Starting phenix.real_space_refine on Wed Mar 4 15:57:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m6p_23703/03_2026/7m6p_23703.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m6p_23703/03_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_23703/03_2026/7m6p_23703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m6p_23703/03_2026/7m6p_23703.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m6p_23703/03_2026/7m6p_23703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m6p_23703/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.47, per 1000 atoms: 0.24 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: 1.33 Conformation dependent library (CDL) restraints added in 528.0 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: 0.54 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: 2.51 Time building geometry restraints manager: 1.71 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: 8329 17.22 - 34.44: 579 34.44 - 51.66: 112 51.66 - 68.88: 20 68.88 - 86.11: 10 Dihedral angle restraints: 9050 sinusoidal: 3740 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 9047 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: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.770 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 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 : 12.688 86.106 5585 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 covalent geometry : bond 0.00804 (15000) covalent geometry : angle 1.26969 (20325) SS BOND : bond 0.00668 ( 5) SS BOND : angle 0.75276 ( 10) hydrogen bonds : bond 0.18857 ( 750) hydrogen bonds : angle 6.47530 ( 2565) link_NAG-ASN : bond 0.00257 ( 5) link_NAG-ASN : angle 2.71776 ( 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 : 0.587 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: 0.1136 time to fit residues: 96.4500 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 : 0.554 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 250 GLN 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.117197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.093348 restraints weight = 32745.649| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.96 r_work: 0.3183 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15010 Z= 0.182 Angle : 0.769 9.410 20350 Z= 0.406 Chirality : 0.049 0.219 2290 Planarity : 0.005 0.046 2545 Dihedral : 5.147 23.150 2060 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.43 % Allowed : 13.58 % Favored : 83.99 % 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: 0.75 (0.27), residues: 380 loop : -1.98 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 400 TYR 0.018 0.002 TYR B 433 PHE 0.037 0.002 PHE B 266 TRP 0.040 0.003 TRP C 267 HIS 0.006 0.001 HIS E 239 Details of bonding type rmsd covalent geometry : bond 0.00399 (15000) covalent geometry : angle 0.76723 (20325) SS BOND : bond 0.00575 ( 5) SS BOND : angle 1.34946 ( 10) hydrogen bonds : bond 0.06564 ( 750) hydrogen bonds : angle 4.61636 ( 2565) link_NAG-ASN : bond 0.00022 ( 5) link_NAG-ASN : angle 1.71046 ( 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 448 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 409 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.8273 (p0) REVERT: A 138 ASP cc_start: 0.7647 (p0) cc_final: 0.7275 (p0) REVERT: A 174 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8058 (mm110) REVERT: A 439 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7492 (tm-30) REVERT: B 105 ASP cc_start: 0.8972 (p0) cc_final: 0.8669 (p0) REVERT: B 113 MET cc_start: 0.8909 (ppp) cc_final: 0.8595 (ppp) REVERT: B 114 LEU cc_start: 0.9299 (mt) cc_final: 0.9007 (tp) REVERT: B 115 ASP cc_start: 0.8988 (p0) cc_final: 0.8787 (p0) REVERT: B 138 ASP cc_start: 0.7255 (p0) cc_final: 0.6808 (p0) REVERT: B 140 LYS cc_start: 0.8971 (mttp) cc_final: 0.8424 (mtmm) REVERT: B 174 GLN cc_start: 0.8423 (mp10) cc_final: 0.8152 (mm110) REVERT: B 201 GLN cc_start: 0.7815 (mp10) cc_final: 0.7263 (mp10) REVERT: B 287 MET cc_start: 0.9586 (mmm) cc_final: 0.9343 (mmp) REVERT: B 420 LEU cc_start: 0.9081 (tp) cc_final: 0.8852 (tp) REVERT: B 422 PHE cc_start: 0.9338 (t80) cc_final: 0.9128 (t80) REVERT: B 423 LEU cc_start: 0.9303 (tp) cc_final: 0.9079 (tt) REVERT: B 426 ASN cc_start: 0.8985 (m-40) cc_final: 0.8592 (m-40) REVERT: B 439 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7630 (tm-30) REVERT: C 39 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8409 (p0) REVERT: C 81 ASP cc_start: 0.9060 (p0) cc_final: 0.8818 (p0) REVERT: C 121 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8181 (p0) REVERT: C 140 LYS cc_start: 0.8934 (mttp) cc_final: 0.8710 (mttp) REVERT: C 210 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8254 (tp-100) REVERT: C 221 TYR cc_start: 0.7734 (m-80) cc_final: 0.7491 (m-10) REVERT: C 300 LYS cc_start: 0.9415 (mttp) cc_final: 0.9052 (mtmm) REVERT: C 426 ASN cc_start: 0.8993 (m-40) cc_final: 0.8768 (m110) REVERT: C 439 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7832 (tm-30) REVERT: D 94 ASP cc_start: 0.8488 (t0) cc_final: 0.8171 (t70) REVERT: D 105 ASP cc_start: 0.9189 (p0) cc_final: 0.8980 (p0) REVERT: D 138 ASP cc_start: 0.7716 (p0) cc_final: 0.6941 (p0) REVERT: D 140 LYS cc_start: 0.9187 (mtpp) cc_final: 0.8649 (mtmm) REVERT: D 243 GLN cc_start: 0.8851 (mp10) cc_final: 0.8544 (mp10) REVERT: D 308 ASP cc_start: 0.9320 (m-30) cc_final: 0.9108 (m-30) REVERT: D 311 MET cc_start: 0.9609 (mmt) cc_final: 0.9406 (mmm) REVERT: D 426 ASN cc_start: 0.9072 (m-40) cc_final: 0.8716 (m110) REVERT: E 39 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8274 (p0) REVERT: E 138 ASP cc_start: 0.7833 (p0) cc_final: 0.7526 (p0) REVERT: E 140 LYS cc_start: 0.8925 (mttp) cc_final: 0.8427 (mtpp) REVERT: E 174 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7931 (mm110) REVERT: E 251 MET cc_start: 0.9122 (mpp) cc_final: 0.8714 (mpp) REVERT: E 270 MET cc_start: 0.7610 (tpp) cc_final: 0.7203 (mmt) REVERT: E 287 MET cc_start: 0.9509 (mmm) cc_final: 0.9308 (mmp) REVERT: E 300 LYS cc_start: 0.9243 (mtmm) cc_final: 0.8786 (mmtm) outliers start: 39 outliers final: 18 residues processed: 434 average time/residue: 0.1008 time to fit residues: 68.4164 Evaluate side-chains 391 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 366 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 121 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 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: 3.9990 chunk 57 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 104 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.115490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.091201 restraints weight = 32965.383| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 4.10 r_work: 0.3165 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15010 Z= 0.179 Angle : 0.702 9.147 20350 Z= 0.367 Chirality : 0.047 0.198 2290 Planarity : 0.004 0.058 2545 Dihedral : 4.883 25.676 2060 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.99 % Allowed : 14.83 % Favored : 82.18 % 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: 0.26 (0.19), residues: 1775 helix: 1.76 (0.18), residues: 700 sheet: 0.77 (0.27), residues: 380 loop : -1.93 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 83 TYR 0.017 0.002 TYR B 429 PHE 0.029 0.002 PHE C 266 TRP 0.058 0.003 TRP E 267 HIS 0.004 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00401 (15000) covalent geometry : angle 0.70098 (20325) SS BOND : bond 0.00648 ( 5) SS BOND : angle 0.66152 ( 10) hydrogen bonds : bond 0.05560 ( 750) hydrogen bonds : angle 4.25589 ( 2565) link_NAG-ASN : bond 0.00257 ( 5) link_NAG-ASN : angle 1.83477 ( 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 433 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 385 time to evaluate : 0.577 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 39 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8234 (p0) REVERT: A 105 ASP cc_start: 0.8903 (p0) cc_final: 0.8631 (p0) REVERT: A 115 ASP cc_start: 0.9008 (p0) cc_final: 0.8729 (p0) REVERT: A 138 ASP cc_start: 0.7751 (p0) cc_final: 0.7375 (p0) REVERT: A 174 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8091 (mm110) REVERT: A 270 MET cc_start: 0.7556 (tpp) cc_final: 0.7009 (tmm) REVERT: A 426 ASN cc_start: 0.9144 (m-40) cc_final: 0.8777 (m110) REVERT: B 105 ASP cc_start: 0.9009 (p0) cc_final: 0.8629 (p0) REVERT: B 113 MET cc_start: 0.8912 (ppp) cc_final: 0.8709 (ppp) REVERT: B 138 ASP cc_start: 0.7478 (p0) cc_final: 0.6577 (p0) REVERT: B 140 LYS cc_start: 0.8922 (mttp) cc_final: 0.8270 (mtmm) REVERT: B 174 GLN cc_start: 0.8516 (mp10) cc_final: 0.8219 (mm110) REVERT: B 201 GLN cc_start: 0.7819 (mp10) cc_final: 0.7214 (mp10) REVERT: B 221 TYR cc_start: 0.7728 (m-80) cc_final: 0.7499 (m-10) REVERT: B 270 MET cc_start: 0.7619 (tpp) cc_final: 0.7004 (tmm) REVERT: B 287 MET cc_start: 0.9591 (mmm) cc_final: 0.9354 (mmp) REVERT: B 420 LEU cc_start: 0.9079 (tp) cc_final: 0.8864 (tp) REVERT: B 423 LEU cc_start: 0.9322 (tp) cc_final: 0.9052 (tt) REVERT: B 426 ASN cc_start: 0.9037 (m-40) cc_final: 0.8674 (m-40) REVERT: B 439 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7740 (tm-30) REVERT: C 39 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8435 (p0) REVERT: C 81 ASP cc_start: 0.9169 (p0) cc_final: 0.8856 (p0) REVERT: C 140 LYS cc_start: 0.8883 (mttp) cc_final: 0.8657 (mttp) REVERT: C 177 ILE cc_start: 0.9288 (mm) cc_final: 0.8904 (mm) REVERT: C 221 TYR cc_start: 0.7976 (m-80) cc_final: 0.7752 (m-10) REVERT: C 300 LYS cc_start: 0.9354 (mttp) cc_final: 0.9074 (mtmm) REVERT: C 422 PHE cc_start: 0.9424 (t80) cc_final: 0.9004 (t80) REVERT: C 426 ASN cc_start: 0.9029 (m-40) cc_final: 0.8455 (m-40) REVERT: C 439 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7761 (tm-30) REVERT: D 94 ASP cc_start: 0.8476 (t0) cc_final: 0.8237 (t70) REVERT: D 105 ASP cc_start: 0.9201 (p0) cc_final: 0.8931 (p0) REVERT: D 138 ASP cc_start: 0.7954 (p0) cc_final: 0.7253 (p0) REVERT: D 140 LYS cc_start: 0.9243 (mtpp) cc_final: 0.8712 (mtmm) REVERT: D 237 ARG cc_start: 0.9056 (mtt-85) cc_final: 0.8773 (mtp85) REVERT: D 243 GLN cc_start: 0.8837 (mp10) cc_final: 0.8578 (mp10) REVERT: D 300 LYS cc_start: 0.9203 (mtmm) cc_final: 0.8926 (mmtp) REVERT: D 439 GLU cc_start: 0.7514 (tm-30) cc_final: 0.7269 (tm-30) REVERT: E 39 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8311 (p0) REVERT: E 138 ASP cc_start: 0.7873 (p0) cc_final: 0.7592 (p0) REVERT: E 174 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7967 (mm110) REVERT: E 251 MET cc_start: 0.9287 (mpp) cc_final: 0.8893 (mpp) REVERT: E 270 MET cc_start: 0.7789 (tpp) cc_final: 0.7277 (mmt) REVERT: E 287 MET cc_start: 0.9480 (mmm) cc_final: 0.9267 (mmp) REVERT: E 308 ASP cc_start: 0.9317 (m-30) cc_final: 0.9060 (m-30) REVERT: E 426 ASN cc_start: 0.9024 (m-40) cc_final: 0.8580 (m110) outliers start: 48 outliers final: 34 residues processed: 416 average time/residue: 0.1028 time to fit residues: 67.0272 Evaluate side-chains 386 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 347 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET 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 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 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 320 SER Chi-restraints excluded: chain D residue 32 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 290 GLN Chi-restraints excluded: chain D residue 307 ILE 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 277 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 53 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 chunk 111 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 85 optimal weight: 0.0870 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN B 210 GLN D 290 GLN E 210 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 = 0.115548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.091297 restraints weight = 32813.329| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 3.95 r_work: 0.3177 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15010 Z= 0.155 Angle : 0.673 10.510 20350 Z= 0.349 Chirality : 0.046 0.171 2290 Planarity : 0.004 0.048 2545 Dihedral : 4.731 29.031 2060 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.87 % Allowed : 16.14 % Favored : 81.00 % 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: 0.40 (0.19), residues: 1775 helix: 2.14 (0.18), residues: 670 sheet: 0.71 (0.26), residues: 380 loop : -1.91 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 83 TYR 0.015 0.002 TYR A 429 PHE 0.026 0.002 PHE A 266 TRP 0.064 0.003 TRP E 267 HIS 0.003 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00346 (15000) covalent geometry : angle 0.67154 (20325) SS BOND : bond 0.00873 ( 5) SS BOND : angle 1.23968 ( 10) hydrogen bonds : bond 0.05005 ( 750) hydrogen bonds : angle 4.06310 ( 2565) link_NAG-ASN : bond 0.00075 ( 5) link_NAG-ASN : angle 1.51618 ( 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 421 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 375 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.8320 (p0) REVERT: A 115 ASP cc_start: 0.8980 (p0) cc_final: 0.8709 (p0) REVERT: A 138 ASP cc_start: 0.7797 (p0) cc_final: 0.7396 (p0) REVERT: A 174 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8054 (mm110) REVERT: A 201 GLN cc_start: 0.7553 (mp10) cc_final: 0.6892 (mp10) REVERT: A 300 LYS cc_start: 0.9150 (mtmm) cc_final: 0.8762 (mmtm) REVERT: A 426 ASN cc_start: 0.9163 (m-40) cc_final: 0.8891 (m110) REVERT: B 105 ASP cc_start: 0.9013 (p0) cc_final: 0.8641 (p0) REVERT: B 138 ASP cc_start: 0.7598 (p0) cc_final: 0.7344 (p0) REVERT: B 140 LYS cc_start: 0.8865 (mttp) cc_final: 0.8599 (mttp) REVERT: B 174 GLN cc_start: 0.8522 (mp10) cc_final: 0.8216 (mm110) REVERT: B 201 GLN cc_start: 0.7774 (mp10) cc_final: 0.7137 (mp10) REVERT: B 221 TYR cc_start: 0.7791 (m-80) cc_final: 0.7586 (m-10) REVERT: B 287 MET cc_start: 0.9613 (mmm) cc_final: 0.9392 (mmp) REVERT: B 420 LEU cc_start: 0.9027 (tp) cc_final: 0.8815 (tp) REVERT: B 423 LEU cc_start: 0.9327 (tp) cc_final: 0.9037 (tt) REVERT: B 426 ASN cc_start: 0.9003 (m-40) cc_final: 0.8788 (m110) REVERT: B 439 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7814 (tm-30) REVERT: C 39 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8437 (p0) REVERT: C 81 ASP cc_start: 0.9183 (p0) cc_final: 0.8849 (p0) REVERT: C 177 ILE cc_start: 0.9262 (mm) cc_final: 0.8828 (mm) REVERT: C 201 GLN cc_start: 0.7616 (mp10) cc_final: 0.7341 (mp10) REVERT: C 221 TYR cc_start: 0.7952 (m-80) cc_final: 0.7728 (m-10) REVERT: C 263 TRP cc_start: 0.7469 (m-10) cc_final: 0.7247 (m-10) REVERT: C 422 PHE cc_start: 0.9428 (t80) cc_final: 0.8954 (t80) REVERT: C 426 ASN cc_start: 0.9033 (m-40) cc_final: 0.8390 (m-40) REVERT: C 439 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7805 (tm-30) REVERT: D 80 MET cc_start: 0.8956 (tpp) cc_final: 0.8645 (tpp) REVERT: D 105 ASP cc_start: 0.9153 (p0) cc_final: 0.8836 (p0) REVERT: D 140 LYS cc_start: 0.9259 (mtpp) cc_final: 0.9000 (mtpp) REVERT: D 201 GLN cc_start: 0.7499 (mp10) cc_final: 0.6607 (mp10) REVERT: D 237 ARG cc_start: 0.9040 (mtt-85) cc_final: 0.8815 (mtp85) REVERT: D 243 GLN cc_start: 0.8878 (mp10) cc_final: 0.8532 (mp10) REVERT: D 251 MET cc_start: 0.8972 (mpp) cc_final: 0.8479 (mpp) REVERT: D 300 LYS cc_start: 0.9205 (mtmm) cc_final: 0.8933 (mmtp) REVERT: D 311 MET cc_start: 0.9495 (mmm) cc_final: 0.9288 (mmm) REVERT: D 439 GLU cc_start: 0.7551 (tm-30) cc_final: 0.7256 (tm-30) REVERT: E 39 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8300 (p0) REVERT: E 41 LEU cc_start: 0.8881 (tp) cc_final: 0.8627 (tp) REVERT: E 138 ASP cc_start: 0.7922 (p0) cc_final: 0.7612 (p0) REVERT: E 174 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7981 (mm110) REVERT: E 251 MET cc_start: 0.9185 (mpp) cc_final: 0.8800 (mpp) REVERT: E 287 MET cc_start: 0.9512 (mmm) cc_final: 0.9286 (mmp) REVERT: E 308 ASP cc_start: 0.9226 (m-30) cc_final: 0.9013 (m-30) REVERT: E 422 PHE cc_start: 0.9393 (t80) cc_final: 0.9175 (t80) REVERT: E 426 ASN cc_start: 0.9013 (m-40) cc_final: 0.8740 (m110) outliers start: 46 outliers final: 32 residues processed: 404 average time/residue: 0.1009 time to fit residues: 64.1359 Evaluate side-chains 390 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 353 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET 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 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 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 45 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 290 GLN Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 416 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 15 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 153 optimal weight: 0.3980 chunk 113 optimal weight: 0.9980 chunk 157 optimal weight: 0.0030 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 GLN D 290 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.115435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.091105 restraints weight = 32753.315| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 3.97 r_work: 0.3171 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3690 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= 0.149 Angle : 0.671 10.921 20350 Z= 0.343 Chirality : 0.045 0.178 2290 Planarity : 0.004 0.047 2545 Dihedral : 4.621 30.795 2060 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.18 % Allowed : 16.82 % Favored : 80.00 % 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: 2.17 (0.18), residues: 670 sheet: 0.74 (0.26), residues: 390 loop : -1.95 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 83 TYR 0.025 0.002 TYR D 152 PHE 0.023 0.002 PHE C 266 TRP 0.074 0.003 TRP A 267 HIS 0.003 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00333 (15000) covalent geometry : angle 0.66932 (20325) SS BOND : bond 0.01261 ( 5) SS BOND : angle 1.24946 ( 10) hydrogen bonds : bond 0.04679 ( 750) hydrogen bonds : angle 3.92525 ( 2565) link_NAG-ASN : bond 0.00125 ( 5) link_NAG-ASN : angle 1.50083 ( 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 422 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 371 time to evaluate : 0.547 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 39 ASP cc_start: 0.8475 (OUTLIER) cc_final: 0.8263 (p0) REVERT: A 138 ASP cc_start: 0.7803 (p0) cc_final: 0.7362 (p0) REVERT: A 174 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8038 (mm110) REVERT: A 201 GLN cc_start: 0.7550 (mp10) cc_final: 0.6926 (mp10) REVERT: A 300 LYS cc_start: 0.9149 (mtmm) cc_final: 0.8881 (mmtm) REVERT: A 426 ASN cc_start: 0.9153 (m-40) cc_final: 0.8861 (m110) REVERT: B 105 ASP cc_start: 0.8950 (p0) cc_final: 0.8516 (p0) REVERT: B 138 ASP cc_start: 0.7664 (p0) cc_final: 0.7372 (p0) REVERT: B 140 LYS cc_start: 0.8888 (mttp) cc_final: 0.8618 (mttp) REVERT: B 174 GLN cc_start: 0.8516 (mp10) cc_final: 0.8197 (mm110) REVERT: B 201 GLN cc_start: 0.7728 (mp10) cc_final: 0.7069 (mp10) REVERT: B 287 MET cc_start: 0.9593 (mmm) cc_final: 0.9378 (mmp) REVERT: B 420 LEU cc_start: 0.9008 (tp) cc_final: 0.8790 (tp) REVERT: B 423 LEU cc_start: 0.9320 (tp) cc_final: 0.9013 (tt) REVERT: B 439 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7811 (tm-30) REVERT: C 39 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8432 (p0) REVERT: C 81 ASP cc_start: 0.9139 (p0) cc_final: 0.8777 (p0) REVERT: C 177 ILE cc_start: 0.9263 (mm) cc_final: 0.8593 (mm) REVERT: C 201 GLN cc_start: 0.7615 (mp10) cc_final: 0.7206 (mp10) REVERT: C 221 TYR cc_start: 0.8039 (m-80) cc_final: 0.7836 (m-10) REVERT: C 235 GLU cc_start: 0.8695 (tt0) cc_final: 0.8478 (tt0) REVERT: C 263 TRP cc_start: 0.7275 (m-10) cc_final: 0.7073 (m-10) REVERT: C 422 PHE cc_start: 0.9452 (t80) cc_final: 0.8979 (t80) REVERT: C 426 ASN cc_start: 0.9032 (m-40) cc_final: 0.8391 (m-40) REVERT: C 439 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7708 (tm-30) REVERT: D 80 MET cc_start: 0.9022 (tpp) cc_final: 0.8656 (tpp) REVERT: D 105 ASP cc_start: 0.9161 (p0) cc_final: 0.8836 (p0) REVERT: D 140 LYS cc_start: 0.9229 (mtpp) cc_final: 0.8895 (mtmm) REVERT: D 201 GLN cc_start: 0.7495 (mp10) cc_final: 0.6631 (mp10) REVERT: D 237 ARG cc_start: 0.9038 (mtt-85) cc_final: 0.8834 (mtp85) REVERT: D 243 GLN cc_start: 0.8829 (mp10) cc_final: 0.8486 (mp10) REVERT: D 251 MET cc_start: 0.9009 (mpp) cc_final: 0.8529 (mpp) REVERT: D 270 MET cc_start: 0.6889 (mmt) cc_final: 0.6390 (tmm) REVERT: D 300 LYS cc_start: 0.9192 (mtmm) cc_final: 0.8881 (mmtp) REVERT: D 439 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7397 (tm-30) REVERT: E 39 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8270 (p0) REVERT: E 41 LEU cc_start: 0.8862 (tp) cc_final: 0.8622 (tp) REVERT: E 90 GLN cc_start: 0.8716 (pt0) cc_final: 0.8294 (mt0) REVERT: E 138 ASP cc_start: 0.7919 (p0) cc_final: 0.7633 (p0) REVERT: E 174 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7938 (mm110) REVERT: E 251 MET cc_start: 0.9214 (mpp) cc_final: 0.8812 (mpp) REVERT: E 287 MET cc_start: 0.9513 (mmm) cc_final: 0.9266 (mmp) REVERT: E 422 PHE cc_start: 0.9417 (t80) cc_final: 0.9184 (t80) REVERT: E 426 ASN cc_start: 0.9024 (m-40) cc_final: 0.8755 (m110) REVERT: E 439 GLU cc_start: 0.8108 (pt0) cc_final: 0.7697 (tm-30) outliers start: 51 outliers final: 35 residues processed: 401 average time/residue: 0.0987 time to fit residues: 62.6435 Evaluate side-chains 396 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 356 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET 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 A residue 290 GLN 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 267 TRP 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 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 290 GLN Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 416 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 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: 3.9990 chunk 137 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 76 optimal weight: 0.0170 chunk 131 optimal weight: 0.0980 chunk 94 optimal weight: 4.9990 chunk 115 optimal weight: 0.2980 chunk 61 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.117330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.093397 restraints weight = 32658.045| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.99 r_work: 0.3194 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15010 Z= 0.128 Angle : 0.666 12.831 20350 Z= 0.338 Chirality : 0.045 0.160 2290 Planarity : 0.003 0.041 2545 Dihedral : 4.448 33.002 2060 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.99 % Allowed : 17.51 % Favored : 79.50 % 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: 2.23 (0.18), residues: 670 sheet: 0.82 (0.27), residues: 380 loop : -1.89 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 295 TYR 0.037 0.001 TYR D 152 PHE 0.019 0.001 PHE D 266 TRP 0.076 0.003 TRP B 267 HIS 0.002 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00280 (15000) covalent geometry : angle 0.66551 (20325) SS BOND : bond 0.01223 ( 5) SS BOND : angle 0.66047 ( 10) hydrogen bonds : bond 0.04370 ( 750) hydrogen bonds : angle 3.77644 ( 2565) link_NAG-ASN : bond 0.00103 ( 5) link_NAG-ASN : angle 1.18600 ( 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 430 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 382 time to evaluate : 0.587 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 39 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8201 (p0) REVERT: A 105 ASP cc_start: 0.8873 (p0) cc_final: 0.8653 (p0) REVERT: A 119 LYS cc_start: 0.9326 (mtmm) cc_final: 0.9044 (mtmm) REVERT: A 138 ASP cc_start: 0.7805 (p0) cc_final: 0.7402 (p0) REVERT: A 174 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8011 (mm110) REVERT: A 201 GLN cc_start: 0.7421 (mp10) cc_final: 0.6876 (mp10) REVERT: A 300 LYS cc_start: 0.9199 (mtmm) cc_final: 0.8896 (mmtm) REVERT: A 426 ASN cc_start: 0.9192 (m-40) cc_final: 0.8882 (m110) REVERT: B 105 ASP cc_start: 0.8975 (p0) cc_final: 0.8565 (p0) REVERT: B 138 ASP cc_start: 0.7615 (p0) cc_final: 0.7309 (p0) REVERT: B 140 LYS cc_start: 0.8893 (mttp) cc_final: 0.8632 (mttp) REVERT: B 174 GLN cc_start: 0.8344 (mp10) cc_final: 0.7991 (mm110) REVERT: B 201 GLN cc_start: 0.7663 (mp10) cc_final: 0.7285 (mp10) REVERT: B 221 TYR cc_start: 0.7433 (m-10) cc_final: 0.7163 (m-10) REVERT: B 287 MET cc_start: 0.9568 (mmm) cc_final: 0.9362 (mmp) REVERT: B 420 LEU cc_start: 0.9013 (tp) cc_final: 0.8799 (tp) REVERT: B 423 LEU cc_start: 0.9335 (tp) cc_final: 0.9040 (tt) REVERT: B 439 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7832 (tm-30) REVERT: C 39 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8380 (p0) REVERT: C 81 ASP cc_start: 0.9174 (p0) cc_final: 0.8728 (p0) REVERT: C 177 ILE cc_start: 0.9257 (mm) cc_final: 0.8828 (mm) REVERT: C 201 GLN cc_start: 0.7595 (mp10) cc_final: 0.7182 (mp10) REVERT: C 263 TRP cc_start: 0.6779 (m-10) cc_final: 0.6572 (m-10) REVERT: C 422 PHE cc_start: 0.9462 (t80) cc_final: 0.9058 (t80) REVERT: C 426 ASN cc_start: 0.9014 (m-40) cc_final: 0.8372 (m-40) REVERT: C 439 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7910 (tm-30) REVERT: D 72 PHE cc_start: 0.8891 (t80) cc_final: 0.8639 (t80) REVERT: D 80 MET cc_start: 0.9026 (tpp) cc_final: 0.8637 (tpp) REVERT: D 105 ASP cc_start: 0.9192 (p0) cc_final: 0.8856 (p0) REVERT: D 140 LYS cc_start: 0.9208 (mtpp) cc_final: 0.8899 (mtmm) REVERT: D 152 TYR cc_start: 0.8467 (t80) cc_final: 0.8126 (t80) REVERT: D 201 GLN cc_start: 0.7439 (mp10) cc_final: 0.6596 (mp10) REVERT: D 221 TYR cc_start: 0.7947 (m-80) cc_final: 0.7700 (m-10) REVERT: D 237 ARG cc_start: 0.9009 (mtt-85) cc_final: 0.8639 (mtp85) REVERT: D 243 GLN cc_start: 0.8764 (mp10) cc_final: 0.8443 (mp10) REVERT: D 251 MET cc_start: 0.8999 (mpp) cc_final: 0.8520 (mpp) REVERT: D 270 MET cc_start: 0.6822 (mmt) cc_final: 0.6275 (tmm) REVERT: D 439 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7489 (tm-30) REVERT: E 39 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8256 (p0) REVERT: E 90 GLN cc_start: 0.8630 (pt0) cc_final: 0.8363 (mt0) REVERT: E 138 ASP cc_start: 0.7991 (p0) cc_final: 0.7749 (p0) REVERT: E 174 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7936 (mm110) REVERT: E 201 GLN cc_start: 0.7588 (mp10) cc_final: 0.7144 (mp10) REVERT: E 251 MET cc_start: 0.9250 (mpp) cc_final: 0.8862 (mpp) REVERT: E 287 MET cc_start: 0.9494 (mmm) cc_final: 0.9239 (mmp) REVERT: E 422 PHE cc_start: 0.9421 (t80) cc_final: 0.9185 (t80) REVERT: E 426 ASN cc_start: 0.9009 (m-40) cc_final: 0.8725 (m110) REVERT: E 439 GLU cc_start: 0.8125 (pt0) cc_final: 0.7717 (tm-30) outliers start: 48 outliers final: 34 residues processed: 410 average time/residue: 0.0987 time to fit residues: 63.0169 Evaluate side-chains 396 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 357 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 234 ILE 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 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 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 121 ASP Chi-restraints excluded: chain C residue 137 THR 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 402 LEU 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 D residue 320 SER Chi-restraints excluded: chain D residue 416 VAL 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 Chi-restraints excluded: chain E residue 277 VAL 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: 0.6980 chunk 42 optimal weight: 9.9990 chunk 63 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 141 optimal weight: 0.0060 chunk 106 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN B 426 ASN C 90 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.116546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.092738 restraints weight = 32770.370| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.94 r_work: 0.3198 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4021 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= 0.133 Angle : 0.666 13.124 20350 Z= 0.335 Chirality : 0.045 0.159 2290 Planarity : 0.003 0.038 2545 Dihedral : 4.391 32.762 2060 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.18 % Allowed : 18.01 % Favored : 78.82 % 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: 0.42 (0.19), residues: 1775 helix: 1.92 (0.19), residues: 700 sheet: 0.87 (0.27), residues: 380 loop : -1.90 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 237 TYR 0.031 0.001 TYR D 152 PHE 0.031 0.001 PHE C 72 TRP 0.064 0.002 TRP B 267 HIS 0.002 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00302 (15000) covalent geometry : angle 0.66458 (20325) SS BOND : bond 0.00888 ( 5) SS BOND : angle 1.44260 ( 10) hydrogen bonds : bond 0.04131 ( 750) hydrogen bonds : angle 3.74659 ( 2565) link_NAG-ASN : bond 0.00033 ( 5) link_NAG-ASN : angle 1.33348 ( 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 423 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 372 time to evaluate : 0.567 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 39 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.8170 (p0) REVERT: A 119 LYS cc_start: 0.9308 (mtmm) cc_final: 0.8891 (mtmm) REVERT: A 174 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8012 (mm110) REVERT: A 201 GLN cc_start: 0.7566 (mp10) cc_final: 0.7028 (mp10) REVERT: A 300 LYS cc_start: 0.9184 (mtmm) cc_final: 0.8897 (mmtm) REVERT: A 426 ASN cc_start: 0.9213 (m-40) cc_final: 0.8906 (m110) REVERT: B 105 ASP cc_start: 0.8917 (p0) cc_final: 0.8482 (p0) REVERT: B 138 ASP cc_start: 0.7650 (p0) cc_final: 0.7362 (p0) REVERT: B 140 LYS cc_start: 0.8855 (mttp) cc_final: 0.8605 (mttp) REVERT: B 174 GLN cc_start: 0.8408 (mp10) cc_final: 0.8061 (mm110) REVERT: B 201 GLN cc_start: 0.7687 (mp10) cc_final: 0.7297 (mp10) REVERT: B 221 TYR cc_start: 0.7464 (m-10) cc_final: 0.7262 (m-10) REVERT: B 287 MET cc_start: 0.9592 (mmm) cc_final: 0.9382 (mmp) REVERT: B 420 LEU cc_start: 0.8979 (tp) cc_final: 0.8757 (tp) REVERT: B 423 LEU cc_start: 0.9324 (tp) cc_final: 0.9027 (tt) REVERT: B 439 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7830 (tm-30) REVERT: C 39 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.8371 (p0) REVERT: C 81 ASP cc_start: 0.9174 (p0) cc_final: 0.8783 (p0) REVERT: C 119 LYS cc_start: 0.9172 (mtmm) cc_final: 0.8877 (mtmm) REVERT: C 201 GLN cc_start: 0.7633 (mp10) cc_final: 0.7204 (mp10) REVERT: C 422 PHE cc_start: 0.9465 (t80) cc_final: 0.9061 (t80) REVERT: C 426 ASN cc_start: 0.9020 (m-40) cc_final: 0.8374 (m-40) REVERT: C 439 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7890 (tm-30) REVERT: D 72 PHE cc_start: 0.8867 (t80) cc_final: 0.8603 (t80) REVERT: D 80 MET cc_start: 0.9037 (tpp) cc_final: 0.8628 (tpp) REVERT: D 105 ASP cc_start: 0.9204 (p0) cc_final: 0.8882 (p0) REVERT: D 140 LYS cc_start: 0.9249 (mtpp) cc_final: 0.8928 (mtmm) REVERT: D 152 TYR cc_start: 0.8503 (t80) cc_final: 0.8012 (t80) REVERT: D 201 GLN cc_start: 0.7486 (mp10) cc_final: 0.6622 (mp10) REVERT: D 221 TYR cc_start: 0.7952 (m-80) cc_final: 0.7698 (m-10) REVERT: D 237 ARG cc_start: 0.9096 (mtt-85) cc_final: 0.8760 (mtp85) REVERT: D 243 GLN cc_start: 0.8824 (mp10) cc_final: 0.8467 (mp10) REVERT: D 251 MET cc_start: 0.9025 (mpp) cc_final: 0.8504 (mpp) REVERT: D 270 MET cc_start: 0.6884 (mmt) cc_final: 0.6322 (tmm) REVERT: D 308 ASP cc_start: 0.9178 (m-30) cc_final: 0.8951 (m-30) REVERT: D 439 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7588 (tm-30) REVERT: E 39 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8232 (p0) REVERT: E 90 GLN cc_start: 0.8659 (pt0) cc_final: 0.8423 (mt0) REVERT: E 138 ASP cc_start: 0.8097 (p0) cc_final: 0.7795 (p0) REVERT: E 174 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7973 (mm110) REVERT: E 201 GLN cc_start: 0.7630 (mp10) cc_final: 0.7179 (mp10) REVERT: E 287 MET cc_start: 0.9519 (mmm) cc_final: 0.9245 (mmp) REVERT: E 308 ASP cc_start: 0.9296 (m-30) cc_final: 0.9093 (m-30) REVERT: E 422 PHE cc_start: 0.9434 (t80) cc_final: 0.9192 (t80) REVERT: E 426 ASN cc_start: 0.9001 (m-40) cc_final: 0.8698 (m110) REVERT: E 439 GLU cc_start: 0.8139 (pt0) cc_final: 0.7722 (tm-30) outliers start: 51 outliers final: 38 residues processed: 401 average time/residue: 0.0986 time to fit residues: 61.7659 Evaluate side-chains 393 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 350 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET 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 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 39 ASP Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 137 THR 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 45 VAL Chi-restraints excluded: chain D residue 71 SER 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 416 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 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: 3.9990 chunk 49 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 105 optimal weight: 0.3980 chunk 40 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.113883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.089949 restraints weight = 33267.637| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.94 r_work: 0.3151 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15010 Z= 0.185 Angle : 0.711 13.258 20350 Z= 0.359 Chirality : 0.045 0.143 2290 Planarity : 0.003 0.035 2545 Dihedral : 4.529 33.188 2060 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.43 % Allowed : 19.00 % Favored : 77.57 % 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: 0.31 (0.19), residues: 1775 helix: 1.84 (0.18), residues: 700 sheet: 0.76 (0.27), residues: 380 loop : -1.93 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 237 TYR 0.027 0.002 TYR D 152 PHE 0.026 0.002 PHE C 72 TRP 0.080 0.003 TRP D 267 HIS 0.003 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00428 (15000) covalent geometry : angle 0.70924 (20325) SS BOND : bond 0.00628 ( 5) SS BOND : angle 1.32808 ( 10) hydrogen bonds : bond 0.04126 ( 750) hydrogen bonds : angle 3.85687 ( 2565) link_NAG-ASN : bond 0.00376 ( 5) link_NAG-ASN : angle 1.95860 ( 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 408 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 353 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8200 (p0) REVERT: A 114 LEU cc_start: 0.9142 (tp) cc_final: 0.8643 (tt) REVERT: A 119 LYS cc_start: 0.9344 (mtmm) cc_final: 0.8842 (mtmm) REVERT: A 174 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8117 (mm110) REVERT: A 201 GLN cc_start: 0.7735 (mp10) cc_final: 0.7151 (mp10) REVERT: A 300 LYS cc_start: 0.9237 (mtmm) cc_final: 0.8882 (mmtm) REVERT: A 426 ASN cc_start: 0.9231 (m-40) cc_final: 0.8998 (m110) REVERT: B 105 ASP cc_start: 0.8917 (p0) cc_final: 0.8457 (p0) REVERT: B 138 ASP cc_start: 0.7891 (p0) cc_final: 0.7570 (p0) REVERT: B 140 LYS cc_start: 0.8837 (mttp) cc_final: 0.8564 (mttp) REVERT: B 174 GLN cc_start: 0.8524 (mp10) cc_final: 0.8147 (mm110) REVERT: B 201 GLN cc_start: 0.7821 (mp10) cc_final: 0.7422 (mp10) REVERT: B 287 MET cc_start: 0.9597 (mmm) cc_final: 0.9363 (mmp) REVERT: B 420 LEU cc_start: 0.9065 (tp) cc_final: 0.8839 (tp) REVERT: B 423 LEU cc_start: 0.9342 (tp) cc_final: 0.9021 (tt) REVERT: B 439 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7932 (tm-30) REVERT: C 81 ASP cc_start: 0.9180 (p0) cc_final: 0.8702 (p0) REVERT: C 119 LYS cc_start: 0.9249 (mtmm) cc_final: 0.9043 (mtmm) REVERT: C 426 ASN cc_start: 0.9029 (m-40) cc_final: 0.8683 (m-40) REVERT: C 439 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7861 (tm-30) REVERT: D 80 MET cc_start: 0.9075 (tpp) cc_final: 0.8628 (tpp) REVERT: D 105 ASP cc_start: 0.9178 (p0) cc_final: 0.8832 (p0) REVERT: D 134 GLU cc_start: 0.7981 (pm20) cc_final: 0.7741 (pm20) REVERT: D 201 GLN cc_start: 0.7623 (mp10) cc_final: 0.6728 (mp10) REVERT: D 221 TYR cc_start: 0.8092 (m-80) cc_final: 0.7827 (m-10) REVERT: D 237 ARG cc_start: 0.9167 (mtt-85) cc_final: 0.8689 (mtt90) REVERT: D 243 GLN cc_start: 0.8846 (mp10) cc_final: 0.8527 (mp10) REVERT: D 251 MET cc_start: 0.9072 (mpp) cc_final: 0.8524 (mpp) REVERT: D 270 MET cc_start: 0.6913 (mmt) cc_final: 0.6474 (tmm) REVERT: D 439 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7606 (tm-30) REVERT: E 39 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8281 (p0) REVERT: E 90 GLN cc_start: 0.8786 (pt0) cc_final: 0.8477 (mt0) REVERT: E 138 ASP cc_start: 0.8244 (p0) cc_final: 0.7986 (p0) REVERT: E 174 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.8053 (mm110) REVERT: E 201 GLN cc_start: 0.7750 (mp10) cc_final: 0.7276 (mp10) REVERT: E 287 MET cc_start: 0.9551 (mmm) cc_final: 0.9258 (mmp) REVERT: E 308 ASP cc_start: 0.9289 (m-30) cc_final: 0.9058 (m-30) REVERT: E 422 PHE cc_start: 0.9462 (t80) cc_final: 0.9232 (t80) REVERT: E 426 ASN cc_start: 0.9027 (m-40) cc_final: 0.8714 (m110) REVERT: E 439 GLU cc_start: 0.8211 (pt0) cc_final: 0.7870 (tm-30) outliers start: 55 outliers final: 41 residues processed: 384 average time/residue: 0.1006 time to fit residues: 60.2622 Evaluate side-chains 393 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 348 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET 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 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 267 TRP 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 88 LEU Chi-restraints excluded: chain C residue 137 THR 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 71 SER 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 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 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: 3.9990 chunk 85 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 169 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN B 85 ASN B 426 ASN ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.115892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.092041 restraints weight = 32914.331| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.93 r_work: 0.3156 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4268 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= 0.143 Angle : 0.709 14.218 20350 Z= 0.353 Chirality : 0.045 0.155 2290 Planarity : 0.003 0.038 2545 Dihedral : 4.488 34.583 2060 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.99 % Allowed : 18.88 % Favored : 78.13 % 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: 0.37 (0.19), residues: 1775 helix: 1.87 (0.19), residues: 700 sheet: 0.81 (0.27), residues: 380 loop : -1.89 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 437 TYR 0.036 0.001 TYR D 152 PHE 0.024 0.001 PHE C 72 TRP 0.076 0.003 TRP D 267 HIS 0.002 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00332 (15000) covalent geometry : angle 0.70815 (20325) SS BOND : bond 0.00564 ( 5) SS BOND : angle 1.24181 ( 10) hydrogen bonds : bond 0.03976 ( 750) hydrogen bonds : angle 3.75669 ( 2565) link_NAG-ASN : bond 0.00016 ( 5) link_NAG-ASN : angle 1.44980 ( 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 412 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 364 time to evaluate : 0.558 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 39 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8255 (p0) REVERT: A 114 LEU cc_start: 0.9081 (tp) cc_final: 0.8698 (tt) REVERT: A 119 LYS cc_start: 0.9357 (mtmm) cc_final: 0.9081 (mtmm) REVERT: A 174 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8031 (mm110) REVERT: A 201 GLN cc_start: 0.7493 (mp10) cc_final: 0.6889 (mp10) REVERT: A 300 LYS cc_start: 0.9167 (mtmm) cc_final: 0.8793 (mmtm) REVERT: A 426 ASN cc_start: 0.9210 (m-40) cc_final: 0.8919 (m110) REVERT: A 437 ARG cc_start: 0.6479 (ptt-90) cc_final: 0.6272 (ptp90) REVERT: B 105 ASP cc_start: 0.9011 (p0) cc_final: 0.8560 (p0) REVERT: B 138 ASP cc_start: 0.7885 (p0) cc_final: 0.7524 (p0) REVERT: B 140 LYS cc_start: 0.8806 (mttp) cc_final: 0.8574 (mttp) REVERT: B 174 GLN cc_start: 0.8473 (mp10) cc_final: 0.8112 (mm110) REVERT: B 185 TYR cc_start: 0.9266 (m-80) cc_final: 0.8960 (m-80) REVERT: B 201 GLN cc_start: 0.7589 (mp10) cc_final: 0.7197 (mp10) REVERT: B 267 TRP cc_start: 0.6666 (OUTLIER) cc_final: 0.6419 (m-90) REVERT: B 287 MET cc_start: 0.9594 (mmm) cc_final: 0.9355 (mmp) REVERT: B 308 ASP cc_start: 0.9412 (m-30) cc_final: 0.9153 (m-30) REVERT: B 420 LEU cc_start: 0.9009 (tp) cc_final: 0.8796 (tp) REVERT: B 423 LEU cc_start: 0.9308 (tp) cc_final: 0.9002 (tt) REVERT: B 439 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7981 (tm-30) REVERT: C 81 ASP cc_start: 0.9101 (p0) cc_final: 0.8623 (p0) REVERT: C 426 ASN cc_start: 0.9001 (m-40) cc_final: 0.8723 (m110) REVERT: C 437 ARG cc_start: 0.6513 (ptt-90) cc_final: 0.6224 (ptp90) REVERT: C 439 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7867 (tm-30) REVERT: D 80 MET cc_start: 0.9081 (tpp) cc_final: 0.8650 (tpp) REVERT: D 105 ASP cc_start: 0.9267 (p0) cc_final: 0.8918 (p0) REVERT: D 134 GLU cc_start: 0.8088 (pm20) cc_final: 0.7832 (pm20) REVERT: D 201 GLN cc_start: 0.7423 (mp10) cc_final: 0.6549 (mp10) REVERT: D 221 TYR cc_start: 0.8153 (m-80) cc_final: 0.7901 (m-10) REVERT: D 237 ARG cc_start: 0.9114 (mtt-85) cc_final: 0.8807 (mtp85) REVERT: D 243 GLN cc_start: 0.8815 (mp10) cc_final: 0.8444 (mp10) REVERT: D 251 MET cc_start: 0.9082 (mpp) cc_final: 0.8525 (mpp) REVERT: D 270 MET cc_start: 0.6854 (mmt) cc_final: 0.6349 (tmm) REVERT: D 439 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7629 (tm-30) REVERT: E 80 MET cc_start: 0.9286 (tpp) cc_final: 0.9004 (tpp) REVERT: E 81 ASP cc_start: 0.9174 (p0) cc_final: 0.8951 (p0) REVERT: E 90 GLN cc_start: 0.8698 (pt0) cc_final: 0.8435 (mt0) REVERT: E 138 ASP cc_start: 0.8327 (p0) cc_final: 0.8041 (p0) REVERT: E 162 CYS cc_start: 0.8287 (t) cc_final: 0.7870 (t) REVERT: E 174 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7946 (mm110) REVERT: E 201 GLN cc_start: 0.7518 (mp10) cc_final: 0.7051 (mp10) REVERT: E 287 MET cc_start: 0.9535 (mmm) cc_final: 0.9228 (mmp) REVERT: E 422 PHE cc_start: 0.9476 (t80) cc_final: 0.9256 (t80) REVERT: E 426 ASN cc_start: 0.9001 (m-40) cc_final: 0.8678 (m110) REVERT: E 439 GLU cc_start: 0.8251 (pt0) cc_final: 0.7892 (tm-30) outliers start: 48 outliers final: 39 residues processed: 390 average time/residue: 0.1019 time to fit residues: 61.4808 Evaluate side-chains 394 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 351 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET 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 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 267 TRP 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 88 LEU 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 45 VAL Chi-restraints excluded: chain D residue 71 SER 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 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 289 THR 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: 1.9990 chunk 41 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 167 optimal weight: 0.0980 chunk 22 optimal weight: 0.0470 chunk 133 optimal weight: 0.9980 chunk 23 optimal weight: 0.0770 chunk 138 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 48 optimal weight: 0.2980 overall best weight: 0.2836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.117640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.093577 restraints weight = 32678.469| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 4.00 r_work: 0.3212 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4452 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= 0.131 Angle : 0.730 15.083 20350 Z= 0.357 Chirality : 0.046 0.162 2290 Planarity : 0.003 0.035 2545 Dihedral : 4.384 35.534 2060 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.74 % Allowed : 19.31 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.38 (0.19), residues: 1775 helix: 1.83 (0.19), residues: 700 sheet: 0.88 (0.27), residues: 380 loop : -1.87 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 437 TYR 0.036 0.001 TYR D 152 PHE 0.022 0.001 PHE C 72 TRP 0.073 0.003 TRP D 267 HIS 0.003 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00300 (15000) covalent geometry : angle 0.72925 (20325) SS BOND : bond 0.00666 ( 5) SS BOND : angle 1.20835 ( 10) hydrogen bonds : bond 0.03786 ( 750) hydrogen bonds : angle 3.68651 ( 2565) link_NAG-ASN : bond 0.00169 ( 5) link_NAG-ASN : angle 1.09386 ( 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 429 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 385 time to evaluate : 0.558 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: 0.8401 (OUTLIER) cc_final: 0.8155 (p0) REVERT: A 119 LYS cc_start: 0.9329 (mtmm) cc_final: 0.9110 (mtmm) REVERT: A 174 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.8026 (mm110) REVERT: A 177 ILE cc_start: 0.9297 (mm) cc_final: 0.9043 (mm) REVERT: A 185 TYR cc_start: 0.9094 (m-80) cc_final: 0.8748 (m-80) REVERT: A 201 GLN cc_start: 0.7573 (mp10) cc_final: 0.6990 (mp10) REVERT: A 221 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.7698 (m-10) REVERT: A 426 ASN cc_start: 0.9255 (m-40) cc_final: 0.9003 (m110) REVERT: A 437 ARG cc_start: 0.6432 (ptt-90) cc_final: 0.6228 (ptp90) REVERT: B 105 ASP cc_start: 0.8913 (p0) cc_final: 0.8509 (p0) REVERT: B 138 ASP cc_start: 0.7882 (p0) cc_final: 0.7577 (p0) REVERT: B 174 GLN cc_start: 0.8489 (mp10) cc_final: 0.8144 (mm110) REVERT: B 181 GLU cc_start: 0.8422 (mp0) cc_final: 0.8210 (mp0) REVERT: B 185 TYR cc_start: 0.9171 (m-80) cc_final: 0.8857 (m-80) REVERT: B 201 GLN cc_start: 0.7621 (mp10) cc_final: 0.7253 (mp10) REVERT: B 287 MET cc_start: 0.9601 (mmm) cc_final: 0.9349 (mmp) REVERT: B 308 ASP cc_start: 0.9335 (m-30) cc_final: 0.9110 (m-30) REVERT: B 439 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7957 (tm-30) REVERT: C 81 ASP cc_start: 0.9079 (p0) cc_final: 0.8668 (p0) REVERT: C 426 ASN cc_start: 0.9000 (m-40) cc_final: 0.8760 (m110) REVERT: C 437 ARG cc_start: 0.6408 (ptt-90) cc_final: 0.5905 (ptp90) REVERT: C 439 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7793 (tm-30) REVERT: D 80 MET cc_start: 0.9084 (tpp) cc_final: 0.8716 (tpp) REVERT: D 105 ASP cc_start: 0.9221 (p0) cc_final: 0.8852 (p0) REVERT: D 140 LYS cc_start: 0.9123 (mtpp) cc_final: 0.8563 (mttp) REVERT: D 201 GLN cc_start: 0.7496 (mp10) cc_final: 0.6628 (mp10) REVERT: D 221 TYR cc_start: 0.8021 (m-80) cc_final: 0.7788 (m-10) REVERT: D 235 GLU cc_start: 0.8990 (tt0) cc_final: 0.8217 (tm-30) REVERT: D 237 ARG cc_start: 0.9167 (mtt-85) cc_final: 0.8774 (mtp85) REVERT: D 243 GLN cc_start: 0.8785 (mp10) cc_final: 0.8469 (mp10) REVERT: D 251 MET cc_start: 0.9041 (mpp) cc_final: 0.8477 (mpp) REVERT: D 270 MET cc_start: 0.6894 (mmt) cc_final: 0.6337 (tmm) REVERT: D 439 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7620 (tm-30) REVERT: E 80 MET cc_start: 0.9233 (tpp) cc_final: 0.8997 (tpp) REVERT: E 138 ASP cc_start: 0.8259 (p0) cc_final: 0.7941 (p0) REVERT: E 162 CYS cc_start: 0.7957 (t) cc_final: 0.7477 (t) REVERT: E 174 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7972 (mm110) REVERT: E 201 GLN cc_start: 0.7612 (mp10) cc_final: 0.7169 (mp10) REVERT: E 235 GLU cc_start: 0.8748 (tt0) cc_final: 0.8266 (tm-30) REVERT: E 308 ASP cc_start: 0.9408 (m-30) cc_final: 0.9128 (m-30) REVERT: E 422 PHE cc_start: 0.9422 (t80) cc_final: 0.9170 (t80) REVERT: E 426 ASN cc_start: 0.8999 (m-40) cc_final: 0.8660 (m110) REVERT: E 439 GLU cc_start: 0.8221 (pt0) cc_final: 0.7871 (tm-30) outliers start: 44 outliers final: 35 residues processed: 409 average time/residue: 0.0986 time to fit residues: 62.0685 Evaluate side-chains 402 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 363 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 221 TYR 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 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 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 71 SER 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 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 261 LEU Chi-restraints excluded: chain E residue 289 THR 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: 4.9990 chunk 105 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN E 210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.115323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.091592 restraints weight = 32672.403| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.94 r_work: 0.3161 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15010 Z= 0.156 Angle : 0.743 14.030 20350 Z= 0.364 Chirality : 0.045 0.200 2290 Planarity : 0.004 0.047 2545 Dihedral : 4.451 36.738 2060 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.43 % Allowed : 20.12 % Favored : 77.45 % 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: 0.31 (0.19), residues: 1775 helix: 1.77 (0.19), residues: 700 sheet: 0.72 (0.27), residues: 390 loop : -1.86 (0.21), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 437 TYR 0.042 0.002 TYR E 152 PHE 0.038 0.002 PHE B 72 TRP 0.073 0.003 TRP A 267 HIS 0.003 0.001 HIS E 335 Details of bonding type rmsd covalent geometry : bond 0.00366 (15000) covalent geometry : angle 0.74127 (20325) SS BOND : bond 0.00566 ( 5) SS BOND : angle 1.63047 ( 10) hydrogen bonds : bond 0.03762 ( 750) hydrogen bonds : angle 3.72898 ( 2565) link_NAG-ASN : bond 0.00231 ( 5) link_NAG-ASN : angle 1.67020 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3329.54 seconds wall clock time: 57 minutes 53.61 seconds (3473.61 seconds total)