Starting phenix.real_space_refine on Fri Jul 3 15:00:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m6p_23703/07_2026/7m6p_23703.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m6p_23703/07_2026/7m6p_23703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7m6p_23703/07_2026/7m6p_23703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m6p_23703/07_2026/7m6p_23703.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7m6p_23703/07_2026/7m6p_23703.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m6p_23703/07_2026/7m6p_23703.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m6p_23703/07_2026/7m6p_23703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m6p_23703/07_2026/7m6p_23703.map" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 9510 2.51 5 N 2400 2.21 5 O 2640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14650 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2911 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2911 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2911 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2911 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2911 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.00, per 1000 atoms: 0.20 Number of scatterers: 14650 At special positions: 0 Unit cell: (96.8, 95.7, 137.5, 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 2640 8.00 N 2400 7.00 C 9510 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 176 " distance=2.04 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 176 " distance=2.04 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 176 " distance=2.04 Simple disulfide: pdb=" SG CYS D 162 " - pdb=" SG CYS D 176 " distance=2.04 Simple disulfide: pdb=" SG CYS E 162 " - pdb=" SG CYS E 176 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 62 " " NAG B 802 " - " ASN B 62 " " NAG C 802 " - " ASN C 62 " " NAG D 802 " - " ASN D 62 " " NAG E 802 " - " ASN E 62 " Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 587.3 milliseconds 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3450 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 25 sheets defined 39.7% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 33 through 42 removed outlier: 3.753A pdb=" N PHE A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 removed outlier: 3.525A pdb=" N ILE A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 268 removed outlier: 3.788A pdb=" N TRP A 267 " --> pdb=" O TRP A 263 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 295 removed outlier: 4.064A pdb=" N VAL A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 281 " --> pdb=" O VAL A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 339 Processing helix chain 'A' and resid 396 through 444 removed outlier: 3.728A pdb=" N LEU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) Proline residue: A 419 - end of helix removed outlier: 3.656A pdb=" N THR A 432 " --> pdb=" O PHE A 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 42 removed outlier: 3.753A pdb=" N PHE B 37 " --> pdb=" O PRO B 33 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 251 removed outlier: 3.526A pdb=" N ILE B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 268 removed outlier: 3.789A pdb=" N TRP B 267 " --> pdb=" O TRP B 263 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 295 removed outlier: 4.063A pdb=" N VAL B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 281 " --> pdb=" O VAL B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 339 Processing helix chain 'B' and resid 396 through 444 removed outlier: 3.727A pdb=" N LEU B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG B 406 " --> pdb=" O LEU B 402 " (cutoff:3.500A) Proline residue: B 419 - end of helix removed outlier: 3.656A pdb=" N THR B 432 " --> pdb=" O PHE B 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 42 removed outlier: 3.753A pdb=" N PHE C 37 " --> pdb=" O PRO C 33 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 251 removed outlier: 3.526A pdb=" N ILE C 249 " --> pdb=" O GLY C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 268 removed outlier: 3.788A pdb=" N TRP C 267 " --> pdb=" O TRP C 263 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE C 268 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 295 removed outlier: 4.063A pdb=" N VAL C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY C 280 " --> pdb=" O ARG C 276 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE C 281 " --> pdb=" O VAL C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 339 Processing helix chain 'C' and resid 396 through 444 removed outlier: 3.728A pdb=" N LEU C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG C 406 " --> pdb=" O LEU C 402 " (cutoff:3.500A) Proline residue: C 419 - end of helix removed outlier: 3.657A pdb=" N THR C 432 " --> pdb=" O PHE C 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 42 removed outlier: 3.754A pdb=" N PHE D 37 " --> pdb=" O PRO D 33 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 removed outlier: 3.526A pdb=" N ILE D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 268 removed outlier: 3.788A pdb=" N TRP D 267 " --> pdb=" O TRP D 263 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE D 268 " --> pdb=" O VAL D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 295 removed outlier: 4.065A pdb=" N VAL D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY D 280 " --> pdb=" O ARG D 276 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE D 281 " --> pdb=" O VAL D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 339 Processing helix chain 'D' and resid 396 through 444 removed outlier: 3.728A pdb=" N LEU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG D 406 " --> pdb=" O LEU D 402 " (cutoff:3.500A) Proline residue: D 419 - end of helix removed outlier: 3.656A pdb=" N THR D 432 " --> pdb=" O PHE D 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 42 removed outlier: 3.753A pdb=" N PHE E 37 " --> pdb=" O PRO E 33 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 251 removed outlier: 3.526A pdb=" N ILE E 249 " --> pdb=" O GLY E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 268 removed outlier: 3.788A pdb=" N TRP E 267 " --> pdb=" O TRP E 263 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE E 268 " --> pdb=" O VAL E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 295 removed outlier: 4.064A pdb=" N VAL E 277 " --> pdb=" O ALA E 273 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY E 280 " --> pdb=" O ARG E 276 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE E 281 " --> pdb=" O VAL E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 339 Processing helix chain 'E' and resid 396 through 444 removed outlier: 3.727A pdb=" N LEU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG E 406 " --> pdb=" O LEU E 402 " (cutoff:3.500A) Proline residue: E 419 - end of helix removed outlier: 3.656A pdb=" N THR E 432 " --> pdb=" O PHE E 428 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 108 removed outlier: 4.046A pdb=" N TRP A 92 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 5.912A 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 128 removed outlier: 3.744A pdb=" N VAL A 159 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TRP A 92 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.816A 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 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 107 through 108 removed outlier: 4.045A pdb=" N TRP B 92 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 5.912A 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 128 removed outlier: 3.744A pdb=" N VAL B 159 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TRP B 92 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.817A 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 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 107 through 108 removed outlier: 4.047A pdb=" N TRP C 92 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 5.911A 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 128 removed outlier: 3.743A pdb=" N VAL C 159 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TRP C 92 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.817A 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 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 107 through 108 removed outlier: 4.046A pdb=" N TRP D 92 " --> pdb=" O VAL D 150 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 5.912A 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 128 removed outlier: 3.743A pdb=" N VAL D 159 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TRP D 92 " --> pdb=" O VAL D 150 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.816A 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 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 107 through 108 removed outlier: 4.046A pdb=" N TRP E 92 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASP E 81 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER E 74 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 5.912A 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 128 removed outlier: 3.744A pdb=" N VAL E 159 " --> pdb=" O LYS E 128 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TRP E 92 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASP E 81 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER E 74 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.818A 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 Processing sheet with id=AC7, first strand: chain 'E' and resid 224 through 225 890 hydrogen bonds defined for protein. 2565 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.31 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4273 1.34 - 1.46: 3791 1.46 - 1.58: 6766 1.58 - 1.71: 0 1.71 - 1.83: 170 Bond restraints: 15000 Sorted by residual: bond pdb=" CB MET C 187 " pdb=" CG MET C 187 " ideal model delta sigma weight residual 1.520 1.447 0.073 3.00e-02 1.11e+03 5.85e+00 bond pdb=" CB MET E 187 " pdb=" CG MET E 187 " ideal model delta sigma weight residual 1.520 1.448 0.072 3.00e-02 1.11e+03 5.81e+00 bond pdb=" CB MET B 187 " pdb=" CG MET B 187 " ideal model delta sigma weight residual 1.520 1.448 0.072 3.00e-02 1.11e+03 5.81e+00 bond pdb=" CB MET D 187 " pdb=" CG MET D 187 " ideal model delta sigma weight residual 1.520 1.448 0.072 3.00e-02 1.11e+03 5.79e+00 bond pdb=" CB MET A 187 " pdb=" CG MET A 187 " ideal model delta sigma weight residual 1.520 1.448 0.072 3.00e-02 1.11e+03 5.76e+00 ... (remaining 14995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 19315 2.57 - 5.14: 823 5.14 - 7.70: 137 7.70 - 10.27: 35 10.27 - 12.84: 15 Bond angle restraints: 20325 Sorted by residual: angle pdb=" C VAL A 135 " pdb=" N THR A 136 " pdb=" CA THR A 136 " ideal model delta sigma weight residual 121.54 131.59 -10.05 1.91e+00 2.74e-01 2.77e+01 angle pdb=" C VAL E 135 " pdb=" N THR E 136 " pdb=" CA THR E 136 " ideal model delta sigma weight residual 121.54 131.58 -10.04 1.91e+00 2.74e-01 2.76e+01 angle pdb=" C VAL B 135 " pdb=" N THR B 136 " pdb=" CA THR B 136 " ideal model delta sigma weight residual 121.54 131.57 -10.03 1.91e+00 2.74e-01 2.76e+01 angle pdb=" C VAL D 135 " pdb=" N THR D 136 " pdb=" CA THR D 136 " ideal model delta sigma weight residual 121.54 131.56 -10.02 1.91e+00 2.74e-01 2.75e+01 angle pdb=" C VAL C 135 " pdb=" N THR C 136 " pdb=" CA THR C 136 " ideal model delta sigma weight residual 121.54 131.53 -9.99 1.91e+00 2.74e-01 2.73e+01 ... (remaining 20320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 8234 17.22 - 34.44: 569 34.44 - 51.66: 112 51.66 - 68.88: 20 68.88 - 86.11: 10 Dihedral angle restraints: 8945 sinusoidal: 3635 harmonic: 5310 Sorted by residual: dihedral pdb=" N PHE B 266 " pdb=" C PHE B 266 " pdb=" CA PHE B 266 " pdb=" CB PHE B 266 " ideal model delta harmonic sigma weight residual 122.80 135.86 -13.06 0 2.50e+00 1.60e-01 2.73e+01 dihedral pdb=" N PHE D 266 " pdb=" C PHE D 266 " pdb=" CA PHE D 266 " pdb=" CB PHE D 266 " ideal model delta harmonic sigma weight residual 122.80 135.85 -13.05 0 2.50e+00 1.60e-01 2.72e+01 dihedral pdb=" N PHE E 266 " pdb=" C PHE E 266 " pdb=" CA PHE E 266 " pdb=" CB PHE E 266 " ideal model delta harmonic sigma weight residual 122.80 135.84 -13.04 0 2.50e+00 1.60e-01 2.72e+01 ... (remaining 8942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1942 0.096 - 0.191: 283 0.191 - 0.287: 56 0.287 - 0.383: 4 0.383 - 0.478: 5 Chirality restraints: 2290 Sorted by residual: chirality pdb=" CA PHE B 266 " pdb=" N PHE B 266 " pdb=" C PHE B 266 " pdb=" CB PHE B 266 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CA PHE D 266 " pdb=" N PHE D 266 " pdb=" C PHE D 266 " pdb=" CB PHE D 266 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.71e+00 chirality pdb=" CA PHE E 266 " pdb=" N PHE E 266 " pdb=" C PHE E 266 " pdb=" CB PHE E 266 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.69e+00 ... (remaining 2287 not shown) Planarity restraints: 2550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 266 " 0.026 2.00e-02 2.50e+03 2.86e-02 1.43e+01 pdb=" CG PHE A 266 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE A 266 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 266 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE A 266 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 PHE A 266 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 266 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 266 " 0.026 2.00e-02 2.50e+03 2.86e-02 1.43e+01 pdb=" CG PHE E 266 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE E 266 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE E 266 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE E 266 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE E 266 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 266 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 266 " -0.026 2.00e-02 2.50e+03 2.85e-02 1.42e+01 pdb=" CG PHE D 266 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE D 266 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE D 266 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE D 266 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE D 266 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 266 " 0.007 2.00e-02 2.50e+03 ... (remaining 2547 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3865 2.81 - 3.34: 13546 3.34 - 3.86: 23842 3.86 - 4.38: 26471 4.38 - 4.90: 46987 Nonbonded interactions: 114711 Sorted by model distance: nonbonded pdb=" OD2 ASP D 110 " pdb=" OG SER D 112 " model vdw 2.293 3.040 nonbonded pdb=" OD2 ASP B 110 " pdb=" OG SER B 112 " model vdw 2.293 3.040 nonbonded pdb=" OD2 ASP C 110 " pdb=" OG SER C 112 " model vdw 2.293 3.040 nonbonded pdb=" OD2 ASP E 110 " pdb=" OG SER E 112 " model vdw 2.293 3.040 nonbonded pdb=" OD2 ASP A 110 " pdb=" OG SER A 112 " model vdw 2.294 3.040 ... (remaining 114706 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 32 through 444) selection = (chain 'B' and resid 32 through 444) selection = (chain 'C' and resid 32 through 444) selection = (chain 'D' and resid 32 through 444) selection = (chain 'E' and resid 32 through 444) } 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 individual isotropic 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.330 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 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 0.080 15010 Z= 0.373 Angle : 1.271 12.840 20350 Z= 0.725 Chirality : 0.075 0.478 2290 Planarity : 0.008 0.060 2545 Dihedral : 12.723 86.106 5480 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.20), residues: 1775 helix: 2.34 (0.19), residues: 650 sheet: 0.19 (0.29), residues: 370 loop : -1.90 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 400 TYR 0.028 0.003 TYR A 325 PHE 0.065 0.005 PHE A 266 TRP 0.018 0.003 TRP D 267 HIS 0.008 0.003 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00804 / 0.37 (15000) covalent geometry : angle 1.26969 / 0.72 (20325) SS BOND : bond 0.00668 / 0.39 ( 5) SS BOND : angle 0.75276 / 0.41 ( 10) hydrogen bonds : bond 0.18857 / 12.54 ( 750) hydrogen bonds : angle 6.47530 / 4.51 ( 2565) link_NAG-ASN : bond 0.00257 / 0.15 ( 5) link_NAG-ASN : angle 2.71776 / 1.64 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 562 time to evaluate : 0.489 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 78 THR cc_start: 0.9152 (p) cc_final: 0.8767 (p) REVERT: A 105 ASP cc_start: 0.7674 (p0) cc_final: 0.7290 (p0) REVERT: A 138 ASP cc_start: 0.7084 (p0) cc_final: 0.6520 (p0) REVERT: A 263 TRP cc_start: 0.6830 (m-10) cc_final: 0.6521 (m-10) REVERT: A 287 MET cc_start: 0.9284 (mmm) cc_final: 0.9051 (mmm) REVERT: B 115 ASP cc_start: 0.7564 (p0) cc_final: 0.7143 (p0) REVERT: B 138 ASP cc_start: 0.6447 (p0) cc_final: 0.6212 (p0) REVERT: B 287 MET cc_start: 0.9395 (mmm) cc_final: 0.9101 (mmp) REVERT: B 408 LYS cc_start: 0.8732 (mmtm) cc_final: 0.8313 (ptpt) REVERT: B 420 LEU cc_start: 0.8881 (tp) cc_final: 0.8644 (tp) REVERT: B 423 LEU cc_start: 0.9261 (tp) cc_final: 0.9025 (tt) REVERT: C 138 ASP cc_start: 0.7296 (p0) cc_final: 0.7089 (p0) REVERT: C 140 LYS cc_start: 0.8699 (mttp) cc_final: 0.8450 (mttp) REVERT: C 287 MET cc_start: 0.9286 (mmm) cc_final: 0.8913 (mmp) REVERT: C 426 ASN cc_start: 0.8587 (m-40) cc_final: 0.7560 (m-40) REVERT: D 78 THR cc_start: 0.9127 (p) cc_final: 0.8791 (p) REVERT: D 153 SER cc_start: 0.8547 (t) cc_final: 0.8314 (p) REVERT: D 164 MET cc_start: 0.8681 (ptp) cc_final: 0.8421 (ptp) REVERT: D 287 MET cc_start: 0.9371 (mmm) cc_final: 0.9036 (mmp) REVERT: D 311 MET cc_start: 0.8855 (mmt) cc_final: 0.8499 (mmm) REVERT: E 78 THR cc_start: 0.9082 (p) cc_final: 0.8722 (p) REVERT: E 138 ASP cc_start: 0.7178 (p0) cc_final: 0.6971 (p0) REVERT: E 287 MET cc_start: 0.9307 (mmm) cc_final: 0.9030 (mmp) REVERT: E 426 ASN cc_start: 0.8696 (m-40) cc_final: 0.8154 (m-40) outliers start: 0 outliers final: 0 residues processed: 562 average time/residue: 0.0977 time to fit residues: 83.2528 Evaluate side-chains 361 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.0770 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 HIS A 250 GLN A 426 ASN B 66 ASN B 85 ASN B 239 HIS B 334 GLN C 179 GLN C 210 GLN C 239 HIS C 250 GLN C 269 ASN D 90 GLN D 210 GLN D 239 HIS D 290 GLN D 426 ASN E 85 ASN E 179 GLN E 239 HIS ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 GLN E 334 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.116901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.092742 restraints weight = 32267.539| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 4.07 r_work: 0.3171 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15010 Z= 0.181 Angle : 0.767 9.346 20350 Z= 0.406 Chirality : 0.049 0.214 2290 Planarity : 0.005 0.048 2545 Dihedral : 4.969 23.294 1955 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.55 % Allowed : 13.40 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.19), residues: 1775 helix: 2.02 (0.18), residues: 670 sheet: 0.78 (0.27), residues: 380 loop : -1.97 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 400 TYR 0.017 0.002 TYR B 433 PHE 0.037 0.002 PHE B 266 TRP 0.040 0.003 TRP C 267 HIS 0.007 0.002 HIS E 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (15000) covalent geometry : angle 0.76585 / 0.41 (20325) SS BOND : bond 0.01184 / 0.76 ( 5) SS BOND : angle 0.99458 / 0.50 ( 10) hydrogen bonds : bond 0.06413 / 4.20 ( 750) hydrogen bonds : angle 4.61042 / 3.20 ( 2565) link_NAG-ASN : bond 0.00046 / 0.03 ( 5) link_NAG-ASN : angle 1.51882 / 0.82 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 410 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8293 (p0) REVERT: A 138 ASP cc_start: 0.7680 (p0) cc_final: 0.7311 (p0) REVERT: A 174 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8038 (mm110) REVERT: B 105 ASP cc_start: 0.9026 (p0) cc_final: 0.8721 (p0) REVERT: B 113 MET cc_start: 0.8904 (ppp) cc_final: 0.8578 (ppp) REVERT: B 114 LEU cc_start: 0.9314 (mt) cc_final: 0.9021 (tp) REVERT: B 138 ASP cc_start: 0.7292 (p0) cc_final: 0.6829 (p0) REVERT: B 140 LYS cc_start: 0.8962 (mttp) cc_final: 0.8407 (mtmm) REVERT: B 174 GLN cc_start: 0.8396 (mp10) cc_final: 0.8120 (mm110) REVERT: B 201 GLN cc_start: 0.7742 (mp10) cc_final: 0.7181 (mp10) REVERT: B 287 MET cc_start: 0.9529 (mmm) cc_final: 0.9299 (mmp) REVERT: B 420 LEU cc_start: 0.9056 (tp) cc_final: 0.8823 (tp) REVERT: B 422 PHE cc_start: 0.9344 (t80) cc_final: 0.9132 (t80) REVERT: B 423 LEU cc_start: 0.9280 (tp) cc_final: 0.9063 (tt) REVERT: B 426 ASN cc_start: 0.8978 (m-40) cc_final: 0.8601 (m-40) REVERT: B 439 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7660 (tm-30) REVERT: C 39 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8419 (p0) REVERT: C 81 ASP cc_start: 0.9081 (p0) cc_final: 0.8832 (p0) REVERT: C 140 LYS cc_start: 0.8926 (mttp) cc_final: 0.8699 (mttp) REVERT: C 210 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8283 (tp-100) REVERT: C 221 TYR cc_start: 0.7774 (m-80) cc_final: 0.7525 (m-10) REVERT: C 300 LYS cc_start: 0.9406 (mttp) cc_final: 0.9019 (mtmm) REVERT: C 426 ASN cc_start: 0.8985 (m-40) cc_final: 0.8764 (m110) REVERT: C 439 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7869 (tm-30) REVERT: D 94 ASP cc_start: 0.8501 (t0) cc_final: 0.8165 (t70) REVERT: D 105 ASP cc_start: 0.9220 (p0) cc_final: 0.9013 (p0) REVERT: D 138 ASP cc_start: 0.7765 (p0) cc_final: 0.7081 (p0) REVERT: D 140 LYS cc_start: 0.9195 (mtpp) cc_final: 0.8707 (mtmm) REVERT: D 237 ARG cc_start: 0.9072 (mtt-85) cc_final: 0.8776 (mtp85) REVERT: D 243 GLN cc_start: 0.8848 (mp10) cc_final: 0.8517 (mp10) REVERT: D 270 MET cc_start: 0.7038 (tpp) cc_final: 0.6818 (mmt) REVERT: D 308 ASP cc_start: 0.9387 (m-30) cc_final: 0.9166 (m-30) REVERT: D 426 ASN cc_start: 0.9052 (m-40) cc_final: 0.8687 (m110) REVERT: E 39 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8291 (p0) REVERT: E 138 ASP cc_start: 0.7855 (p0) cc_final: 0.7532 (p0) REVERT: E 140 LYS cc_start: 0.8920 (mttp) cc_final: 0.8409 (mtpp) REVERT: E 174 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7906 (mm110) REVERT: E 251 MET cc_start: 0.9110 (mpp) cc_final: 0.8681 (mpp) REVERT: E 270 MET cc_start: 0.7583 (tpp) cc_final: 0.7131 (mmt) REVERT: E 300 LYS cc_start: 0.9235 (mtmm) cc_final: 0.8739 (mmtm) outliers start: 41 outliers final: 19 residues processed: 435 average time/residue: 0.0908 time to fit residues: 61.5957 Evaluate side-chains 394 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 369 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 290 GLN Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 269 ASN Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 435 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 158 optimal weight: 0.1980 chunk 143 optimal weight: 2.9990 chunk 37 optimal weight: 0.0070 chunk 104 optimal weight: 0.1980 chunk 9 optimal weight: 0.9990 overall best weight: 0.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.118344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.094179 restraints weight = 32537.583| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 4.10 r_work: 0.3206 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15010 Z= 0.147 Angle : 0.698 10.582 20350 Z= 0.361 Chirality : 0.046 0.190 2290 Planarity : 0.004 0.059 2545 Dihedral : 4.744 25.265 1955 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.24 % Allowed : 15.26 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.19), residues: 1775 helix: 1.81 (0.18), residues: 700 sheet: 0.90 (0.27), residues: 380 loop : -1.88 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 400 TYR 0.016 0.001 TYR B 429 PHE 0.028 0.002 PHE C 266 TRP 0.060 0.003 TRP A 267 HIS 0.002 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (15000) covalent geometry : angle 0.69731 / 0.36 (20325) SS BOND : bond 0.00549 / 0.33 ( 5) SS BOND : angle 0.68294 / 0.36 ( 10) hydrogen bonds : bond 0.05515 / 3.61 ( 750) hydrogen bonds : angle 4.16739 / 2.88 ( 2565) link_NAG-ASN : bond 0.00116 / 0.07 ( 5) link_NAG-ASN : angle 1.19785 / 0.65 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 402 time to evaluate : 0.562 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 39 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.8294 (p0) REVERT: A 80 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8620 (mmm) REVERT: A 94 ASP cc_start: 0.8404 (t0) cc_final: 0.8167 (t0) REVERT: A 105 ASP cc_start: 0.8899 (p0) cc_final: 0.8628 (p0) REVERT: A 115 ASP cc_start: 0.8976 (p0) cc_final: 0.8673 (p0) REVERT: A 138 ASP cc_start: 0.7591 (p0) cc_final: 0.7225 (p0) REVERT: A 174 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8051 (mm110) REVERT: A 270 MET cc_start: 0.7461 (tpp) cc_final: 0.6896 (tmm) REVERT: A 426 ASN cc_start: 0.9132 (m-40) cc_final: 0.8926 (m110) REVERT: B 105 ASP cc_start: 0.8973 (p0) cc_final: 0.8670 (p0) REVERT: B 138 ASP cc_start: 0.7309 (p0) cc_final: 0.7077 (p0) REVERT: B 140 LYS cc_start: 0.8905 (mttp) cc_final: 0.8625 (mttp) REVERT: B 174 GLN cc_start: 0.8421 (mp10) cc_final: 0.8137 (mm110) REVERT: B 201 GLN cc_start: 0.7771 (mp10) cc_final: 0.7175 (mp10) REVERT: B 221 TYR cc_start: 0.7556 (m-80) cc_final: 0.7222 (m-10) REVERT: B 270 MET cc_start: 0.7444 (tpp) cc_final: 0.6775 (tmm) REVERT: B 287 MET cc_start: 0.9546 (mmm) cc_final: 0.9321 (mmp) REVERT: B 420 LEU cc_start: 0.9022 (tp) cc_final: 0.8815 (tp) REVERT: B 422 PHE cc_start: 0.9336 (t80) cc_final: 0.9117 (t80) REVERT: B 423 LEU cc_start: 0.9297 (tp) cc_final: 0.9046 (tt) REVERT: B 426 ASN cc_start: 0.9010 (m-40) cc_final: 0.8618 (m-40) REVERT: B 439 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7512 (tm-30) REVERT: C 39 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8382 (p0) REVERT: C 81 ASP cc_start: 0.9112 (p0) cc_final: 0.8816 (p0) REVERT: C 177 ILE cc_start: 0.9259 (mm) cc_final: 0.8878 (mm) REVERT: C 221 TYR cc_start: 0.7798 (m-80) cc_final: 0.7491 (m-10) REVERT: C 263 TRP cc_start: 0.7459 (m-10) cc_final: 0.7249 (m-10) REVERT: C 300 LYS cc_start: 0.9345 (mttp) cc_final: 0.9073 (mtmm) REVERT: C 422 PHE cc_start: 0.9398 (t80) cc_final: 0.8979 (t80) REVERT: C 426 ASN cc_start: 0.8986 (m-40) cc_final: 0.8364 (m-40) REVERT: C 439 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7755 (tm-30) REVERT: D 72 PHE cc_start: 0.8930 (t80) cc_final: 0.8698 (t80) REVERT: D 80 MET cc_start: 0.8911 (tpp) cc_final: 0.8699 (tpp) REVERT: D 94 ASP cc_start: 0.8440 (t0) cc_final: 0.8168 (t70) REVERT: D 105 ASP cc_start: 0.9211 (p0) cc_final: 0.8933 (p0) REVERT: D 138 ASP cc_start: 0.7872 (p0) cc_final: 0.7177 (p0) REVERT: D 140 LYS cc_start: 0.9189 (mtpp) cc_final: 0.8658 (mtmm) REVERT: D 237 ARG cc_start: 0.9058 (mtt-85) cc_final: 0.8799 (mtp85) REVERT: D 243 GLN cc_start: 0.8804 (mp10) cc_final: 0.8575 (mp10) REVERT: D 300 LYS cc_start: 0.9199 (mtmm) cc_final: 0.8947 (mmtp) REVERT: D 311 MET cc_start: 0.9498 (mmm) cc_final: 0.8785 (mmm) REVERT: D 439 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7273 (tm-30) REVERT: E 39 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8316 (p0) REVERT: E 174 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7946 (mm110) REVERT: E 300 LYS cc_start: 0.9227 (mtmm) cc_final: 0.8794 (mmtm) REVERT: E 308 ASP cc_start: 0.9312 (m-30) cc_final: 0.9085 (m-30) REVERT: E 426 ASN cc_start: 0.8973 (m-40) cc_final: 0.8516 (m110) outliers start: 36 outliers final: 20 residues processed: 422 average time/residue: 0.0853 time to fit residues: 56.3453 Evaluate side-chains 390 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 364 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 269 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 53 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 104 optimal weight: 0.0170 chunk 66 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 GLN ** D 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.117254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.093270 restraints weight = 32477.337| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.97 r_work: 0.3193 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15010 Z= 0.154 Angle : 0.667 10.630 20350 Z= 0.344 Chirality : 0.046 0.173 2290 Planarity : 0.004 0.063 2545 Dihedral : 4.653 27.953 1955 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.12 % Allowed : 16.26 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.19), residues: 1775 helix: 2.16 (0.18), residues: 670 sheet: 0.77 (0.27), residues: 380 loop : -1.83 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 295 TYR 0.016 0.002 TYR B 152 PHE 0.026 0.002 PHE C 266 TRP 0.065 0.003 TRP A 267 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (15000) covalent geometry : angle 0.66524 / 0.34 (20325) SS BOND : bond 0.00401 / 0.24 ( 5) SS BOND : angle 1.50177 / 0.83 ( 10) hydrogen bonds : bond 0.04912 / 3.24 ( 750) hydrogen bonds : angle 4.02281 / 2.78 ( 2565) link_NAG-ASN : bond 0.00143 / 0.08 ( 5) link_NAG-ASN : angle 1.39566 / 0.78 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 375 time to evaluate : 0.521 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 115 ASP cc_start: 0.8978 (p0) cc_final: 0.8673 (p0) REVERT: A 138 ASP cc_start: 0.7623 (p0) cc_final: 0.7211 (p0) REVERT: A 174 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8081 (mm110) REVERT: A 201 GLN cc_start: 0.7604 (mp10) cc_final: 0.6841 (mp10) REVERT: A 426 ASN cc_start: 0.9173 (m-40) cc_final: 0.8915 (m110) REVERT: B 105 ASP cc_start: 0.8981 (p0) cc_final: 0.8594 (p0) REVERT: B 138 ASP cc_start: 0.7389 (p0) cc_final: 0.7152 (p0) REVERT: B 140 LYS cc_start: 0.8867 (mttp) cc_final: 0.8598 (mttp) REVERT: B 174 GLN cc_start: 0.8489 (mp10) cc_final: 0.8175 (mm110) REVERT: B 187 MET cc_start: 0.8872 (mmm) cc_final: 0.8581 (tpp) REVERT: B 201 GLN cc_start: 0.7802 (mp10) cc_final: 0.7186 (mp10) REVERT: B 221 TYR cc_start: 0.7680 (m-80) cc_final: 0.7411 (m-10) REVERT: B 287 MET cc_start: 0.9585 (mmm) cc_final: 0.9368 (mmp) REVERT: B 420 LEU cc_start: 0.8973 (tp) cc_final: 0.8757 (tp) REVERT: B 422 PHE cc_start: 0.9392 (t80) cc_final: 0.9186 (t80) REVERT: B 423 LEU cc_start: 0.9305 (tp) cc_final: 0.9029 (tt) REVERT: B 426 ASN cc_start: 0.9036 (m-40) cc_final: 0.8681 (m-40) REVERT: B 439 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7802 (tm-30) REVERT: C 39 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8434 (p0) REVERT: C 80 MET cc_start: 0.9185 (mmm) cc_final: 0.8954 (mtp) REVERT: C 81 ASP cc_start: 0.9180 (p0) cc_final: 0.8840 (p0) REVERT: C 177 ILE cc_start: 0.9261 (mm) cc_final: 0.8809 (mm) REVERT: C 201 GLN cc_start: 0.7605 (mp10) cc_final: 0.7194 (mp10) REVERT: C 221 TYR cc_start: 0.7931 (m-80) cc_final: 0.7685 (m-10) REVERT: C 263 TRP cc_start: 0.7412 (m-10) cc_final: 0.7180 (m-10) REVERT: C 422 PHE cc_start: 0.9418 (t80) cc_final: 0.8961 (t80) REVERT: C 426 ASN cc_start: 0.9042 (m-40) cc_final: 0.8399 (m-40) REVERT: C 439 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7774 (tm-30) REVERT: D 72 PHE cc_start: 0.8910 (t80) cc_final: 0.8650 (t80) REVERT: D 105 ASP cc_start: 0.9159 (p0) cc_final: 0.8827 (p0) REVERT: D 140 LYS cc_start: 0.9244 (mtpp) cc_final: 0.8991 (mtpp) REVERT: D 201 GLN cc_start: 0.7490 (mp10) cc_final: 0.6614 (mp10) REVERT: D 237 ARG cc_start: 0.9056 (mtt-85) cc_final: 0.8834 (mtp85) REVERT: D 243 GLN cc_start: 0.8844 (mp10) cc_final: 0.8512 (mp10) REVERT: D 251 MET cc_start: 0.8991 (mpp) cc_final: 0.8531 (mpp) REVERT: D 300 LYS cc_start: 0.9221 (mtmm) cc_final: 0.8928 (mmtp) REVERT: D 311 MET cc_start: 0.9497 (mmm) cc_final: 0.9284 (mmm) REVERT: D 439 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7200 (tm-30) REVERT: E 39 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8274 (p0) REVERT: E 41 LEU cc_start: 0.8882 (tp) cc_final: 0.8659 (tp) REVERT: E 174 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7996 (mm110) REVERT: E 251 MET cc_start: 0.9119 (mpp) cc_final: 0.8684 (mpp) REVERT: E 308 ASP cc_start: 0.9288 (m-30) cc_final: 0.9072 (m-30) REVERT: E 422 PHE cc_start: 0.9403 (t80) cc_final: 0.9194 (t80) REVERT: E 426 ASN cc_start: 0.8964 (m-40) cc_final: 0.8711 (m110) outliers start: 50 outliers final: 32 residues processed: 407 average time/residue: 0.0866 time to fit residues: 55.2523 Evaluate side-chains 392 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 356 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 269 ASN Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 15 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 165 optimal weight: 0.2980 chunk 97 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 153 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 157 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN C 210 GLN ** C 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.117223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.093024 restraints weight = 32773.860| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 4.00 r_work: 0.3194 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15010 Z= 0.141 Angle : 0.673 11.215 20350 Z= 0.343 Chirality : 0.045 0.168 2290 Planarity : 0.004 0.045 2545 Dihedral : 4.582 30.131 1955 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.18 % Allowed : 16.70 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.19), residues: 1775 helix: 2.15 (0.18), residues: 670 sheet: 0.93 (0.27), residues: 370 loop : -1.84 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 295 TYR 0.032 0.002 TYR B 152 PHE 0.024 0.002 PHE A 266 TRP 0.078 0.003 TRP A 267 HIS 0.003 0.001 HIS A 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (15000) covalent geometry : angle 0.67241 / 0.34 (20325) SS BOND : bond 0.00765 / 0.42 ( 5) SS BOND : angle 0.85916 / 0.46 ( 10) hydrogen bonds : bond 0.04557 / 3.02 ( 750) hydrogen bonds : angle 3.87434 / 2.67 ( 2565) link_NAG-ASN : bond 0.00030 / 0.02 ( 5) link_NAG-ASN : angle 1.21298 / 0.67 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 377 time to evaluate : 0.450 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 138 ASP cc_start: 0.7600 (p0) cc_final: 0.7261 (p0) REVERT: A 174 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8028 (mm110) REVERT: A 201 GLN cc_start: 0.7608 (mp10) cc_final: 0.6904 (mp10) REVERT: A 300 LYS cc_start: 0.9220 (mtmm) cc_final: 0.8905 (mmtm) REVERT: A 426 ASN cc_start: 0.9183 (m-40) cc_final: 0.8898 (m110) REVERT: B 105 ASP cc_start: 0.8961 (p0) cc_final: 0.8550 (p0) REVERT: B 138 ASP cc_start: 0.7478 (p0) cc_final: 0.7216 (p0) REVERT: B 140 LYS cc_start: 0.8873 (mttp) cc_final: 0.8636 (mttp) REVERT: B 174 GLN cc_start: 0.8478 (mp10) cc_final: 0.8154 (mm110) REVERT: B 201 GLN cc_start: 0.7798 (mp10) cc_final: 0.7142 (mp10) REVERT: B 287 MET cc_start: 0.9581 (mmm) cc_final: 0.9371 (mmp) REVERT: B 420 LEU cc_start: 0.8977 (tp) cc_final: 0.8764 (tp) REVERT: B 422 PHE cc_start: 0.9388 (t80) cc_final: 0.9151 (t80) REVERT: B 423 LEU cc_start: 0.9307 (tp) cc_final: 0.9019 (tt) REVERT: B 426 ASN cc_start: 0.9035 (m-40) cc_final: 0.8644 (m-40) REVERT: B 439 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7813 (tm-30) REVERT: C 39 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8418 (p0) REVERT: C 81 ASP cc_start: 0.9223 (p0) cc_final: 0.8851 (p0) REVERT: C 177 ILE cc_start: 0.9253 (mm) cc_final: 0.8556 (mm) REVERT: C 201 GLN cc_start: 0.7590 (mp10) cc_final: 0.7163 (mp10) REVERT: C 235 GLU cc_start: 0.8695 (tt0) cc_final: 0.8468 (tt0) REVERT: C 263 TRP cc_start: 0.7208 (m-10) cc_final: 0.6992 (m-10) REVERT: C 422 PHE cc_start: 0.9450 (t80) cc_final: 0.8992 (t80) REVERT: C 426 ASN cc_start: 0.9037 (m-40) cc_final: 0.8407 (m-40) REVERT: C 439 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7746 (tm-30) REVERT: D 72 PHE cc_start: 0.8886 (t80) cc_final: 0.8613 (t80) REVERT: D 80 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.7997 (mpp) REVERT: D 105 ASP cc_start: 0.9168 (p0) cc_final: 0.8832 (p0) REVERT: D 201 GLN cc_start: 0.7487 (mp10) cc_final: 0.6595 (mp10) REVERT: D 237 ARG cc_start: 0.9064 (mtt-85) cc_final: 0.8590 (mtp85) REVERT: D 243 GLN cc_start: 0.8789 (mp10) cc_final: 0.8476 (mp10) REVERT: D 251 MET cc_start: 0.9006 (mpp) cc_final: 0.8525 (mpp) REVERT: D 300 LYS cc_start: 0.9168 (mtmm) cc_final: 0.8852 (mmtp) REVERT: D 426 ASN cc_start: 0.9106 (m-40) cc_final: 0.8834 (m110) REVERT: D 439 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7385 (tm-30) REVERT: E 39 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.8246 (p0) REVERT: E 41 LEU cc_start: 0.8858 (tp) cc_final: 0.8651 (tp) REVERT: E 174 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7831 (mm110) REVERT: E 201 GLN cc_start: 0.7639 (mp10) cc_final: 0.7179 (mp10) REVERT: E 237 ARG cc_start: 0.9223 (mtt-85) cc_final: 0.9002 (mtp85) REVERT: E 251 MET cc_start: 0.9096 (mpp) cc_final: 0.8629 (mpp) REVERT: E 287 MET cc_start: 0.9552 (mmp) cc_final: 0.9321 (mmp) REVERT: E 422 PHE cc_start: 0.9400 (t80) cc_final: 0.9178 (t80) REVERT: E 426 ASN cc_start: 0.9014 (m-40) cc_final: 0.8749 (m110) REVERT: E 439 GLU cc_start: 0.8105 (pt0) cc_final: 0.7709 (tm-30) outliers start: 51 outliers final: 39 residues processed: 404 average time/residue: 0.0824 time to fit residues: 52.1297 Evaluate side-chains 399 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 355 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 267 TRP Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 269 ASN Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 143 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.116058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.091976 restraints weight = 32949.040| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 3.97 r_work: 0.3177 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15010 Z= 0.163 Angle : 0.681 11.747 20350 Z= 0.346 Chirality : 0.045 0.157 2290 Planarity : 0.004 0.042 2545 Dihedral : 4.600 32.113 1955 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.55 % Allowed : 16.76 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.19), residues: 1775 helix: 2.19 (0.18), residues: 670 sheet: 0.79 (0.26), residues: 380 loop : -1.87 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 437 TYR 0.040 0.002 TYR D 152 PHE 0.018 0.002 PHE A 266 TRP 0.074 0.003 TRP D 267 HIS 0.003 0.001 HIS A 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (15000) covalent geometry : angle 0.68020 / 0.35 (20325) SS BOND : bond 0.00569 / 0.36 ( 5) SS BOND : angle 0.84689 / 0.40 ( 10) hydrogen bonds : bond 0.04349 / 2.89 ( 750) hydrogen bonds : angle 3.84533 / 2.66 ( 2565) link_NAG-ASN : bond 0.00248 / 0.15 ( 5) link_NAG-ASN : angle 1.56390 / 0.88 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 365 time to evaluate : 0.424 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 138 ASP cc_start: 0.7713 (p0) cc_final: 0.7325 (p0) REVERT: A 174 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8100 (mm110) REVERT: A 201 GLN cc_start: 0.7683 (mp10) cc_final: 0.7001 (mp10) REVERT: A 300 LYS cc_start: 0.9232 (mtmm) cc_final: 0.8899 (mmtm) REVERT: A 426 ASN cc_start: 0.9176 (m-40) cc_final: 0.8957 (m110) REVERT: B 105 ASP cc_start: 0.8931 (p0) cc_final: 0.8487 (p0) REVERT: B 138 ASP cc_start: 0.7677 (p0) cc_final: 0.7371 (p0) REVERT: B 140 LYS cc_start: 0.8922 (mttp) cc_final: 0.8642 (mttp) REVERT: B 174 GLN cc_start: 0.8401 (mp10) cc_final: 0.8046 (mm110) REVERT: B 201 GLN cc_start: 0.7771 (mp10) cc_final: 0.7097 (mp10) REVERT: B 221 TYR cc_start: 0.7455 (m-10) cc_final: 0.7187 (m-10) REVERT: B 287 MET cc_start: 0.9609 (mmm) cc_final: 0.9381 (mmp) REVERT: B 420 LEU cc_start: 0.9041 (tp) cc_final: 0.8827 (tp) REVERT: B 423 LEU cc_start: 0.9339 (tp) cc_final: 0.9024 (tt) REVERT: B 439 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7852 (tm-30) REVERT: C 81 ASP cc_start: 0.9271 (p0) cc_final: 0.8860 (p0) REVERT: C 177 ILE cc_start: 0.9285 (mm) cc_final: 0.8847 (mm) REVERT: C 201 GLN cc_start: 0.7695 (mp10) cc_final: 0.7256 (mp10) REVERT: C 221 TYR cc_start: 0.8113 (m-80) cc_final: 0.7875 (m-10) REVERT: C 422 PHE cc_start: 0.9482 (t80) cc_final: 0.9073 (t80) REVERT: C 426 ASN cc_start: 0.9021 (m-40) cc_final: 0.8385 (m-40) REVERT: C 439 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7709 (tm-30) REVERT: D 105 ASP cc_start: 0.9168 (p0) cc_final: 0.8834 (p0) REVERT: D 140 LYS cc_start: 0.9217 (mtpp) cc_final: 0.8948 (mtmm) REVERT: D 152 TYR cc_start: 0.8512 (t80) cc_final: 0.8290 (t80) REVERT: D 201 GLN cc_start: 0.7591 (mp10) cc_final: 0.6705 (mp10) REVERT: D 221 TYR cc_start: 0.7964 (m-80) cc_final: 0.7720 (m-10) REVERT: D 237 ARG cc_start: 0.9122 (mtt-85) cc_final: 0.8694 (mtt90) REVERT: D 243 GLN cc_start: 0.8781 (mp10) cc_final: 0.8409 (mp10) REVERT: D 251 MET cc_start: 0.9050 (mpp) cc_final: 0.8566 (mpp) REVERT: D 267 TRP cc_start: 0.6856 (m-90) cc_final: 0.6650 (m-90) REVERT: D 426 ASN cc_start: 0.9142 (m-40) cc_final: 0.8832 (m110) REVERT: D 439 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7435 (tm-30) REVERT: E 39 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8295 (p0) REVERT: E 174 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7994 (mm110) REVERT: E 201 GLN cc_start: 0.7712 (mp10) cc_final: 0.7246 (mp10) REVERT: E 422 PHE cc_start: 0.9424 (t80) cc_final: 0.9194 (t80) REVERT: E 426 ASN cc_start: 0.9046 (m-40) cc_final: 0.8742 (m110) REVERT: E 439 GLU cc_start: 0.8126 (pt0) cc_final: 0.7731 (tm-30) outliers start: 57 outliers final: 41 residues processed: 397 average time/residue: 0.0890 time to fit residues: 55.3210 Evaluate side-chains 391 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 347 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 267 TRP Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 269 ASN Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 107 optimal weight: 0.0870 chunk 42 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 141 optimal weight: 0.0010 chunk 106 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.9968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN B 90 GLN B 426 ASN ** C 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.115194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.091167 restraints weight = 32856.068| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.94 r_work: 0.3172 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15010 Z= 0.152 Angle : 0.679 12.792 20350 Z= 0.344 Chirality : 0.045 0.145 2290 Planarity : 0.004 0.043 2545 Dihedral : 4.564 32.487 1955 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.55 % Allowed : 18.32 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.19), residues: 1775 helix: 1.91 (0.19), residues: 700 sheet: 0.82 (0.27), residues: 380 loop : -1.88 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 83 TYR 0.031 0.002 TYR D 152 PHE 0.018 0.001 PHE B 266 TRP 0.065 0.003 TRP B 267 HIS 0.003 0.001 HIS A 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (15000) covalent geometry : angle 0.67820 / 0.34 (20325) SS BOND : bond 0.00430 / 0.29 ( 5) SS BOND : angle 1.07380 / 0.60 ( 10) hydrogen bonds : bond 0.04170 / 2.77 ( 750) hydrogen bonds : angle 3.77702 / 2.62 ( 2565) link_NAG-ASN : bond 0.00129 / 0.08 ( 5) link_NAG-ASN : angle 1.45708 / 0.82 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 353 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8076 (mm110) REVERT: A 187 MET cc_start: 0.8950 (mmm) cc_final: 0.8367 (tpp) REVERT: A 201 GLN cc_start: 0.7706 (mp10) cc_final: 0.7026 (mp10) REVERT: A 234 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8477 (mm) REVERT: A 300 LYS cc_start: 0.9204 (mtmm) cc_final: 0.8887 (mmtm) REVERT: A 426 ASN cc_start: 0.9154 (m-40) cc_final: 0.8845 (m110) REVERT: B 105 ASP cc_start: 0.8925 (p0) cc_final: 0.8461 (p0) REVERT: B 138 ASP cc_start: 0.7773 (p0) cc_final: 0.6386 (p0) REVERT: B 140 LYS cc_start: 0.8878 (mttp) cc_final: 0.8206 (mtmm) REVERT: B 174 GLN cc_start: 0.8475 (mp10) cc_final: 0.8126 (mm110) REVERT: B 201 GLN cc_start: 0.7787 (mp10) cc_final: 0.7390 (mp10) REVERT: B 263 TRP cc_start: 0.6725 (m-10) cc_final: 0.6459 (m-10) REVERT: B 287 MET cc_start: 0.9607 (mmm) cc_final: 0.9366 (mmp) REVERT: B 420 LEU cc_start: 0.9074 (tp) cc_final: 0.8846 (tp) REVERT: B 423 LEU cc_start: 0.9355 (tp) cc_final: 0.9063 (tt) REVERT: B 439 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7917 (tm-30) REVERT: C 81 ASP cc_start: 0.9220 (p0) cc_final: 0.8777 (p0) REVERT: C 177 ILE cc_start: 0.9286 (mm) cc_final: 0.8854 (mm) REVERT: C 422 PHE cc_start: 0.9501 (t80) cc_final: 0.9096 (t80) REVERT: C 426 ASN cc_start: 0.9027 (m-40) cc_final: 0.8416 (m-40) REVERT: C 439 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7860 (tm-30) REVERT: D 105 ASP cc_start: 0.9190 (p0) cc_final: 0.8839 (p0) REVERT: D 134 GLU cc_start: 0.7997 (pm20) cc_final: 0.7750 (pm20) REVERT: D 140 LYS cc_start: 0.9190 (mtpp) cc_final: 0.8980 (mtmm) REVERT: D 201 GLN cc_start: 0.7581 (mp10) cc_final: 0.6726 (mp10) REVERT: D 221 TYR cc_start: 0.8033 (m-80) cc_final: 0.7796 (m-10) REVERT: D 237 ARG cc_start: 0.9139 (mtt-85) cc_final: 0.8701 (mtt90) REVERT: D 243 GLN cc_start: 0.8825 (mp10) cc_final: 0.8456 (mp10) REVERT: D 251 MET cc_start: 0.9050 (mpp) cc_final: 0.8555 (mpp) REVERT: D 426 ASN cc_start: 0.9123 (m-40) cc_final: 0.8819 (m110) REVERT: D 439 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7621 (tm-30) REVERT: E 174 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.8029 (mm110) REVERT: E 251 MET cc_start: 0.9217 (mpp) cc_final: 0.8854 (mpp) REVERT: E 287 MET cc_start: 0.9547 (mmp) cc_final: 0.9332 (mmp) REVERT: E 422 PHE cc_start: 0.9449 (t80) cc_final: 0.9219 (t80) REVERT: E 426 ASN cc_start: 0.9028 (m-40) cc_final: 0.8720 (m110) REVERT: E 439 GLU cc_start: 0.8239 (pt0) cc_final: 0.7824 (tm-30) outliers start: 57 outliers final: 40 residues processed: 386 average time/residue: 0.0892 time to fit residues: 54.0247 Evaluate side-chains 385 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 342 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 267 TRP Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 75 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 15 optimal weight: 0.2980 chunk 119 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 GLN B 426 ASN C 90 GLN C 139 ASN ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.116385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.092382 restraints weight = 32972.659| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 4.02 r_work: 0.3183 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15010 Z= 0.137 Angle : 0.681 13.500 20350 Z= 0.343 Chirality : 0.045 0.150 2290 Planarity : 0.003 0.043 2545 Dihedral : 4.532 32.797 1955 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.93 % Allowed : 19.07 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.19), residues: 1775 helix: 1.90 (0.19), residues: 700 sheet: 0.85 (0.27), residues: 380 loop : -1.85 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.041 0.001 TYR D 152 PHE 0.015 0.001 PHE B 266 TRP 0.061 0.003 TRP E 267 HIS 0.002 0.001 HIS A 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (15000) covalent geometry : angle 0.68013 / 0.34 (20325) SS BOND : bond 0.00525 / 0.32 ( 5) SS BOND : angle 1.32586 / 0.67 ( 10) hydrogen bonds : bond 0.04002 / 2.66 ( 750) hydrogen bonds : angle 3.70935 / 2.58 ( 2565) link_NAG-ASN : bond 0.00030 / 0.02 ( 5) link_NAG-ASN : angle 1.30025 / 0.73 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 367 time to evaluate : 0.529 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 174 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8043 (mm110) REVERT: A 185 TYR cc_start: 0.9204 (m-80) cc_final: 0.8834 (m-80) REVERT: A 187 MET cc_start: 0.8960 (mmm) cc_final: 0.8387 (tpp) REVERT: A 201 GLN cc_start: 0.7800 (mp10) cc_final: 0.7151 (mp10) REVERT: A 234 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8416 (mm) REVERT: A 300 LYS cc_start: 0.9181 (mtmm) cc_final: 0.8865 (mmtm) REVERT: A 426 ASN cc_start: 0.9205 (m-40) cc_final: 0.8968 (m110) REVERT: B 105 ASP cc_start: 0.8936 (p0) cc_final: 0.8463 (p0) REVERT: B 138 ASP cc_start: 0.7786 (p0) cc_final: 0.7492 (p0) REVERT: B 140 LYS cc_start: 0.8868 (mttp) cc_final: 0.8600 (mttp) REVERT: B 174 GLN cc_start: 0.8483 (mp10) cc_final: 0.8130 (mm110) REVERT: B 201 GLN cc_start: 0.7735 (mp10) cc_final: 0.7353 (mp10) REVERT: B 287 MET cc_start: 0.9609 (mmm) cc_final: 0.9362 (mmp) REVERT: B 420 LEU cc_start: 0.9078 (tp) cc_final: 0.8859 (tp) REVERT: B 423 LEU cc_start: 0.9317 (tp) cc_final: 0.9018 (tt) REVERT: B 437 ARG cc_start: 0.6198 (ptt-90) cc_final: 0.5935 (ptp90) REVERT: B 439 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7933 (tm-30) REVERT: C 81 ASP cc_start: 0.9234 (p0) cc_final: 0.8714 (p0) REVERT: C 201 GLN cc_start: 0.7708 (mp10) cc_final: 0.7265 (mp10) REVERT: C 439 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7796 (tm-30) REVERT: D 105 ASP cc_start: 0.9194 (p0) cc_final: 0.8843 (p0) REVERT: D 134 GLU cc_start: 0.7983 (pm20) cc_final: 0.7704 (pm20) REVERT: D 201 GLN cc_start: 0.7550 (mp10) cc_final: 0.6697 (mp10) REVERT: D 221 TYR cc_start: 0.8026 (m-80) cc_final: 0.7809 (m-10) REVERT: D 235 GLU cc_start: 0.8845 (tt0) cc_final: 0.8159 (tm-30) REVERT: D 237 ARG cc_start: 0.9146 (mtt-85) cc_final: 0.8602 (mtp85) REVERT: D 243 GLN cc_start: 0.8801 (mp10) cc_final: 0.8431 (mp10) REVERT: D 251 MET cc_start: 0.9025 (mpp) cc_final: 0.8530 (mpp) REVERT: D 426 ASN cc_start: 0.9138 (m-40) cc_final: 0.8823 (m110) REVERT: D 439 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7623 (tm-30) REVERT: E 41 LEU cc_start: 0.8860 (tp) cc_final: 0.8658 (tp) REVERT: E 174 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.8024 (mm110) REVERT: E 251 MET cc_start: 0.9223 (mpp) cc_final: 0.8864 (mpp) REVERT: E 422 PHE cc_start: 0.9448 (t80) cc_final: 0.9216 (t80) REVERT: E 426 ASN cc_start: 0.9020 (m-40) cc_final: 0.8694 (m110) REVERT: E 439 GLU cc_start: 0.8203 (pt0) cc_final: 0.7873 (tm-30) outliers start: 47 outliers final: 42 residues processed: 392 average time/residue: 0.0906 time to fit residues: 55.4766 Evaluate side-chains 390 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 345 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 267 TRP Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 37 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 83 optimal weight: 0.0010 chunk 35 optimal weight: 0.0070 chunk 169 optimal weight: 2.9990 chunk 36 optimal weight: 0.0980 chunk 71 optimal weight: 0.0970 chunk 115 optimal weight: 3.9990 chunk 122 optimal weight: 0.0670 overall best weight: 0.0540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 139 ASN ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN C 290 GLN C 426 ASN D 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.118427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.094660 restraints weight = 32733.020| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 4.00 r_work: 0.3223 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15010 Z= 0.128 Angle : 0.708 14.845 20350 Z= 0.349 Chirality : 0.045 0.167 2290 Planarity : 0.003 0.042 2545 Dihedral : 4.407 34.113 1955 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.43 % Allowed : 20.06 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.19), residues: 1775 helix: 1.90 (0.19), residues: 700 sheet: 1.08 (0.27), residues: 370 loop : -1.84 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 83 TYR 0.032 0.001 TYR D 152 PHE 0.016 0.001 PHE C 425 TRP 0.057 0.003 TRP B 267 HIS 0.002 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (15000) covalent geometry : angle 0.70803 / 0.35 (20325) SS BOND : bond 0.00478 / 0.29 ( 5) SS BOND : angle 1.10399 / 0.54 ( 10) hydrogen bonds : bond 0.03785 / 2.50 ( 750) hydrogen bonds : angle 3.61055 / 2.50 ( 2565) link_NAG-ASN : bond 0.00304 / 0.18 ( 5) link_NAG-ASN : angle 0.79900 / 0.44 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 383 time to evaluate : 0.497 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 174 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8003 (mm110) REVERT: A 185 TYR cc_start: 0.9118 (m-80) cc_final: 0.8816 (m-80) REVERT: A 187 MET cc_start: 0.8913 (mmm) cc_final: 0.8304 (tpp) REVERT: A 201 GLN cc_start: 0.7772 (mp10) cc_final: 0.7126 (mp10) REVERT: A 426 ASN cc_start: 0.9214 (m-40) cc_final: 0.8972 (m110) REVERT: B 105 ASP cc_start: 0.8997 (p0) cc_final: 0.8577 (p0) REVERT: B 138 ASP cc_start: 0.7702 (p0) cc_final: 0.7404 (p0) REVERT: B 140 LYS cc_start: 0.8869 (mttp) cc_final: 0.8615 (mttp) REVERT: B 174 GLN cc_start: 0.8439 (mp10) cc_final: 0.8080 (mm110) REVERT: B 185 TYR cc_start: 0.9171 (m-80) cc_final: 0.8853 (m-80) REVERT: B 201 GLN cc_start: 0.7600 (mp10) cc_final: 0.7233 (mp10) REVERT: B 287 MET cc_start: 0.9607 (mmm) cc_final: 0.9365 (mmp) REVERT: B 420 LEU cc_start: 0.8951 (tp) cc_final: 0.8738 (tp) REVERT: B 423 LEU cc_start: 0.9322 (tp) cc_final: 0.9029 (tt) REVERT: B 439 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7855 (tm-30) REVERT: C 81 ASP cc_start: 0.9264 (p0) cc_final: 0.8792 (p0) REVERT: C 177 ILE cc_start: 0.9251 (mm) cc_final: 0.8769 (mm) REVERT: C 201 GLN cc_start: 0.7562 (mp10) cc_final: 0.7147 (mp10) REVERT: C 439 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7818 (tm-30) REVERT: D 105 ASP cc_start: 0.9226 (p0) cc_final: 0.8873 (p0) REVERT: D 134 GLU cc_start: 0.7987 (pm20) cc_final: 0.7683 (pm20) REVERT: D 140 LYS cc_start: 0.9102 (mtmm) cc_final: 0.8767 (ptpp) REVERT: D 201 GLN cc_start: 0.7412 (mp10) cc_final: 0.6575 (mp10) REVERT: D 221 TYR cc_start: 0.7962 (m-80) cc_final: 0.7758 (m-10) REVERT: D 235 GLU cc_start: 0.8865 (tt0) cc_final: 0.8228 (tm-30) REVERT: D 237 ARG cc_start: 0.9144 (mtt-85) cc_final: 0.8734 (mtp85) REVERT: D 243 GLN cc_start: 0.8737 (mp10) cc_final: 0.8370 (mp10) REVERT: D 251 MET cc_start: 0.9002 (mpp) cc_final: 0.8496 (mpp) REVERT: D 308 ASP cc_start: 0.9253 (m-30) cc_final: 0.9041 (m-30) REVERT: D 426 ASN cc_start: 0.9126 (m-40) cc_final: 0.8799 (m110) REVERT: D 439 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7647 (tm-30) REVERT: E 174 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.8000 (mm110) REVERT: E 251 MET cc_start: 0.9207 (mpp) cc_final: 0.8895 (mpp) REVERT: E 422 PHE cc_start: 0.9412 (t80) cc_final: 0.9176 (t80) REVERT: E 426 ASN cc_start: 0.9004 (m-40) cc_final: 0.8675 (m110) REVERT: E 439 GLU cc_start: 0.8211 (pt0) cc_final: 0.7814 (tm-30) outliers start: 39 outliers final: 30 residues processed: 404 average time/residue: 0.0923 time to fit residues: 58.0086 Evaluate side-chains 388 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 356 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 267 TRP Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 130 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 167 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 23 optimal weight: 0.0000 chunk 138 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN B 426 ASN C 139 ASN ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN ** C 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.117913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.093953 restraints weight = 33018.258| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 4.00 r_work: 0.3217 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15010 Z= 0.133 Angle : 0.731 14.427 20350 Z= 0.357 Chirality : 0.045 0.188 2290 Planarity : 0.004 0.041 2545 Dihedral : 4.425 33.526 1955 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.18 % Allowed : 21.06 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.19), residues: 1775 helix: 1.80 (0.19), residues: 700 sheet: 0.93 (0.27), residues: 380 loop : -1.82 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 437 TYR 0.047 0.001 TYR E 152 PHE 0.034 0.001 PHE B 72 TRP 0.059 0.003 TRP A 267 HIS 0.002 0.001 HIS E 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (15000) covalent geometry : angle 0.73036 / 0.36 (20325) SS BOND : bond 0.00447 / 0.28 ( 5) SS BOND : angle 0.97369 / 0.45 ( 10) hydrogen bonds : bond 0.03724 / 2.47 ( 750) hydrogen bonds : angle 3.65777 / 2.53 ( 2565) link_NAG-ASN : bond 0.00013 / 0.01 ( 5) link_NAG-ASN : angle 1.10893 / 0.62 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 369 time to evaluate : 0.440 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 126 ASN cc_start: 0.8353 (p0) cc_final: 0.7868 (p0) REVERT: A 174 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8036 (mm110) REVERT: A 187 MET cc_start: 0.8918 (mmm) cc_final: 0.8695 (tpp) REVERT: A 201 GLN cc_start: 0.7807 (mp10) cc_final: 0.7154 (mp10) REVERT: A 426 ASN cc_start: 0.9226 (m-40) cc_final: 0.8991 (m110) REVERT: B 105 ASP cc_start: 0.9003 (p0) cc_final: 0.8558 (p0) REVERT: B 138 ASP cc_start: 0.7761 (p0) cc_final: 0.7464 (p0) REVERT: B 140 LYS cc_start: 0.8930 (mttp) cc_final: 0.8677 (mttp) REVERT: B 174 GLN cc_start: 0.8461 (mp10) cc_final: 0.8117 (mm110) REVERT: B 181 GLU cc_start: 0.8308 (mp0) cc_final: 0.8035 (mp0) REVERT: B 185 TYR cc_start: 0.9148 (m-80) cc_final: 0.8885 (m-80) REVERT: B 201 GLN cc_start: 0.7676 (mp10) cc_final: 0.7299 (mp10) REVERT: B 287 MET cc_start: 0.9593 (mmm) cc_final: 0.9373 (mmp) REVERT: B 420 LEU cc_start: 0.8959 (tp) cc_final: 0.8728 (tp) REVERT: B 423 LEU cc_start: 0.9313 (tp) cc_final: 0.9013 (tt) REVERT: B 437 ARG cc_start: 0.6083 (ptt-90) cc_final: 0.5801 (ptt-90) REVERT: B 439 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7966 (tm-30) REVERT: C 81 ASP cc_start: 0.9215 (p0) cc_final: 0.8736 (p0) REVERT: C 177 ILE cc_start: 0.9225 (mm) cc_final: 0.8744 (mm) REVERT: C 201 GLN cc_start: 0.7628 (mp10) cc_final: 0.7205 (mp10) REVERT: C 237 ARG cc_start: 0.8965 (mtt-85) cc_final: 0.8730 (mtt-85) REVERT: C 439 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7803 (tm-30) REVERT: D 105 ASP cc_start: 0.9234 (p0) cc_final: 0.8927 (p0) REVERT: D 140 LYS cc_start: 0.9085 (mtmm) cc_final: 0.8593 (ptpp) REVERT: D 201 GLN cc_start: 0.7409 (mp10) cc_final: 0.6504 (mp10) REVERT: D 221 TYR cc_start: 0.7973 (m-80) cc_final: 0.7762 (m-10) REVERT: D 235 GLU cc_start: 0.8866 (tt0) cc_final: 0.8290 (tm-30) REVERT: D 237 ARG cc_start: 0.9147 (mtt-85) cc_final: 0.8934 (mtp85) REVERT: D 243 GLN cc_start: 0.8737 (mp10) cc_final: 0.8361 (mp10) REVERT: D 251 MET cc_start: 0.9014 (mpp) cc_final: 0.8497 (mpp) REVERT: D 263 TRP cc_start: 0.6476 (m-10) cc_final: 0.6102 (m-10) REVERT: D 426 ASN cc_start: 0.9136 (m-40) cc_final: 0.8805 (m110) REVERT: D 439 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7666 (tm-30) REVERT: E 174 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.8017 (mm110) REVERT: E 237 ARG cc_start: 0.9240 (mtp85) cc_final: 0.8557 (mtt-85) REVERT: E 251 MET cc_start: 0.9237 (mpp) cc_final: 0.8866 (mpp) REVERT: E 422 PHE cc_start: 0.9402 (t80) cc_final: 0.9169 (t80) REVERT: E 426 ASN cc_start: 0.9011 (m-40) cc_final: 0.8662 (m110) REVERT: E 439 GLU cc_start: 0.8227 (pt0) cc_final: 0.7892 (tm-30) outliers start: 35 outliers final: 30 residues processed: 390 average time/residue: 0.0858 time to fit residues: 51.8836 Evaluate side-chains 387 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 355 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 267 TRP Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 39 optimal weight: 2.9990 chunk 105 optimal weight: 0.2980 chunk 38 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 172 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 90 GLN C 139 ASN ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN ** C 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.117256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.093246 restraints weight = 32993.024| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 4.02 r_work: 0.3213 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15010 Z= 0.138 Angle : 0.734 14.346 20350 Z= 0.357 Chirality : 0.045 0.195 2290 Planarity : 0.003 0.037 2545 Dihedral : 4.434 35.124 1955 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.12 % Allowed : 20.93 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.19), residues: 1775 helix: 1.79 (0.19), residues: 700 sheet: 0.84 (0.27), residues: 390 loop : -1.79 (0.21), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 437 TYR 0.040 0.002 TYR E 152 PHE 0.030 0.001 PHE B 72 TRP 0.058 0.003 TRP A 267 HIS 0.002 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (15000) covalent geometry : angle 0.73290 / 0.36 (20325) SS BOND : bond 0.00539 / 0.32 ( 5) SS BOND : angle 1.10775 / 0.56 ( 10) hydrogen bonds : bond 0.03661 / 2.43 ( 750) hydrogen bonds : angle 3.66731 / 2.55 ( 2565) link_NAG-ASN : bond 0.00034 / 0.02 ( 5) link_NAG-ASN : angle 1.21631 / 0.69 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3068.73 seconds wall clock time: 53 minutes 26.35 seconds (3206.35 seconds total)