cc_start: 0.7324 (mp0) cc_final: 0.6701 (mp0) REVERT: C 270 MET cc_start: 0.7420 (ppp) cc_final: 0.6993 (ppp) REVERT: C 300 LYS cc_start: 0.9128 (mptt) cc_final: 0.8554 (mmtp) REVERT: C 309 ILE cc_start: 0.8928 (mt) cc_final: 0.8677 (mt) REVERT: C 406 ARG cc_start: 0.7965 (ttm170) cc_final: 0.7395 (mmp-170) REVERT: C 410 ILE cc_start: 0.8656 (mm) cc_final: 0.8397 (mm) REVERT: D 113 MET cc_start: 0.8692 (pmm) cc_final: 0.8035 (pmm) REVERT: D 114 LEU cc_start: 0.8706 (mt) cc_final: 0.8389 (tp) REVERT: D 138 ASP cc_start: 0.8051 (p0) cc_final: 0.7673 (p0) REVERT: D 177 ILE cc_start: 0.8745 (mt) cc_final: 0.8539 (mm) REVERT: D 190 LEU cc_start: 0.9101 (tp) cc_final: 0.8691 (tp) REVERT: D 193 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7623 (mm-30) REVERT: D 210 GLN cc_start: 0.8076 (mp10) cc_final: 0.7807 (mp10) REVERT: D 214 LYS cc_start: 0.8750 (mmtp) cc_final: 0.8449 (mmmm) REVERT: D 235 GLU cc_start: 0.7863 (tt0) cc_final: 0.7539 (tt0) REVERT: D 241 GLU cc_start: 0.7300 (mp0) cc_final: 0.6615 (mp0) REVERT: D 300 LYS cc_start: 0.8987 (mttt) cc_final: 0.8526 (mmtp) REVERT: D 399 MET cc_start: 0.5943 (mpp) cc_final: 0.5240 (mpp) REVERT: D 403 PHE cc_start: 0.7282 (m-80) cc_final: 0.6766 (m-80) REVERT: D 406 ARG cc_start: 0.7901 (ttm170) cc_final: 0.7463 (mmp-170) REVERT: E 104 ASP cc_start: 0.9011 (p0) cc_final: 0.8780 (p0) REVERT: E 144 ILE cc_start: 0.9306 (mt) cc_final: 0.9019 (mm) REVERT: E 149 ASN cc_start: 0.8909 (m-40) cc_final: 0.8692 (m-40) REVERT: E 181 GLU cc_start: 0.6832 (pm20) cc_final: 0.6049 (pm20) REVERT: E 190 LEU cc_start: 0.8991 (tp) cc_final: 0.8627 (tp) REVERT: E 193 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7590 (mm-30) REVERT: E 214 LYS cc_start: 0.8891 (mmmm) cc_final: 0.8411 (mmmm) REVERT: E 235 GLU cc_start: 0.7732 (tt0) cc_final: 0.7164 (tt0) REVERT: E 237 ARG cc_start: 0.7992 (mtt-85) cc_final: 0.7396 (mtt-85) REVERT: E 241 GLU cc_start: 0.7184 (mp0) cc_final: 0.6353 (mp0) REVERT: E 247 TYR cc_start: 0.8756 (m-80) cc_final: 0.8502 (m-80) REVERT: E 263 TRP cc_start: 0.7695 (m-10) cc_final: 0.7172 (m-10) REVERT: E 287 MET cc_start: 0.8922 (tpp) cc_final: 0.8396 (tpp) REVERT: E 314 CYS cc_start: 0.7977 (p) cc_final: 0.7371 (p) REVERT: E 322 LEU cc_start: 0.9403 (mt) cc_final: 0.9119 (mp) REVERT: E 422 PHE cc_start: 0.8545 (t80) cc_final: 0.8293 (t80) outliers start: 46 outliers final: 32 residues processed: 481 average time/residue: 0.2391 time to fit residues: 169.8939 Evaluate side-chains 493 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 455 time to evaluate : 1.640 ------------------------------------------------------------------------------- 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 138 ASP 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 287 MET 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 32 MET Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 138 ASP 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 187 MET Chi-restraints excluded: chain D residue 233 CYS Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 418 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 3.9990 chunk 152 optimal weight: 0.8980 chunk 33 optimal weight: 0.0980 chunk 99 optimal weight: 3.9990 chunk 41 optimal weight: 0.0010 chunk 169 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 GLN C 243 GLN D 243 GLN E 55 ASN ** E 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14645 Z= 0.186 Angle : 0.673 8.817 19845 Z= 0.342 Chirality : 0.045 0.229 2230 Planarity : 0.004 0.047 2485 Dihedral : 4.529 46.765 2015 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.18 % Allowed : 19.30 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.20), residues: 1730 helix: 2.24 (0.21), residues: 620 sheet: 1.04 (0.26), residues: 365 loop : -1.77 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 263 HIS 0.008 0.001 HIS B 239 PHE 0.013 0.001 PHE B 418 TYR 0.014 0.001 TYR E 429 ARG 0.003 0.000 ARG B 237 *********************** 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 506 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 456 time to evaluate : 1.737 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 104 ASP cc_start: 0.8997 (p0) cc_final: 0.8683 (p0) REVERT: A 114 LEU cc_start: 0.8705 (mt) cc_final: 0.7940 (tp) REVERT: A 119 LYS cc_start: 0.8941 (mtmm) cc_final: 0.8220 (mtmt) REVERT: A 140 LYS cc_start: 0.8906 (mttp) cc_final: 0.8250 (mtmm) REVERT: A 181 GLU cc_start: 0.6754 (pm20) cc_final: 0.6147 (pm20) REVERT: A 190 LEU cc_start: 0.9023 (tp) cc_final: 0.8343 (tt) REVERT: A 193 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7687 (mm-30) REVERT: A 214 LYS cc_start: 0.8788 (mmtp) cc_final: 0.8449 (mmmm) REVERT: A 235 GLU cc_start: 0.7764 (tt0) cc_final: 0.7383 (tt0) REVERT: A 241 GLU cc_start: 0.7295 (mp0) cc_final: 0.6559 (mp0) REVERT: A 317 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.8104 (m-10) REVERT: A 322 LEU cc_start: 0.9385 (mt) cc_final: 0.9130 (mp) REVERT: A 403 PHE cc_start: 0.7398 (m-80) cc_final: 0.6849 (m-80) REVERT: A 406 ARG cc_start: 0.7851 (ttm170) cc_final: 0.7404 (mmt180) REVERT: B 42 MET cc_start: 0.8673 (pmm) cc_final: 0.8395 (pmm) REVERT: B 81 ASP cc_start: 0.7943 (p0) cc_final: 0.7632 (p0) REVERT: B 102 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.8366 (m-80) REVERT: B 138 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7628 (p0) REVERT: B 144 ILE cc_start: 0.9208 (mt) cc_final: 0.8960 (mm) REVERT: B 174 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7514 (mm-40) REVERT: B 179 GLN cc_start: 0.8693 (mt0) cc_final: 0.8394 (mt0) REVERT: B 181 GLU cc_start: 0.7158 (pm20) cc_final: 0.6290 (pm20) REVERT: B 190 LEU cc_start: 0.9163 (tp) cc_final: 0.8486 (tp) REVERT: B 193 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7576 (mm-30) REVERT: B 214 LYS cc_start: 0.8715 (mmtp) cc_final: 0.8475 (mmmm) REVERT: B 287 MET cc_start: 0.8849 (tpp) cc_final: 0.8570 (tpp) REVERT: B 322 LEU cc_start: 0.9372 (mt) cc_final: 0.9130 (mp) REVERT: C 104 ASP cc_start: 0.8989 (p0) cc_final: 0.8603 (p0) REVERT: C 114 LEU cc_start: 0.8478 (mt) cc_final: 0.8071 (mp) REVERT: C 119 LYS cc_start: 0.8900 (mtmm) cc_final: 0.8640 (mttm) REVERT: C 127 GLU cc_start: 0.6719 (tm-30) cc_final: 0.6320 (tm-30) REVERT: C 140 LYS cc_start: 0.8811 (mttp) cc_final: 0.8253 (mtmm) REVERT: C 142 LEU cc_start: 0.8713 (tp) cc_final: 0.8384 (tt) REVERT: C 149 ASN cc_start: 0.8815 (m-40) cc_final: 0.8558 (m110) REVERT: C 154 ILE cc_start: 0.8633 (mm) cc_final: 0.8357 (mm) REVERT: C 181 GLU cc_start: 0.6803 (pm20) cc_final: 0.6283 (pm20) REVERT: C 190 LEU cc_start: 0.9092 (tp) cc_final: 0.8445 (tp) REVERT: C 235 GLU cc_start: 0.7612 (tt0) cc_final: 0.7374 (tt0) REVERT: C 241 GLU cc_start: 0.7327 (mp0) cc_final: 0.6704 (mp0) REVERT: C 270 MET cc_start: 0.7461 (ppp) cc_final: 0.7132 (ppp) REVERT: C 300 LYS cc_start: 0.9114 (mptt) cc_final: 0.8620 (mmtp) REVERT: C 309 ILE cc_start: 0.8944 (mt) cc_final: 0.8695 (mt) REVERT: C 406 ARG cc_start: 0.7989 (ttm170) cc_final: 0.7343 (mmp-170) REVERT: C 410 ILE cc_start: 0.8647 (mm) cc_final: 0.8387 (mm) REVERT: D 49 ASP cc_start: 0.9019 (t0) cc_final: 0.8608 (t0) REVERT: D 134 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8375 (mm-30) REVERT: D 138 ASP cc_start: 0.8044 (p0) cc_final: 0.7591 (p0) REVERT: D 144 ILE cc_start: 0.9296 (mt) cc_final: 0.9010 (mm) REVERT: D 190 LEU cc_start: 0.9105 (tp) cc_final: 0.8709 (tp) REVERT: D 193 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7611 (mm-30) REVERT: D 210 GLN cc_start: 0.8076 (mp10) cc_final: 0.7802 (mp10) REVERT: D 214 LYS cc_start: 0.8777 (mmtp) cc_final: 0.8494 (mmmm) REVERT: D 235 GLU cc_start: 0.7825 (tt0) cc_final: 0.7536 (tt0) REVERT: D 241 GLU cc_start: 0.7325 (mp0) cc_final: 0.6656 (mp0) REVERT: D 270 MET cc_start: 0.7850 (ppp) cc_final: 0.6969 (ppp) REVERT: D 300 LYS cc_start: 0.8976 (mttt) cc_final: 0.8534 (mmtp) REVERT: D 406 ARG cc_start: 0.7913 (ttm170) cc_final: 0.7545 (mmp-170) REVERT: E 144 ILE cc_start: 0.9309 (mt) cc_final: 0.9032 (mm) REVERT: E 181 GLU cc_start: 0.6957 (pm20) cc_final: 0.5971 (pm20) REVERT: E 190 LEU cc_start: 0.9012 (tp) cc_final: 0.8647 (tp) REVERT: E 193 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7599 (mm-30) REVERT: E 214 LYS cc_start: 0.8892 (mmmm) cc_final: 0.8404 (mmmm) REVERT: E 235 GLU cc_start: 0.7722 (tt0) cc_final: 0.7300 (tt0) REVERT: E 237 ARG cc_start: 0.7967 (mtt-85) cc_final: 0.7653 (mtt-85) REVERT: E 241 GLU cc_start: 0.7194 (mp0) cc_final: 0.6338 (mp0) REVERT: E 247 TYR cc_start: 0.8745 (m-80) cc_final: 0.8508 (m-80) REVERT: E 263 TRP cc_start: 0.7768 (m-10) cc_final: 0.7292 (m-10) REVERT: E 287 MET cc_start: 0.8919 (tpp) cc_final: 0.8637 (tpt) REVERT: E 422 PHE cc_start: 0.8577 (t80) cc_final: 0.8369 (t80) outliers start: 50 outliers final: 38 residues processed: 478 average time/residue: 0.2498 time to fit residues: 179.3819 Evaluate side-chains 488 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 447 time to evaluate : 1.683 ------------------------------------------------------------------------------- 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 138 ASP 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 32 MET Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 79 THR 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 314 CYS 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 142 optimal weight: 0.0050 chunk 94 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 HIS D 243 GLN E 55 ASN E 149 ASN ** E 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14645 Z= 0.194 Angle : 0.685 9.477 19845 Z= 0.347 Chirality : 0.045 0.210 2230 Planarity : 0.004 0.045 2485 Dihedral : 4.523 48.907 2015 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.74 % Allowed : 20.96 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.20), residues: 1730 helix: 2.19 (0.21), residues: 620 sheet: 1.07 (0.27), residues: 365 loop : -1.79 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 263 HIS 0.008 0.001 HIS B 239 PHE 0.016 0.001 PHE B 169 TYR 0.015 0.001 TYR E 429 ARG 0.003 0.000 ARG C 276 *********************** 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 504 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 461 time to evaluate : 1.662 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 104 ASP cc_start: 0.9030 (p0) cc_final: 0.8709 (p0) REVERT: A 114 LEU cc_start: 0.8733 (mt) cc_final: 0.8233 (mm) REVERT: A 119 LYS cc_start: 0.8938 (mtmm) cc_final: 0.8398 (mtmt) REVERT: A 140 LYS cc_start: 0.8907 (mttp) cc_final: 0.8323 (mtmm) REVERT: A 181 GLU cc_start: 0.6807 (pm20) cc_final: 0.6154 (pm20) REVERT: A 190 LEU cc_start: 0.9028 (tp) cc_final: 0.8360 (tt) REVERT: A 193 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7676 (mm-30) REVERT: A 214 LYS cc_start: 0.8817 (mmtp) cc_final: 0.8465 (mmmm) REVERT: A 235 GLU cc_start: 0.7760 (tt0) cc_final: 0.7473 (tt0) REVERT: A 240 LEU cc_start: 0.8833 (mp) cc_final: 0.8598 (mt) REVERT: A 241 GLU cc_start: 0.7298 (mp0) cc_final: 0.6521 (mp0) REVERT: A 270 MET cc_start: 0.8217 (ppp) cc_final: 0.7878 (ppp) REVERT: A 317 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8156 (m-80) REVERT: A 322 LEU cc_start: 0.9420 (mt) cc_final: 0.9165 (mp) REVERT: A 403 PHE cc_start: 0.7369 (m-80) cc_final: 0.6832 (m-80) REVERT: A 406 ARG cc_start: 0.7853 (ttm170) cc_final: 0.7405 (mmt180) REVERT: B 42 MET cc_start: 0.8660 (pmm) cc_final: 0.8352 (pmm) REVERT: B 81 ASP cc_start: 0.7961 (p0) cc_final: 0.7678 (p0) REVERT: B 101 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7747 (tm-30) REVERT: B 102 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.8360 (m-80) REVERT: B 138 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.6757 (p0) REVERT: B 140 LYS cc_start: 0.8807 (mttp) cc_final: 0.8325 (mtmm) REVERT: B 144 ILE cc_start: 0.9215 (mt) cc_final: 0.8966 (mm) REVERT: B 174 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7578 (mm-40) REVERT: B 179 GLN cc_start: 0.8681 (mt0) cc_final: 0.8358 (mt0) REVERT: B 181 GLU cc_start: 0.7200 (pm20) cc_final: 0.6319 (pm20) REVERT: B 190 LEU cc_start: 0.9187 (tp) cc_final: 0.8534 (tp) REVERT: B 193 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7516 (mm-30) REVERT: B 214 LYS cc_start: 0.8833 (mmtp) cc_final: 0.8503 (mmmm) REVERT: B 270 MET cc_start: 0.7967 (ppp) cc_final: 0.7598 (ppp) REVERT: B 287 MET cc_start: 0.8842 (tpp) cc_final: 0.8532 (tpp) REVERT: B 322 LEU cc_start: 0.9391 (mt) cc_final: 0.9151 (mp) REVERT: C 104 ASP cc_start: 0.8925 (p0) cc_final: 0.8604 (p0) REVERT: C 114 LEU cc_start: 0.8489 (mt) cc_final: 0.8249 (mm) REVERT: C 119 LYS cc_start: 0.8903 (mtmm) cc_final: 0.8659 (mttt) REVERT: C 127 GLU cc_start: 0.6800 (tm-30) cc_final: 0.6425 (tm-30) REVERT: C 140 LYS cc_start: 0.8812 (mttp) cc_final: 0.8305 (mtmm) REVERT: C 142 LEU cc_start: 0.8718 (tp) cc_final: 0.8397 (tt) REVERT: C 149 ASN cc_start: 0.8792 (m-40) cc_final: 0.8561 (m110) REVERT: C 154 ILE cc_start: 0.8585 (mm) cc_final: 0.8326 (mm) REVERT: C 181 GLU cc_start: 0.6825 (pm20) cc_final: 0.6264 (pm20) REVERT: C 190 LEU cc_start: 0.9101 (tp) cc_final: 0.8449 (tp) REVERT: C 197 LYS cc_start: 0.8609 (mmtt) cc_final: 0.8260 (ptpp) REVERT: C 235 GLU cc_start: 0.7698 (tt0) cc_final: 0.7464 (tt0) REVERT: C 241 GLU cc_start: 0.7343 (mp0) cc_final: 0.6706 (mp0) REVERT: C 270 MET cc_start: 0.7562 (ppp) cc_final: 0.7260 (ppp) REVERT: C 300 LYS cc_start: 0.9105 (mptt) cc_final: 0.8608 (mmtp) REVERT: C 406 ARG cc_start: 0.7999 (ttm170) cc_final: 0.7339 (mmp-170) REVERT: C 410 ILE cc_start: 0.8665 (mm) cc_final: 0.8409 (mm) REVERT: D 134 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8399 (mm-30) REVERT: D 190 LEU cc_start: 0.9118 (tp) cc_final: 0.8738 (tp) REVERT: D 193 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7590 (mm-30) REVERT: D 214 LYS cc_start: 0.8787 (mmtp) cc_final: 0.8547 (mmmm) REVERT: D 235 GLU cc_start: 0.7885 (tt0) cc_final: 0.7666 (tt0) REVERT: D 241 GLU cc_start: 0.7385 (mp0) cc_final: 0.6727 (mp0) REVERT: D 270 MET cc_start: 0.7878 (ppp) cc_final: 0.7083 (ppp) REVERT: D 300 LYS cc_start: 0.8963 (mttt) cc_final: 0.8518 (mmtp) REVERT: D 399 MET cc_start: 0.5460 (mpp) cc_final: 0.4437 (mpp) REVERT: D 403 PHE cc_start: 0.7322 (m-80) cc_final: 0.6821 (m-80) REVERT: D 406 ARG cc_start: 0.7939 (ttm170) cc_final: 0.7573 (mmp-170) REVERT: E 102 TYR cc_start: 0.8959 (m-80) cc_final: 0.8664 (m-80) REVERT: E 144 ILE cc_start: 0.9299 (mt) cc_final: 0.9040 (mm) REVERT: E 181 GLU cc_start: 0.6947 (pm20) cc_final: 0.5933 (pm20) REVERT: E 190 LEU cc_start: 0.9017 (tp) cc_final: 0.8654 (tp) REVERT: E 193 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7600 (mm-30) REVERT: E 214 LYS cc_start: 0.8891 (mmmm) cc_final: 0.8422 (mmmm) REVERT: E 235 GLU cc_start: 0.7718 (tt0) cc_final: 0.7267 (tt0) REVERT: E 237 ARG cc_start: 0.7978 (mtt-85) cc_final: 0.7677 (mtt-85) REVERT: E 241 GLU cc_start: 0.7213 (mp0) cc_final: 0.6354 (mp0) REVERT: E 263 TRP cc_start: 0.7862 (m-10) cc_final: 0.7402 (m-10) REVERT: E 287 MET cc_start: 0.8934 (tpp) cc_final: 0.8455 (tpp) REVERT: E 314 CYS cc_start: 0.8025 (p) cc_final: 0.7795 (p) outliers start: 43 outliers final: 38 residues processed: 479 average time/residue: 0.2357 time to fit residues: 168.0789 Evaluate side-chains 484 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 443 time to evaluate : 1.508 ------------------------------------------------------------------------------- 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 138 ASP Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 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 149 ASN Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 418 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 107 optimal weight: 0.0070 chunk 114 optimal weight: 0.8980 chunk 83 optimal weight: 0.0970 chunk 15 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 153 optimal weight: 0.0980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN ** C 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN D 90 GLN E 55 ASN ** E 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14645 Z= 0.186 Angle : 0.697 9.451 19845 Z= 0.352 Chirality : 0.045 0.208 2230 Planarity : 0.004 0.046 2485 Dihedral : 4.539 47.712 2015 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.06 % Allowed : 21.40 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.20), residues: 1730 helix: 2.17 (0.21), residues: 615 sheet: 1.02 (0.27), residues: 365 loop : -1.80 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 263 HIS 0.004 0.001 HIS C 335 PHE 0.018 0.001 PHE E 422 TYR 0.017 0.001 TYR E 429 ARG 0.002 0.000 ARG B 242 *********************** 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 503 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 455 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8995 (p0) cc_final: 0.8713 (p0) REVERT: A 114 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8212 (mm) REVERT: A 119 LYS cc_start: 0.8925 (mtmm) cc_final: 0.8396 (mtmt) REVERT: A 138 ASP cc_start: 0.8188 (p0) cc_final: 0.7899 (p0) REVERT: A 140 LYS cc_start: 0.8901 (mttp) cc_final: 0.8351 (mtmm) REVERT: A 147 ASN cc_start: 0.8758 (p0) cc_final: 0.8436 (p0) REVERT: A 181 GLU cc_start: 0.6854 (pm20) cc_final: 0.6180 (pm20) REVERT: A 190 LEU cc_start: 0.8969 (tp) cc_final: 0.8313 (tt) REVERT: A 193 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7677 (mm-30) REVERT: A 214 LYS cc_start: 0.8793 (mmtp) cc_final: 0.8392 (mmmm) REVERT: A 235 GLU cc_start: 0.7736 (tt0) cc_final: 0.7201 (tt0) REVERT: A 237 ARG cc_start: 0.7846 (mtt-85) cc_final: 0.7371 (mtt-85) REVERT: A 240 LEU cc_start: 0.8856 (mp) cc_final: 0.8645 (mt) REVERT: A 241 GLU cc_start: 0.7282 (mp0) cc_final: 0.6390 (mp0) REVERT: A 270 MET cc_start: 0.8221 (ppp) cc_final: 0.7929 (ppp) REVERT: A 317 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.8096 (m-80) REVERT: A 403 PHE cc_start: 0.7351 (m-80) cc_final: 0.6825 (m-80) REVERT: A 406 ARG cc_start: 0.7827 (ttm170) cc_final: 0.7389 (mmt180) REVERT: B 42 MET cc_start: 0.8650 (pmm) cc_final: 0.8337 (pmm) REVERT: B 81 ASP cc_start: 0.7962 (p0) cc_final: 0.7677 (p0) REVERT: B 101 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7729 (tm-30) REVERT: B 102 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.8352 (m-80) REVERT: B 138 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7312 (p0) REVERT: B 140 LYS cc_start: 0.8806 (mttp) cc_final: 0.8220 (mtmm) REVERT: B 144 ILE cc_start: 0.9222 (mt) cc_final: 0.8987 (mm) REVERT: B 174 GLN cc_start: 0.7967 (mm-40) cc_final: 0.7605 (mm-40) REVERT: B 179 GLN cc_start: 0.8672 (mt0) cc_final: 0.8384 (mt0) REVERT: B 181 GLU cc_start: 0.7222 (pm20) cc_final: 0.6324 (pm20) REVERT: B 190 LEU cc_start: 0.9163 (tp) cc_final: 0.8494 (tp) REVERT: B 193 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7505 (mm-30) REVERT: B 214 LYS cc_start: 0.8848 (mmtp) cc_final: 0.8493 (mmmm) REVERT: B 270 MET cc_start: 0.7998 (ppp) cc_final: 0.7665 (ppp) REVERT: B 287 MET cc_start: 0.8837 (tpp) cc_final: 0.8529 (tpp) REVERT: B 322 LEU cc_start: 0.9386 (mt) cc_final: 0.9149 (mp) REVERT: C 114 LEU cc_start: 0.8452 (mt) cc_final: 0.8220 (mm) REVERT: C 119 LYS cc_start: 0.8892 (mtmm) cc_final: 0.8643 (mttt) REVERT: C 127 GLU cc_start: 0.6792 (tm-30) cc_final: 0.6382 (tm-30) REVERT: C 140 LYS cc_start: 0.8751 (mttp) cc_final: 0.8244 (mtmm) REVERT: C 142 LEU cc_start: 0.8694 (tp) cc_final: 0.8375 (tt) REVERT: C 149 ASN cc_start: 0.8797 (m-40) cc_final: 0.8566 (m110) REVERT: C 154 ILE cc_start: 0.8559 (mm) cc_final: 0.8287 (mm) REVERT: C 190 LEU cc_start: 0.9089 (tp) cc_final: 0.8461 (tp) REVERT: C 197 LYS cc_start: 0.8617 (mmtt) cc_final: 0.8239 (ptpp) REVERT: C 241 GLU cc_start: 0.7351 (mp0) cc_final: 0.6723 (mp0) REVERT: C 270 MET cc_start: 0.7535 (ppp) cc_final: 0.7267 (ppp) REVERT: C 300 LYS cc_start: 0.9105 (mptt) cc_final: 0.8602 (mmtp) REVERT: C 309 ILE cc_start: 0.8925 (mt) cc_final: 0.8691 (mt) REVERT: C 406 ARG cc_start: 0.7977 (ttm170) cc_final: 0.7325 (mmp-170) REVERT: C 410 ILE cc_start: 0.8688 (mm) cc_final: 0.8420 (mm) REVERT: D 49 ASP cc_start: 0.9039 (t0) cc_final: 0.8701 (t0) REVERT: D 104 ASP cc_start: 0.8994 (p0) cc_final: 0.8408 (p0) REVERT: D 126 ASN cc_start: 0.8502 (p0) cc_final: 0.8069 (p0) REVERT: D 138 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7352 (p0) REVERT: D 140 LYS cc_start: 0.8799 (mttp) cc_final: 0.8315 (mtmm) REVERT: D 149 ASN cc_start: 0.8954 (m-40) cc_final: 0.8697 (m110) REVERT: D 190 LEU cc_start: 0.9115 (tp) cc_final: 0.8702 (tp) REVERT: D 193 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7587 (mm-30) REVERT: D 214 LYS cc_start: 0.8784 (mmtp) cc_final: 0.8524 (mmmm) REVERT: D 241 GLU cc_start: 0.7391 (mp0) cc_final: 0.6699 (mp0) REVERT: D 270 MET cc_start: 0.7878 (ppp) cc_final: 0.7126 (ppp) REVERT: D 300 LYS cc_start: 0.8930 (mttt) cc_final: 0.8493 (mmtp) REVERT: D 399 MET cc_start: 0.5536 (mpp) cc_final: 0.4640 (mpp) REVERT: D 403 PHE cc_start: 0.7317 (m-80) cc_final: 0.6831 (m-80) REVERT: D 406 ARG cc_start: 0.7881 (ttm170) cc_final: 0.7515 (mmp-170) REVERT: E 144 ILE cc_start: 0.9326 (mt) cc_final: 0.9055 (mm) REVERT: E 181 GLU cc_start: 0.6920 (pm20) cc_final: 0.5841 (pm20) REVERT: E 190 LEU cc_start: 0.9012 (tp) cc_final: 0.8654 (tp) REVERT: E 193 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7546 (mm-30) REVERT: E 214 LYS cc_start: 0.8892 (mmmm) cc_final: 0.8469 (mmmm) REVERT: E 235 GLU cc_start: 0.7708 (tt0) cc_final: 0.7173 (tt0) REVERT: E 237 ARG cc_start: 0.7970 (mtt-85) cc_final: 0.7576 (mtt-85) REVERT: E 241 GLU cc_start: 0.7206 (mp0) cc_final: 0.6360 (mp0) REVERT: E 248 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8868 (pp) REVERT: E 263 TRP cc_start: 0.7885 (m-10) cc_final: 0.7448 (m-10) REVERT: E 287 MET cc_start: 0.8895 (tpp) cc_final: 0.8342 (tpp) REVERT: E 314 CYS cc_start: 0.8045 (p) cc_final: 0.7245 (p) outliers start: 48 outliers final: 37 residues processed: 475 average time/residue: 0.2316 time to fit residues: 163.8876 Evaluate side-chains 491 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 448 time to evaluate : 1.730 ------------------------------------------------------------------------------- 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 153 SER Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 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 138 ASP Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 233 CYS Chi-restraints excluded: chain D residue 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 149 ASN Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 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 161 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 chunk 157 optimal weight: 0.0010 chunk 94 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 48 optimal weight: 0.0970 chunk 142 optimal weight: 0.0770 chunk 148 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 overall best weight: 0.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN ** C 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN D 90 GLN E 90 GLN E 243 GLN ** E 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14645 Z= 0.195 Angle : 0.702 10.437 19845 Z= 0.356 Chirality : 0.045 0.252 2230 Planarity : 0.004 0.046 2485 Dihedral : 4.505 45.901 2015 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.87 % Allowed : 21.85 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.20), residues: 1730 helix: 2.12 (0.21), residues: 615 sheet: 0.93 (0.26), residues: 365 loop : -1.80 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP B 263 HIS 0.006 0.001 HIS C 335 PHE 0.029 0.001 PHE A 418 TYR 0.025 0.001 TYR E 429 ARG 0.004 0.000 ARG D 276 *********************** 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 500 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 455 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8246 (mm) REVERT: A 119 LYS cc_start: 0.8929 (mtmm) cc_final: 0.8394 (mtmt) REVERT: A 138 ASP cc_start: 0.8140 (p0) cc_final: 0.7876 (p0) REVERT: A 140 LYS cc_start: 0.8903 (mttp) cc_final: 0.8347 (mtmm) REVERT: A 181 GLU cc_start: 0.6909 (pm20) cc_final: 0.6185 (pm20) REVERT: A 190 LEU cc_start: 0.8969 (tp) cc_final: 0.8270 (tt) REVERT: A 193 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7667 (mm-30) REVERT: A 214 LYS cc_start: 0.8811 (mmtp) cc_final: 0.8407 (mmmm) REVERT: A 235 GLU cc_start: 0.7733 (tt0) cc_final: 0.7202 (tt0) REVERT: A 237 ARG cc_start: 0.7842 (mtt-85) cc_final: 0.7364 (mtt-85) REVERT: A 240 LEU cc_start: 0.8808 (mp) cc_final: 0.8601 (mt) REVERT: A 241 GLU cc_start: 0.7294 (mp0) cc_final: 0.6463 (mp0) REVERT: A 270 MET cc_start: 0.8282 (ppp) cc_final: 0.8004 (ppp) REVERT: A 287 MET cc_start: 0.9060 (tpp) cc_final: 0.8771 (tpt) REVERT: A 313 VAL cc_start: 0.8817 (p) cc_final: 0.8548 (m) REVERT: A 317 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.8070 (m-80) REVERT: A 403 PHE cc_start: 0.7400 (m-80) cc_final: 0.6844 (m-80) REVERT: A 406 ARG cc_start: 0.7824 (ttm170) cc_final: 0.7384 (mmt180) REVERT: B 42 MET cc_start: 0.8639 (pmm) cc_final: 0.8356 (pmm) REVERT: B 81 ASP cc_start: 0.7976 (p0) cc_final: 0.7633 (p0) REVERT: B 101 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7723 (tm-30) REVERT: B 102 TYR cc_start: 0.8729 (OUTLIER) cc_final: 0.8301 (m-80) REVERT: B 113 MET cc_start: 0.8408 (pmm) cc_final: 0.7464 (pmm) REVERT: B 138 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7299 (p0) REVERT: B 140 LYS cc_start: 0.8799 (mttp) cc_final: 0.8215 (mtmm) REVERT: B 144 ILE cc_start: 0.9228 (mt) cc_final: 0.8990 (mm) REVERT: B 174 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7653 (mm-40) REVERT: B 179 GLN cc_start: 0.8643 (mt0) cc_final: 0.8346 (mt0) REVERT: B 181 GLU cc_start: 0.7261 (pm20) cc_final: 0.6327 (pm20) REVERT: B 190 LEU cc_start: 0.9169 (tp) cc_final: 0.8505 (tp) REVERT: B 193 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7488 (mm-30) REVERT: B 214 LYS cc_start: 0.8895 (mmtp) cc_final: 0.8564 (mmmm) REVERT: B 270 MET cc_start: 0.8025 (ppp) cc_final: 0.7694 (ppp) REVERT: B 287 MET cc_start: 0.8832 (tpp) cc_final: 0.8464 (tpp) REVERT: B 322 LEU cc_start: 0.9386 (mt) cc_final: 0.9154 (mp) REVERT: C 104 ASP cc_start: 0.8884 (p0) cc_final: 0.8626 (p0) REVERT: C 114 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8240 (mm) REVERT: C 119 LYS cc_start: 0.8896 (mtmm) cc_final: 0.8644 (mttt) REVERT: C 127 GLU cc_start: 0.6825 (tm-30) cc_final: 0.6434 (tm-30) REVERT: C 140 LYS cc_start: 0.8745 (mttp) cc_final: 0.8243 (mtmm) REVERT: C 142 LEU cc_start: 0.8688 (tp) cc_final: 0.8375 (tt) REVERT: C 149 ASN cc_start: 0.8785 (m-40) cc_final: 0.8560 (m110) REVERT: C 154 ILE cc_start: 0.8543 (mm) cc_final: 0.8275 (mm) REVERT: C 166 LEU cc_start: 0.8805 (mt) cc_final: 0.8490 (mm) REVERT: C 181 GLU cc_start: 0.7245 (pm20) cc_final: 0.6649 (pm20) REVERT: C 190 LEU cc_start: 0.9091 (tp) cc_final: 0.8482 (tp) REVERT: C 197 LYS cc_start: 0.8580 (mmtt) cc_final: 0.8177 (ptpp) REVERT: C 241 GLU cc_start: 0.7377 (mp0) cc_final: 0.6782 (mp0) REVERT: C 270 MET cc_start: 0.7584 (ppp) cc_final: 0.7329 (ppp) REVERT: C 300 LYS cc_start: 0.9118 (mptt) cc_final: 0.8605 (mmtp) REVERT: C 309 ILE cc_start: 0.8939 (mt) cc_final: 0.8705 (mt) REVERT: C 311 MET cc_start: 0.9256 (mmm) cc_final: 0.9025 (mmm) REVERT: C 314 CYS cc_start: 0.8736 (m) cc_final: 0.8311 (p) REVERT: C 406 ARG cc_start: 0.7967 (ttm170) cc_final: 0.7315 (mmp-170) REVERT: C 410 ILE cc_start: 0.8675 (mm) cc_final: 0.8408 (mm) REVERT: C 423 LEU cc_start: 0.8669 (mt) cc_final: 0.8436 (pp) REVERT: D 49 ASP cc_start: 0.9018 (t0) cc_final: 0.8672 (t0) REVERT: D 104 ASP cc_start: 0.8987 (p0) cc_final: 0.8441 (p0) REVERT: D 126 ASN cc_start: 0.8499 (p0) cc_final: 0.7735 (p0) REVERT: D 138 ASP cc_start: 0.8137 (p0) cc_final: 0.7766 (p0) REVERT: D 140 LYS cc_start: 0.8824 (mttp) cc_final: 0.8351 (mtmm) REVERT: D 190 LEU cc_start: 0.9126 (tp) cc_final: 0.8723 (tp) REVERT: D 193 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7560 (mm-30) REVERT: D 197 LYS cc_start: 0.8560 (mmtm) cc_final: 0.8337 (mmtt) REVERT: D 214 LYS cc_start: 0.8803 (mmtp) cc_final: 0.8513 (mmmm) REVERT: D 241 GLU cc_start: 0.7405 (mp0) cc_final: 0.6701 (mp0) REVERT: D 270 MET cc_start: 0.7839 (ppp) cc_final: 0.7201 (ppp) REVERT: D 300 LYS cc_start: 0.8934 (mttt) cc_final: 0.8516 (mmtp) REVERT: D 399 MET cc_start: 0.5301 (mpp) cc_final: 0.4434 (mpp) REVERT: D 403 PHE cc_start: 0.7345 (m-80) cc_final: 0.6834 (m-80) REVERT: D 406 ARG cc_start: 0.7872 (ttm170) cc_final: 0.7509 (mmp-170) REVERT: E 81 ASP cc_start: 0.8197 (p0) cc_final: 0.7948 (p0) REVERT: E 102 TYR cc_start: 0.9071 (m-80) cc_final: 0.8509 (m-80) REVERT: E 104 ASP cc_start: 0.9025 (p0) cc_final: 0.8801 (p0) REVERT: E 144 ILE cc_start: 0.9317 (mt) cc_final: 0.9049 (mm) REVERT: E 181 GLU cc_start: 0.6941 (pm20) cc_final: 0.5833 (pm20) REVERT: E 190 LEU cc_start: 0.9010 (tp) cc_final: 0.8658 (tp) REVERT: E 193 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7542 (mm-30) REVERT: E 214 LYS cc_start: 0.8900 (mmmm) cc_final: 0.8473 (mmmm) REVERT: E 235 GLU cc_start: 0.7714 (tt0) cc_final: 0.7179 (tt0) REVERT: E 237 ARG cc_start: 0.7990 (mtt-85) cc_final: 0.7595 (mtt-85) REVERT: E 241 GLU cc_start: 0.7211 (mp0) cc_final: 0.6369 (mp0) REVERT: E 248 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8867 (pp) REVERT: E 263 TRP cc_start: 0.7930 (m-10) cc_final: 0.7486 (m-10) REVERT: E 270 MET cc_start: 0.7670 (ppp) cc_final: 0.7373 (ppp) REVERT: E 287 MET cc_start: 0.8896 (tpp) cc_final: 0.8567 (tpt) REVERT: E 403 PHE cc_start: 0.7208 (m-80) cc_final: 0.6853 (m-80) outliers start: 45 outliers final: 35 residues processed: 474 average time/residue: 0.2411 time to fit residues: 169.9099 Evaluate side-chains 488 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 447 time to evaluate : 1.528 ------------------------------------------------------------------------------- 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 153 SER 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 324 GLU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 114 LEU 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 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 265 SER Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 418 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 174 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14645 Z= 0.233 Angle : 0.719 9.686 19845 Z= 0.366 Chirality : 0.046 0.233 2230 Planarity : 0.004 0.045 2485 Dihedral : 4.586 46.946 2015 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.61 % Allowed : 22.36 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.20), residues: 1730 helix: 2.17 (0.21), residues: 615 sheet: 0.67 (0.26), residues: 375 loop : -1.81 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B 263 HIS 0.006 0.001 HIS C 335 PHE 0.032 0.002 PHE B 418 TYR 0.018 0.001 TYR E 429 ARG 0.004 0.000 ARG D 276 ********************** 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 493 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 452 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8989 (p0) cc_final: 0.8729 (p0) REVERT: A 114 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8287 (mm) REVERT: A 119 LYS cc_start: 0.8944 (mtmm) cc_final: 0.8410 (mtmt) REVERT: A 138 ASP cc_start: 0.8209 (p0) cc_final: 0.7514 (p0) REVERT: A 140 LYS cc_start: 0.8874 (mttp) cc_final: 0.8345 (mtmm) REVERT: A 181 GLU cc_start: 0.7046 (pm20) cc_final: 0.6192 (pm20) REVERT: A 190 LEU cc_start: 0.9058 (tp) cc_final: 0.8378 (tt) REVERT: A 193 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7675 (mm-30) REVERT: A 214 LYS cc_start: 0.8845 (mmtp) cc_final: 0.8461 (mmmm) REVERT: A 235 GLU cc_start: 0.7704 (tt0) cc_final: 0.7439 (tt0) REVERT: A 240 LEU cc_start: 0.8815 (mp) cc_final: 0.8580 (mt) REVERT: A 241 GLU cc_start: 0.7339 (mp0) cc_final: 0.6568 (mp0) REVERT: A 270 MET cc_start: 0.8268 (ppp) cc_final: 0.7866 (ppp) REVERT: A 287 MET cc_start: 0.9050 (tpp) cc_final: 0.8721 (tpt) REVERT: A 313 VAL cc_start: 0.8828 (p) cc_final: 0.8550 (m) REVERT: A 403 PHE cc_start: 0.7421 (m-80) cc_final: 0.6869 (m-80) REVERT: A 406 ARG cc_start: 0.7855 (ttm170) cc_final: 0.7395 (mmt180) REVERT: B 42 MET cc_start: 0.8655 (pmm) cc_final: 0.8338 (pmm) REVERT: B 81 ASP cc_start: 0.8081 (p0) cc_final: 0.7742 (p0) REVERT: B 102 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.8336 (m-80) REVERT: B 113 MET cc_start: 0.8431 (pmm) cc_final: 0.7579 (pmm) REVERT: B 138 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7288 (p0) REVERT: B 140 LYS cc_start: 0.8816 (mttp) cc_final: 0.8237 (mtmm) REVERT: B 144 ILE cc_start: 0.9236 (mt) cc_final: 0.9022 (mm) REVERT: B 174 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7693 (mm-40) REVERT: B 179 GLN cc_start: 0.8656 (mt0) cc_final: 0.8344 (mt0) REVERT: B 181 GLU cc_start: 0.7299 (pm20) cc_final: 0.6335 (pm20) REVERT: B 190 LEU cc_start: 0.9204 (tp) cc_final: 0.8600 (tp) REVERT: B 193 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7445 (mm-30) REVERT: B 214 LYS cc_start: 0.8924 (mmtp) cc_final: 0.8553 (mmmm) REVERT: B 270 MET cc_start: 0.8118 (ppp) cc_final: 0.7816 (ppp) REVERT: B 287 MET cc_start: 0.8834 (tpp) cc_final: 0.8572 (tpp) REVERT: B 322 LEU cc_start: 0.9361 (mt) cc_final: 0.9128 (mp) REVERT: C 104 ASP cc_start: 0.8903 (p0) cc_final: 0.8601 (p0) REVERT: C 119 LYS cc_start: 0.8909 (mtmm) cc_final: 0.8658 (mtmt) REVERT: C 127 GLU cc_start: 0.6920 (tm-30) cc_final: 0.6533 (tm-30) REVERT: C 140 LYS cc_start: 0.8753 (mttp) cc_final: 0.8259 (mtmm) REVERT: C 142 LEU cc_start: 0.8732 (tp) cc_final: 0.8409 (tt) REVERT: C 149 ASN cc_start: 0.8791 (m-40) cc_final: 0.8580 (m110) REVERT: C 154 ILE cc_start: 0.8609 (mm) cc_final: 0.8342 (mm) REVERT: C 181 GLU cc_start: 0.7331 (pm20) cc_final: 0.6751 (pm20) REVERT: C 190 LEU cc_start: 0.9163 (tp) cc_final: 0.8583 (tp) REVERT: C 241 GLU cc_start: 0.7438 (mp0) cc_final: 0.6828 (mp0) REVERT: C 270 MET cc_start: 0.7741 (ppp) cc_final: 0.7509 (ppp) REVERT: C 300 LYS cc_start: 0.9113 (mptt) cc_final: 0.8604 (mmtp) REVERT: C 311 MET cc_start: 0.9265 (mmm) cc_final: 0.8775 (mmm) REVERT: C 314 CYS cc_start: 0.8741 (m) cc_final: 0.8324 (p) REVERT: C 406 ARG cc_start: 0.7966 (ttm170) cc_final: 0.7312 (mmp-170) REVERT: C 410 ILE cc_start: 0.8677 (mm) cc_final: 0.8412 (mm) REVERT: D 49 ASP cc_start: 0.9073 (t0) cc_final: 0.8740 (t0) REVERT: D 102 TYR cc_start: 0.9142 (m-80) cc_final: 0.8637 (m-80) REVERT: D 104 ASP cc_start: 0.8994 (p0) cc_final: 0.8355 (p0) REVERT: D 114 LEU cc_start: 0.9022 (tp) cc_final: 0.8809 (mt) REVERT: D 126 ASN cc_start: 0.8547 (p0) cc_final: 0.7856 (p0) REVERT: D 138 ASP cc_start: 0.8248 (p0) cc_final: 0.7692 (p0) REVERT: D 140 LYS cc_start: 0.8820 (mttp) cc_final: 0.8355 (mtmm) REVERT: D 190 LEU cc_start: 0.9160 (tp) cc_final: 0.8744 (tp) REVERT: D 193 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7535 (mm-30) REVERT: D 214 LYS cc_start: 0.8788 (mmtp) cc_final: 0.8513 (mmmm) REVERT: D 241 GLU cc_start: 0.7404 (mp0) cc_final: 0.6673 (mp0) REVERT: D 270 MET cc_start: 0.7818 (ppp) cc_final: 0.7283 (ppp) REVERT: D 300 LYS cc_start: 0.8956 (mttt) cc_final: 0.8542 (mmtp) REVERT: D 399 MET cc_start: 0.5356 (mpp) cc_final: 0.4519 (mpp) REVERT: D 403 PHE cc_start: 0.7373 (m-80) cc_final: 0.6873 (m-80) REVERT: D 406 ARG cc_start: 0.7894 (ttm170) cc_final: 0.7546 (mmp-170) REVERT: E 81 ASP cc_start: 0.8235 (p0) cc_final: 0.7961 (p0) REVERT: E 101 GLU cc_start: 0.8155 (pp20) cc_final: 0.7731 (pp20) REVERT: E 102 TYR cc_start: 0.9091 (m-80) cc_final: 0.8554 (m-80) REVERT: E 104 ASP cc_start: 0.9036 (p0) cc_final: 0.8803 (p0) REVERT: E 144 ILE cc_start: 0.9319 (mt) cc_final: 0.9051 (mm) REVERT: E 181 GLU cc_start: 0.7040 (pm20) cc_final: 0.6270 (pm20) REVERT: E 190 LEU cc_start: 0.9038 (tp) cc_final: 0.8692 (tp) REVERT: E 193 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7552 (mm-30) REVERT: E 214 LYS cc_start: 0.8924 (mmmm) cc_final: 0.8474 (mmmm) REVERT: E 215 GLU cc_start: 0.8218 (pt0) cc_final: 0.8007 (pt0) REVERT: E 235 GLU cc_start: 0.7715 (tt0) cc_final: 0.7270 (tt0) REVERT: E 237 ARG cc_start: 0.8022 (mtt-85) cc_final: 0.7604 (mtt-85) REVERT: E 241 GLU cc_start: 0.7258 (mp0) cc_final: 0.6415 (mp0) REVERT: E 263 TRP cc_start: 0.7983 (m-10) cc_final: 0.7550 (m-10) REVERT: E 287 MET cc_start: 0.8901 (tpp) cc_final: 0.8224 (tpp) REVERT: E 314 CYS cc_start: 0.7994 (p) cc_final: 0.7080 (p) REVERT: E 403 PHE cc_start: 0.7311 (m-80) cc_final: 0.6954 (m-80) outliers start: 41 outliers final: 34 residues processed: 470 average time/residue: 0.2349 time to fit residues: 164.8530 Evaluate side-chains 480 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 443 time to evaluate : 1.760 ------------------------------------------------------------------------------- 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 324 GLU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 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 323 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain D residue 79 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 265 SER Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 418 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 58 optimal weight: 0.0980 chunk 142 optimal weight: 0.0040 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN ** E 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.102590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.085024 restraints weight = 32667.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.088098 restraints weight = 15400.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.089997 restraints weight = 8720.722| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14645 Z= 0.193 Angle : 0.715 9.041 19845 Z= 0.362 Chirality : 0.046 0.288 2230 Planarity : 0.004 0.057 2485 Dihedral : 4.500 45.889 2015 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.55 % Allowed : 22.48 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.20), residues: 1730 helix: 2.17 (0.21), residues: 615 sheet: 0.67 (0.26), residues: 375 loop : -1.79 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP C 263 HIS 0.006 0.001 HIS C 335 PHE 0.024 0.001 PHE C 418 TYR 0.020 0.001 TYR E 429 ARG 0.008 0.000 ARG D 437 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3732.36 seconds wall clock time: 67 minutes 26.69 seconds (4046.69 seconds total)