Starting phenix.real_space_refine on Fri Jul 3 16:30:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m6q_23704/07_2026/7m6q_23704.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m6q_23704/07_2026/7m6q_23704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7m6q_23704/07_2026/7m6q_23704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m6q_23704/07_2026/7m6q_23704.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7m6q_23704/07_2026/7m6q_23704.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m6q_23704/07_2026/7m6q_23704.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m6q_23704/07_2026/7m6q_23704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m6q_23704/07_2026/7m6q_23704.map" } resolution = 2.91 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 9590 2.51 5 N 2390 2.21 5 O 2645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14725 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2903 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2903 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 2903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2903 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 2903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2903 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 2903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2903 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 1, 'TCI': 1} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'TCI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'TCI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'TCI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'TCI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.39, per 1000 atoms: 0.16 Number of scatterers: 14725 At special positions: 0 Unit cell: (94.6, 92.4, 139.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2645 8.00 N 2390 7.00 C 9590 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 802 " - " ASN A 62 " " NAG B 802 " - " ASN B 62 " " NAG C 802 " - " ASN C 62 " " NAG D 802 " - " ASN D 62 " " NAG E 501 " - " ASN E 62 " Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 591.8 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 40.0% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 33 through 43 removed outlier: 3.545A pdb=" N PHE A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 251 removed outlier: 3.893A pdb=" N ILE A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 269 removed outlier: 3.510A pdb=" N SER A 255 " --> pdb=" O MET A 251 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N PHE A 266 " --> pdb=" O SER A 262 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP A 267 " --> pdb=" O TRP A 263 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 295 removed outlier: 3.812A pdb=" N GLY A 278 " --> pdb=" O PRO A 274 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 341 Processing helix chain 'A' and resid 395 through 442 removed outlier: 3.962A pdb=" N MET A 399 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Proline residue: A 419 - end of helix removed outlier: 3.528A pdb=" N SER A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 43 removed outlier: 3.544A pdb=" N PHE B 37 " --> pdb=" O PRO B 33 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 251 removed outlier: 3.893A pdb=" N ILE B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 269 removed outlier: 3.510A pdb=" N SER B 255 " --> pdb=" O MET B 251 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE B 266 " --> pdb=" O SER B 262 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TRP B 267 " --> pdb=" O TRP B 263 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 295 removed outlier: 3.812A pdb=" N GLY B 278 " --> pdb=" O PRO B 274 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 341 Processing helix chain 'B' and resid 395 through 442 removed outlier: 3.962A pdb=" N MET B 399 " --> pdb=" O THR B 395 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) Proline residue: B 419 - end of helix removed outlier: 3.528A pdb=" N SER B 438 " --> pdb=" O LYS B 434 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 43 removed outlier: 3.544A pdb=" N PHE C 37 " --> pdb=" O PRO C 33 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 251 removed outlier: 3.894A pdb=" N ILE C 249 " --> pdb=" O GLY C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 269 removed outlier: 3.511A pdb=" N SER C 255 " --> pdb=" O MET C 251 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE C 266 " --> pdb=" O SER C 262 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TRP C 267 " --> pdb=" O TRP C 263 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE C 268 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 295 removed outlier: 3.812A pdb=" N GLY C 278 " --> pdb=" O PRO C 274 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 341 Processing helix chain 'C' and resid 395 through 442 removed outlier: 3.962A pdb=" N MET C 399 " --> pdb=" O THR C 395 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) Proline residue: C 419 - end of helix removed outlier: 3.528A pdb=" N SER C 438 " --> pdb=" O LYS C 434 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 43 removed outlier: 3.545A pdb=" N PHE D 37 " --> pdb=" O PRO D 33 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 251 removed outlier: 3.894A pdb=" N ILE D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 269 removed outlier: 3.511A pdb=" N SER D 255 " --> pdb=" O MET D 251 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER D 265 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP D 267 " --> pdb=" O TRP D 263 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE D 268 " --> pdb=" O VAL D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 295 removed outlier: 3.812A pdb=" N GLY D 278 " --> pdb=" O PRO D 274 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 341 Processing helix chain 'D' and resid 395 through 442 removed outlier: 3.963A pdb=" N MET D 399 " --> pdb=" O THR D 395 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) Proline residue: D 419 - end of helix removed outlier: 3.528A pdb=" N SER D 438 " --> pdb=" O LYS D 434 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS D 442 " --> pdb=" O SER D 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 43 removed outlier: 3.545A pdb=" N PHE E 37 " --> pdb=" O PRO E 33 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 251 removed outlier: 3.894A pdb=" N ILE E 249 " --> pdb=" O GLY E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 269 removed outlier: 3.511A pdb=" N SER E 255 " --> pdb=" O MET E 251 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER E 265 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE E 266 " --> pdb=" O SER E 262 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP E 267 " --> pdb=" O TRP E 263 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE E 268 " --> pdb=" O VAL E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 295 removed outlier: 3.812A pdb=" N GLY E 278 " --> pdb=" O PRO E 274 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG E 295 " --> pdb=" O SER E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 341 Processing helix chain 'E' and resid 395 through 442 removed outlier: 3.962A pdb=" N MET E 399 " --> pdb=" O THR E 395 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) Proline residue: E 419 - end of helix removed outlier: 3.527A pdb=" N SER E 438 " --> pdb=" O LYS E 434 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS E 442 " --> pdb=" O SER E 438 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 106 through 108 removed outlier: 3.959A pdb=" N TRP A 92 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 5.895A 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 131 removed outlier: 3.661A pdb=" N VAL A 159 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA A 130 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N THR A 157 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TRP A 92 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 123 through 124 Processing sheet with id=AA4, first strand: chain 'A' and resid 123 through 124 removed outlier: 3.565A pdb=" N ARG A 220 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA6, first strand: chain 'B' and resid 106 through 108 removed outlier: 3.959A pdb=" N TRP B 92 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 5.894A 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 131 removed outlier: 3.662A pdb=" N VAL B 159 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA B 130 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N THR B 157 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TRP B 92 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AA9, first strand: chain 'B' and resid 123 through 124 removed outlier: 3.565A pdb=" N ARG B 220 " --> pdb=" O GLU B 235 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AB2, first strand: chain 'C' and resid 106 through 108 removed outlier: 3.959A pdb=" N TRP C 92 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 5.895A 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 131 removed outlier: 3.663A pdb=" N VAL C 159 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA C 130 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N THR C 157 " --> pdb=" O ALA C 130 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TRP C 92 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 123 through 124 Processing sheet with id=AB5, first strand: chain 'C' and resid 123 through 124 removed outlier: 3.565A pdb=" N ARG C 220 " --> pdb=" O GLU C 235 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AB7, first strand: chain 'D' and resid 106 through 108 removed outlier: 3.958A pdb=" N TRP D 92 " --> pdb=" O VAL D 150 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 5.894A 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 131 removed outlier: 3.662A pdb=" N VAL D 159 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA D 130 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N THR D 157 " --> pdb=" O ALA D 130 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TRP D 92 " --> pdb=" O VAL D 150 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 123 through 124 Processing sheet with id=AC1, first strand: chain 'D' and resid 123 through 124 removed outlier: 3.565A pdb=" N ARG D 220 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AC3, first strand: chain 'E' and resid 106 through 108 removed outlier: 3.959A pdb=" N TRP E 92 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 5.894A 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 131 removed outlier: 3.662A pdb=" N VAL E 159 " --> pdb=" O LYS E 128 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA E 130 " --> pdb=" O THR E 157 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N THR E 157 " --> pdb=" O ALA E 130 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TRP E 92 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 123 through 124 Processing sheet with id=AC6, first strand: chain 'E' and resid 123 through 124 removed outlier: 3.566A pdb=" N ARG E 220 " --> pdb=" O GLU E 235 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 224 through 225 860 hydrogen bonds defined for protein. 2505 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: 2.55 Time building geometry restraints manager: 1.56 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: 4487 1.34 - 1.46: 3294 1.46 - 1.58: 7134 1.58 - 1.70: 0 1.70 - 1.82: 170 Bond restraints: 15085 Sorted by residual: bond pdb=" CB VAL C 259 " pdb=" CG2 VAL C 259 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.46e+00 bond pdb=" CB VAL B 259 " pdb=" CG2 VAL B 259 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.40e+00 bond pdb=" CB VAL E 259 " pdb=" CG2 VAL E 259 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.40e+00 bond pdb=" CB VAL D 259 " pdb=" CG2 VAL D 259 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.38e+00 bond pdb=" CB VAL A 259 " pdb=" CG2 VAL A 259 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.32e+00 ... (remaining 15080 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 19277 2.28 - 4.56: 1000 4.56 - 6.83: 123 6.83 - 9.11: 55 9.11 - 11.39: 10 Bond angle restraints: 20465 Sorted by residual: angle pdb=" CA GLU B 215 " pdb=" CB GLU B 215 " pdb=" CG GLU B 215 " ideal model delta sigma weight residual 114.10 122.90 -8.80 2.00e+00 2.50e-01 1.94e+01 angle pdb=" CA GLU A 215 " pdb=" CB GLU A 215 " pdb=" CG GLU A 215 " ideal model delta sigma weight residual 114.10 122.86 -8.76 2.00e+00 2.50e-01 1.92e+01 angle pdb=" CA GLU C 215 " pdb=" CB GLU C 215 " pdb=" CG GLU C 215 " ideal model delta sigma weight residual 114.10 122.86 -8.76 2.00e+00 2.50e-01 1.92e+01 angle pdb=" CA GLU D 215 " pdb=" CB GLU D 215 " pdb=" CG GLU D 215 " ideal model delta sigma weight residual 114.10 122.85 -8.75 2.00e+00 2.50e-01 1.91e+01 angle pdb=" CA GLU E 215 " pdb=" CB GLU E 215 " pdb=" CG GLU E 215 " ideal model delta sigma weight residual 114.10 122.84 -8.74 2.00e+00 2.50e-01 1.91e+01 ... (remaining 20460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.83: 8396 19.83 - 39.66: 459 39.66 - 59.49: 60 59.49 - 79.31: 25 79.31 - 99.14: 10 Dihedral angle restraints: 8950 sinusoidal: 3640 harmonic: 5310 Sorted by residual: dihedral pdb=" N PHE E 418 " pdb=" C PHE E 418 " pdb=" CA PHE E 418 " pdb=" CB PHE E 418 " ideal model delta harmonic sigma weight residual 122.80 134.04 -11.24 0 2.50e+00 1.60e-01 2.02e+01 dihedral pdb=" N PHE A 418 " pdb=" C PHE A 418 " pdb=" CA PHE A 418 " pdb=" CB PHE A 418 " ideal model delta harmonic sigma weight residual 122.80 133.99 -11.19 0 2.50e+00 1.60e-01 2.01e+01 dihedral pdb=" N PHE C 418 " pdb=" C PHE C 418 " pdb=" CA PHE C 418 " pdb=" CB PHE C 418 " ideal model delta harmonic sigma weight residual 122.80 133.99 -11.19 0 2.50e+00 1.60e-01 2.00e+01 ... (remaining 8947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1868 0.088 - 0.177: 411 0.177 - 0.265: 11 0.265 - 0.354: 0 0.354 - 0.442: 10 Chirality restraints: 2300 Sorted by residual: chirality pdb=" CA PHE E 418 " pdb=" N PHE E 418 " pdb=" C PHE E 418 " pdb=" CB PHE E 418 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.88e+00 chirality pdb=" CA PHE A 418 " pdb=" N PHE A 418 " pdb=" C PHE A 418 " pdb=" CB PHE A 418 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.83e+00 chirality pdb=" CA PHE C 418 " pdb=" N PHE C 418 " pdb=" C PHE C 418 " pdb=" CB PHE C 418 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.79e+00 ... (remaining 2297 not shown) Planarity restraints: 2550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR E 283 " 0.021 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C THR E 283 " -0.071 2.00e-02 2.50e+03 pdb=" O THR E 283 " 0.026 2.00e-02 2.50e+03 pdb=" N VAL E 284 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 283 " 0.021 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C THR A 283 " -0.071 2.00e-02 2.50e+03 pdb=" O THR A 283 " 0.026 2.00e-02 2.50e+03 pdb=" N VAL A 284 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 283 " -0.020 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C THR C 283 " 0.070 2.00e-02 2.50e+03 pdb=" O THR C 283 " -0.026 2.00e-02 2.50e+03 pdb=" N VAL C 284 " -0.024 2.00e-02 2.50e+03 ... (remaining 2547 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3832 2.81 - 3.33: 13838 3.33 - 3.86: 23538 3.86 - 4.38: 25372 4.38 - 4.90: 44769 Nonbonded interactions: 111349 Sorted by model distance: nonbonded pdb=" OG1 THR C 186 " pdb=" OD1 ASN C 188 " model vdw 2.289 3.040 nonbonded pdb=" OG1 THR D 186 " pdb=" OD1 ASN D 188 " model vdw 2.289 3.040 nonbonded pdb=" OG1 THR A 186 " pdb=" OD1 ASN A 188 " model vdw 2.289 3.040 nonbonded pdb=" OG1 THR E 186 " pdb=" OD1 ASN E 188 " model vdw 2.290 3.040 nonbonded pdb=" OG1 THR B 186 " pdb=" OD1 ASN B 188 " model vdw 2.290 3.040 ... (remaining 111344 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 442 or resid 802 through 803)) selection = (chain 'B' and (resid 32 through 442 or resid 802 through 803)) selection = (chain 'C' and (resid 32 through 442 or resid 802 through 803)) selection = (chain 'D' and (resid 32 through 442 or resid 802 through 803)) selection = chain 'E' } 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: 2.050 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: 0.050 Set scattering table: 0.030 Process input model: 12.470 Find NCS groups from input model: 0.250 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:5.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 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 : 0.009 0.071 15095 Z= 0.370 Angle : 1.161 11.390 20490 Z= 0.632 Chirality : 0.070 0.442 2300 Planarity : 0.008 0.065 2545 Dihedral : 12.989 99.142 5485 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % 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: -0.39 (0.19), residues: 1775 helix: 1.54 (0.19), residues: 665 sheet: 0.19 (0.27), residues: 380 loop : -2.33 (0.19), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 220 TYR 0.027 0.003 TYR A 433 PHE 0.033 0.004 PHE E 169 TRP 0.011 0.002 TRP C 430 HIS 0.004 0.001 HIS C 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00853 / 0.37 (15085) covalent geometry : angle 1.15894 / 0.63 (20465) SS BOND : bond 0.01046 / 0.62 ( 5) SS BOND : angle 1.15600 / 0.64 ( 10) hydrogen bonds : bond 0.19442 / 13.22 ( 720) hydrogen bonds : angle 6.80224 / 4.80 ( 2505) link_NAG-ASN : bond 0.00417 / 0.24 ( 5) link_NAG-ASN : angle 2.56188 / 1.44 ( 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 230 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.371 Fit side-chains REVERT: A 267 TRP cc_start: 0.6770 (t-100) cc_final: 0.6330 (t-100) REVERT: A 428 PHE cc_start: 0.8463 (t80) cc_final: 0.8139 (m-80) REVERT: A 437 ARG cc_start: 0.7604 (mtp180) cc_final: 0.6383 (mtt180) REVERT: B 266 PHE cc_start: 0.6845 (m-10) cc_final: 0.6068 (m-80) REVERT: B 287 MET cc_start: 0.9094 (tpp) cc_final: 0.8809 (tpt) REVERT: B 428 PHE cc_start: 0.8589 (t80) cc_final: 0.8012 (t80) REVERT: B 437 ARG cc_start: 0.7359 (mtp180) cc_final: 0.6465 (mtt180) REVERT: C 257 LEU cc_start: 0.8513 (tp) cc_final: 0.8140 (mt) REVERT: C 287 MET cc_start: 0.8974 (tpp) cc_final: 0.8633 (tpt) REVERT: C 428 PHE cc_start: 0.8587 (t80) cc_final: 0.7996 (t80) REVERT: C 437 ARG cc_start: 0.7408 (mtp180) cc_final: 0.6335 (mtm180) REVERT: D 190 LEU cc_start: 0.8641 (tt) cc_final: 0.8415 (tm) REVERT: D 287 MET cc_start: 0.9063 (tpp) cc_final: 0.8850 (tpt) REVERT: D 428 PHE cc_start: 0.8651 (t80) cc_final: 0.8095 (t80) REVERT: D 437 ARG cc_start: 0.7423 (mtp180) cc_final: 0.6463 (mtm180) REVERT: E 113 MET cc_start: 0.8532 (pmm) cc_final: 0.8165 (ppp) REVERT: E 308 ASP cc_start: 0.8690 (m-30) cc_final: 0.8356 (m-30) REVERT: E 428 PHE cc_start: 0.8630 (t80) cc_final: 0.8110 (t80) REVERT: E 437 ARG cc_start: 0.7489 (mtp180) cc_final: 0.6586 (mtm180) outliers start: 0 outliers final: 6 residues processed: 230 average time/residue: 0.5158 time to fit residues: 130.2360 Evaluate side-chains 132 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 115 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.0040 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.0970 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 85 ASN D 85 ASN E 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.094161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.070519 restraints weight = 32732.068| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.57 r_work: 0.2917 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15095 Z= 0.160 Angle : 0.707 9.740 20490 Z= 0.367 Chirality : 0.046 0.165 2300 Planarity : 0.004 0.046 2545 Dihedral : 8.779 100.585 2007 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.38 % Allowed : 10.97 % Favored : 86.65 % 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: 0.22 (0.19), residues: 1775 helix: 2.28 (0.19), residues: 645 sheet: 0.77 (0.27), residues: 380 loop : -2.27 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 415 TYR 0.022 0.002 TYR E 325 PHE 0.011 0.001 PHE D 87 TRP 0.025 0.002 TRP E 267 HIS 0.004 0.001 HIS D 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (15085) covalent geometry : angle 0.70648 / 0.37 (20465) SS BOND : bond 0.00524 / 0.31 ( 5) SS BOND : angle 0.16352 / 0.09 ( 10) hydrogen bonds : bond 0.07207 / 4.81 ( 720) hydrogen bonds : angle 5.00995 / 3.53 ( 2505) link_NAG-ASN : bond 0.00267 / 0.16 ( 5) link_NAG-ASN : angle 0.98340 / 0.53 ( 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 190 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 0.359 Fit side-chains REVERT: A 113 MET cc_start: 0.8568 (ppp) cc_final: 0.8365 (ppp) REVERT: A 171 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8413 (mpp) REVERT: A 267 TRP cc_start: 0.6623 (t-100) cc_final: 0.6165 (t-100) REVERT: A 426 ASN cc_start: 0.8606 (t0) cc_final: 0.8392 (t0) REVERT: A 428 PHE cc_start: 0.8730 (t80) cc_final: 0.8306 (m-80) REVERT: A 437 ARG cc_start: 0.7241 (mtp180) cc_final: 0.6084 (mtm180) REVERT: B 79 THR cc_start: 0.8932 (m) cc_final: 0.8348 (p) REVERT: B 81 ASP cc_start: 0.8489 (p0) cc_final: 0.8109 (p0) REVERT: B 196 GLU cc_start: 0.8596 (pm20) cc_final: 0.8348 (pm20) REVERT: B 257 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7717 (tp) REVERT: B 266 PHE cc_start: 0.6209 (m-10) cc_final: 0.5753 (m-10) REVERT: B 428 PHE cc_start: 0.8775 (t80) cc_final: 0.8194 (t80) REVERT: B 437 ARG cc_start: 0.7071 (mtp180) cc_final: 0.6164 (mtt180) REVERT: C 308 ASP cc_start: 0.8867 (m-30) cc_final: 0.8584 (m-30) REVERT: C 428 PHE cc_start: 0.8809 (t80) cc_final: 0.8111 (t80) REVERT: C 437 ARG cc_start: 0.7047 (mtp180) cc_final: 0.6056 (mtt180) REVERT: D 79 THR cc_start: 0.8957 (m) cc_final: 0.8399 (p) REVERT: D 81 ASP cc_start: 0.8580 (p0) cc_final: 0.8316 (p0) REVERT: D 113 MET cc_start: 0.8337 (ppp) cc_final: 0.7992 (ppp) REVERT: D 243 GLN cc_start: 0.9078 (mm-40) cc_final: 0.8855 (mt0) REVERT: D 428 PHE cc_start: 0.8879 (t80) cc_final: 0.8306 (t80) REVERT: D 437 ARG cc_start: 0.7098 (mtp180) cc_final: 0.6209 (mtt180) REVERT: E 79 THR cc_start: 0.9036 (m) cc_final: 0.8580 (p) REVERT: E 81 ASP cc_start: 0.8457 (p0) cc_final: 0.8203 (p0) REVERT: E 113 MET cc_start: 0.8621 (pmm) cc_final: 0.8078 (ppp) REVERT: E 187 MET cc_start: 0.8674 (mmm) cc_final: 0.8444 (tpp) REVERT: E 308 ASP cc_start: 0.9066 (m-30) cc_final: 0.8722 (m-30) REVERT: E 428 PHE cc_start: 0.8843 (t80) cc_final: 0.8264 (t80) REVERT: E 437 ARG cc_start: 0.7201 (mtp180) cc_final: 0.6201 (mtm180) outliers start: 38 outliers final: 14 residues processed: 176 average time/residue: 0.4879 time to fit residues: 94.9220 Evaluate side-chains 151 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 204 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 20 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 121 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.091448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.067097 restraints weight = 33305.236| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.60 r_work: 0.2841 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15095 Z= 0.173 Angle : 0.661 7.466 20490 Z= 0.341 Chirality : 0.045 0.154 2300 Planarity : 0.004 0.043 2545 Dihedral : 7.742 98.710 2001 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.01 % Allowed : 11.35 % Favored : 85.64 % 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: 0.41 (0.19), residues: 1775 helix: 2.40 (0.19), residues: 645 sheet: 0.90 (0.25), residues: 380 loop : -2.14 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 242 TYR 0.020 0.002 TYR B 325 PHE 0.016 0.002 PHE D 87 TRP 0.013 0.001 TRP E 267 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (15085) covalent geometry : angle 0.66013 / 0.34 (20465) SS BOND : bond 0.00521 / 0.30 ( 5) SS BOND : angle 0.47561 / 0.24 ( 10) hydrogen bonds : bond 0.06343 / 4.23 ( 720) hydrogen bonds : angle 4.46426 / 3.12 ( 2505) link_NAG-ASN : bond 0.00055 / 0.04 ( 5) link_NAG-ASN : angle 1.14498 / 0.61 ( 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 194 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 146 time to evaluate : 0.491 Fit side-chains REVERT: A 113 MET cc_start: 0.8677 (ppp) cc_final: 0.8039 (ppp) REVERT: A 171 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8367 (mpp) REVERT: A 267 TRP cc_start: 0.6665 (t-100) cc_final: 0.6428 (t-100) REVERT: A 428 PHE cc_start: 0.8845 (t80) cc_final: 0.8125 (t80) REVERT: A 437 ARG cc_start: 0.7253 (mtp180) cc_final: 0.6093 (mtm180) REVERT: B 79 THR cc_start: 0.8994 (m) cc_final: 0.8660 (p) REVERT: B 266 PHE cc_start: 0.6592 (m-10) cc_final: 0.6333 (m-10) REVERT: B 428 PHE cc_start: 0.8790 (t80) cc_final: 0.8178 (t80) REVERT: C 266 PHE cc_start: 0.7028 (m-10) cc_final: 0.6756 (m-80) REVERT: C 428 PHE cc_start: 0.8824 (t80) cc_final: 0.8130 (t80) REVERT: C 437 ARG cc_start: 0.6967 (mtp180) cc_final: 0.5822 (mtm180) REVERT: D 113 MET cc_start: 0.8434 (ppp) cc_final: 0.8070 (ppp) REVERT: D 428 PHE cc_start: 0.8837 (t80) cc_final: 0.8269 (t80) REVERT: D 437 ARG cc_start: 0.7091 (mtp180) cc_final: 0.6147 (mtm180) REVERT: E 79 THR cc_start: 0.9019 (m) cc_final: 0.8689 (p) REVERT: E 113 MET cc_start: 0.8587 (pmm) cc_final: 0.8152 (ppp) REVERT: E 308 ASP cc_start: 0.9071 (m-30) cc_final: 0.8815 (m-30) REVERT: E 428 PHE cc_start: 0.8859 (t80) cc_final: 0.8241 (t80) REVERT: E 437 ARG cc_start: 0.7198 (mtp180) cc_final: 0.6070 (mtm180) outliers start: 48 outliers final: 16 residues processed: 179 average time/residue: 0.5041 time to fit residues: 99.6337 Evaluate side-chains 149 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 264 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 137 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 GLN ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN D 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.092092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.067783 restraints weight = 32776.324| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.58 r_work: 0.2851 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15095 Z= 0.141 Angle : 0.624 8.171 20490 Z= 0.321 Chirality : 0.044 0.136 2300 Planarity : 0.003 0.047 2545 Dihedral : 7.472 98.913 1997 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.07 % Allowed : 12.79 % Favored : 84.14 % 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: 0.57 (0.19), residues: 1775 helix: 2.53 (0.19), residues: 645 sheet: 0.93 (0.25), residues: 380 loop : -2.01 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 333 TYR 0.017 0.002 TYR D 325 PHE 0.012 0.001 PHE D 87 TRP 0.017 0.001 TRP E 267 HIS 0.004 0.001 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (15085) covalent geometry : angle 0.62373 / 0.32 (20465) SS BOND : bond 0.00377 / 0.22 ( 5) SS BOND : angle 0.29250 / 0.15 ( 10) hydrogen bonds : bond 0.05607 / 3.73 ( 720) hydrogen bonds : angle 4.14335 / 2.88 ( 2505) link_NAG-ASN : bond 0.00165 / 0.10 ( 5) link_NAG-ASN : angle 0.81914 / 0.44 ( 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 192 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 143 time to evaluate : 0.757 Fit side-chains revert: symmetry clash REVERT: A 113 MET cc_start: 0.8528 (ppp) cc_final: 0.8089 (ppp) REVERT: A 428 PHE cc_start: 0.8824 (t80) cc_final: 0.8108 (t80) REVERT: A 437 ARG cc_start: 0.7176 (mtp180) cc_final: 0.6009 (mtm180) REVERT: B 196 GLU cc_start: 0.8551 (pm20) cc_final: 0.8278 (pm20) REVERT: B 266 PHE cc_start: 0.6625 (m-10) cc_final: 0.6350 (m-80) REVERT: B 428 PHE cc_start: 0.8772 (t80) cc_final: 0.8164 (t80) REVERT: C 266 PHE cc_start: 0.7052 (m-10) cc_final: 0.6776 (m-10) REVERT: C 428 PHE cc_start: 0.8841 (t80) cc_final: 0.8165 (t80) REVERT: C 437 ARG cc_start: 0.6882 (mtp180) cc_final: 0.5874 (mtm180) REVERT: D 113 MET cc_start: 0.8402 (ppp) cc_final: 0.7992 (ppp) REVERT: D 181 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8015 (pp20) REVERT: D 428 PHE cc_start: 0.8805 (t80) cc_final: 0.8250 (t80) REVERT: D 437 ARG cc_start: 0.7122 (mtp180) cc_final: 0.6233 (mtm180) REVERT: E 79 THR cc_start: 0.8941 (m) cc_final: 0.8575 (p) REVERT: E 113 MET cc_start: 0.8530 (pmm) cc_final: 0.8032 (ppp) REVERT: E 308 ASP cc_start: 0.9053 (m-30) cc_final: 0.8792 (m-30) REVERT: E 428 PHE cc_start: 0.8847 (t80) cc_final: 0.8227 (t80) REVERT: E 437 ARG cc_start: 0.7115 (mtp180) cc_final: 0.6086 (mtm180) outliers start: 49 outliers final: 21 residues processed: 172 average time/residue: 0.5485 time to fit residues: 104.0611 Evaluate side-chains 154 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 48 optimal weight: 0.0670 chunk 164 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN C 179 GLN E 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.091331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.066720 restraints weight = 33129.797| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.59 r_work: 0.2826 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 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 : 0.003 0.039 15095 Z= 0.148 Angle : 0.620 8.913 20490 Z= 0.318 Chirality : 0.043 0.141 2300 Planarity : 0.003 0.038 2545 Dihedral : 7.403 99.348 1997 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.76 % Allowed : 14.29 % Favored : 82.95 % 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: 0.65 (0.19), residues: 1775 helix: 2.86 (0.18), residues: 615 sheet: 0.78 (0.24), residues: 410 loop : -2.01 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 333 TYR 0.017 0.002 TYR B 325 PHE 0.013 0.001 PHE C 87 TRP 0.018 0.001 TRP B 267 HIS 0.003 0.001 HIS A 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (15085) covalent geometry : angle 0.61934 / 0.32 (20465) SS BOND : bond 0.00354 / 0.21 ( 5) SS BOND : angle 0.34460 / 0.17 ( 10) hydrogen bonds : bond 0.05332 / 3.55 ( 720) hydrogen bonds : angle 4.02212 / 2.77 ( 2505) link_NAG-ASN : bond 0.00098 / 0.06 ( 5) link_NAG-ASN : angle 0.93168 / 0.51 ( 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 184 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 140 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8536 (ppp) cc_final: 0.8181 (ppp) REVERT: A 428 PHE cc_start: 0.8823 (t80) cc_final: 0.8105 (t80) REVERT: B 79 THR cc_start: 0.9019 (m) cc_final: 0.8602 (p) REVERT: B 428 PHE cc_start: 0.8751 (t80) cc_final: 0.8138 (t80) REVERT: C 113 MET cc_start: 0.8425 (ppp) cc_final: 0.8154 (ppp) REVERT: C 181 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8245 (pp20) REVERT: C 196 GLU cc_start: 0.8396 (pm20) cc_final: 0.7548 (pm20) REVERT: C 197 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8006 (pmtt) REVERT: C 266 PHE cc_start: 0.7119 (m-10) cc_final: 0.6792 (m-10) REVERT: C 428 PHE cc_start: 0.8861 (t80) cc_final: 0.8424 (t80) REVERT: D 113 MET cc_start: 0.8463 (ppp) cc_final: 0.8106 (ppp) REVERT: D 428 PHE cc_start: 0.8791 (t80) cc_final: 0.8228 (t80) REVERT: E 79 THR cc_start: 0.8952 (m) cc_final: 0.8574 (p) REVERT: E 113 MET cc_start: 0.8499 (pmm) cc_final: 0.8133 (ppp) REVERT: E 308 ASP cc_start: 0.9055 (m-30) cc_final: 0.8811 (m-30) REVERT: E 428 PHE cc_start: 0.8796 (t80) cc_final: 0.8165 (t80) REVERT: E 437 ARG cc_start: 0.7077 (mtp180) cc_final: 0.6076 (mtm180) outliers start: 44 outliers final: 23 residues processed: 167 average time/residue: 0.5089 time to fit residues: 93.8175 Evaluate side-chains 156 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 123 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 101 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 8 optimal weight: 0.0770 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.090654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.065949 restraints weight = 32872.896| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 3.59 r_work: 0.2811 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15095 Z= 0.157 Angle : 0.631 9.433 20490 Z= 0.325 Chirality : 0.043 0.155 2300 Planarity : 0.003 0.036 2545 Dihedral : 7.396 99.609 1997 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.63 % Allowed : 15.61 % Favored : 81.76 % 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: 0.66 (0.19), residues: 1775 helix: 2.87 (0.18), residues: 615 sheet: 0.74 (0.24), residues: 410 loop : -1.99 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 242 TYR 0.016 0.002 TYR D 325 PHE 0.013 0.001 PHE D 87 TRP 0.020 0.001 TRP B 267 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (15085) covalent geometry : angle 0.63049 / 0.32 (20465) SS BOND : bond 0.00350 / 0.21 ( 5) SS BOND : angle 0.37252 / 0.19 ( 10) hydrogen bonds : bond 0.05270 / 3.51 ( 720) hydrogen bonds : angle 3.87395 / 2.67 ( 2505) link_NAG-ASN : bond 0.00066 / 0.04 ( 5) link_NAG-ASN : angle 0.92196 / 0.50 ( 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 175 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 133 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8522 (ppp) cc_final: 0.8165 (ppp) REVERT: A 181 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8213 (tm-30) REVERT: A 428 PHE cc_start: 0.8819 (t80) cc_final: 0.8101 (t80) REVERT: B 221 TYR cc_start: 0.8627 (OUTLIER) cc_final: 0.8247 (p90) REVERT: B 428 PHE cc_start: 0.8766 (t80) cc_final: 0.8135 (t80) REVERT: C 181 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8226 (pp20) REVERT: C 221 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.8072 (p90) REVERT: C 266 PHE cc_start: 0.7168 (m-10) cc_final: 0.6768 (m-10) REVERT: C 428 PHE cc_start: 0.8873 (t80) cc_final: 0.8438 (t80) REVERT: D 113 MET cc_start: 0.8428 (ppp) cc_final: 0.8051 (ppp) REVERT: D 221 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.8330 (p90) REVERT: D 428 PHE cc_start: 0.8825 (t80) cc_final: 0.8278 (t80) REVERT: E 79 THR cc_start: 0.8954 (m) cc_final: 0.8708 (p) REVERT: E 113 MET cc_start: 0.8484 (pmm) cc_final: 0.8089 (ppp) REVERT: E 221 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.8256 (p90) REVERT: E 308 ASP cc_start: 0.9051 (m-30) cc_final: 0.8809 (m-30) REVERT: E 428 PHE cc_start: 0.8792 (t80) cc_final: 0.8154 (t80) outliers start: 42 outliers final: 25 residues processed: 156 average time/residue: 0.4797 time to fit residues: 82.9340 Evaluate side-chains 164 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 145 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 101 optimal weight: 20.0000 chunk 137 optimal weight: 4.9990 chunk 6 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.091408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.066711 restraints weight = 32638.151| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.58 r_work: 0.2826 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15095 Z= 0.134 Angle : 0.622 10.446 20490 Z= 0.317 Chirality : 0.043 0.142 2300 Planarity : 0.003 0.032 2545 Dihedral : 7.275 98.997 1997 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.82 % Allowed : 16.11 % Favored : 81.07 % 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: 0.75 (0.19), residues: 1775 helix: 2.99 (0.18), residues: 615 sheet: 0.76 (0.25), residues: 400 loop : -1.92 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 333 TYR 0.015 0.001 TYR A 433 PHE 0.011 0.001 PHE A 87 TRP 0.012 0.001 TRP B 267 HIS 0.003 0.001 HIS A 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (15085) covalent geometry : angle 0.62164 / 0.32 (20465) SS BOND : bond 0.00320 / 0.19 ( 5) SS BOND : angle 0.26775 / 0.13 ( 10) hydrogen bonds : bond 0.04878 / 3.25 ( 720) hydrogen bonds : angle 3.71257 / 2.56 ( 2505) link_NAG-ASN : bond 0.00155 / 0.09 ( 5) link_NAG-ASN : angle 0.76409 / 0.42 ( 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 185 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 140 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 113 MET cc_start: 0.8507 (ppp) cc_final: 0.8031 (ppp) REVERT: A 181 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8169 (tm-30) REVERT: A 196 GLU cc_start: 0.8339 (pm20) cc_final: 0.7983 (pm20) REVERT: A 197 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8356 (pmtt) REVERT: A 263 TRP cc_start: 0.7696 (m-10) cc_final: 0.7467 (m-10) REVERT: A 428 PHE cc_start: 0.8762 (t80) cc_final: 0.8102 (t80) REVERT: B 181 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8526 (pp20) REVERT: B 196 GLU cc_start: 0.8304 (pm20) cc_final: 0.7935 (pm20) REVERT: B 197 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8167 (pmtt) REVERT: B 428 PHE cc_start: 0.8742 (t80) cc_final: 0.8124 (t80) REVERT: C 181 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8198 (pp20) REVERT: C 196 GLU cc_start: 0.8312 (pm20) cc_final: 0.7580 (pm20) REVERT: C 197 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8039 (pmtt) REVERT: C 221 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.8012 (p90) REVERT: C 266 PHE cc_start: 0.7135 (m-10) cc_final: 0.6903 (m-10) REVERT: C 428 PHE cc_start: 0.8854 (t80) cc_final: 0.8412 (t80) REVERT: D 113 MET cc_start: 0.8432 (ppp) cc_final: 0.8060 (ppp) REVERT: D 428 PHE cc_start: 0.8800 (t80) cc_final: 0.8245 (t80) REVERT: E 79 THR cc_start: 0.8881 (m) cc_final: 0.8629 (p) REVERT: E 113 MET cc_start: 0.8433 (pmm) cc_final: 0.8082 (ppp) REVERT: E 221 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.8187 (p90) REVERT: E 308 ASP cc_start: 0.9060 (m-30) cc_final: 0.8817 (m-30) REVERT: E 428 PHE cc_start: 0.8777 (t80) cc_final: 0.8184 (t80) outliers start: 45 outliers final: 24 residues processed: 165 average time/residue: 0.4935 time to fit residues: 90.0733 Evaluate side-chains 168 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 42 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 148 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.091677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.066906 restraints weight = 32652.301| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.59 r_work: 0.2827 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15095 Z= 0.130 Angle : 0.619 11.317 20490 Z= 0.312 Chirality : 0.043 0.143 2300 Planarity : 0.003 0.033 2545 Dihedral : 7.052 98.291 1995 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.76 % Allowed : 16.49 % Favored : 80.75 % 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: 0.79 (0.19), residues: 1775 helix: 3.04 (0.19), residues: 615 sheet: 0.75 (0.25), residues: 390 loop : -1.86 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 333 TYR 0.016 0.001 TYR A 433 PHE 0.012 0.001 PHE D 266 TRP 0.009 0.001 TRP B 267 HIS 0.002 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (15085) covalent geometry : angle 0.61863 / 0.31 (20465) SS BOND : bond 0.00312 / 0.18 ( 5) SS BOND : angle 0.27093 / 0.14 ( 10) hydrogen bonds : bond 0.04690 / 3.12 ( 720) hydrogen bonds : angle 3.65040 / 2.51 ( 2505) link_NAG-ASN : bond 0.00128 / 0.08 ( 5) link_NAG-ASN : angle 0.76688 / 0.42 ( 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 182 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 138 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 113 MET cc_start: 0.8541 (ppp) cc_final: 0.8098 (ppp) REVERT: A 181 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8169 (tm-30) REVERT: A 196 GLU cc_start: 0.8299 (pm20) cc_final: 0.7742 (pm20) REVERT: A 197 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8239 (pmtt) REVERT: A 221 TYR cc_start: 0.8461 (OUTLIER) cc_final: 0.7864 (p90) REVERT: A 263 TRP cc_start: 0.7644 (m-10) cc_final: 0.7359 (m-10) REVERT: A 428 PHE cc_start: 0.8770 (t80) cc_final: 0.8118 (t80) REVERT: B 181 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8529 (pp20) REVERT: B 196 GLU cc_start: 0.8252 (pm20) cc_final: 0.8031 (pm20) REVERT: B 428 PHE cc_start: 0.8746 (t80) cc_final: 0.8127 (t80) REVERT: C 181 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8193 (pp20) REVERT: C 221 TYR cc_start: 0.8464 (OUTLIER) cc_final: 0.7921 (p90) REVERT: C 266 PHE cc_start: 0.7130 (m-10) cc_final: 0.6772 (m-10) REVERT: C 428 PHE cc_start: 0.8855 (t80) cc_final: 0.8421 (t80) REVERT: D 113 MET cc_start: 0.8436 (ppp) cc_final: 0.8082 (ppp) REVERT: D 221 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.8203 (p90) REVERT: D 270 MET cc_start: 0.4036 (pmm) cc_final: 0.3818 (mmm) REVERT: D 428 PHE cc_start: 0.8797 (t80) cc_final: 0.8244 (t80) REVERT: E 79 THR cc_start: 0.8893 (m) cc_final: 0.8640 (p) REVERT: E 113 MET cc_start: 0.8426 (pmm) cc_final: 0.8074 (ppp) REVERT: E 221 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.8182 (p90) REVERT: E 263 TRP cc_start: 0.7954 (m-10) cc_final: 0.7495 (m-10) REVERT: E 308 ASP cc_start: 0.9031 (m-30) cc_final: 0.8792 (m-30) REVERT: E 428 PHE cc_start: 0.8811 (t80) cc_final: 0.8228 (t80) outliers start: 44 outliers final: 25 residues processed: 165 average time/residue: 0.4835 time to fit residues: 88.6556 Evaluate side-chains 169 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 GLN E 290 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.092558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.067720 restraints weight = 32325.533| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.46 r_work: 0.2859 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15095 Z= 0.130 Angle : 0.614 9.945 20490 Z= 0.309 Chirality : 0.043 0.143 2300 Planarity : 0.003 0.032 2545 Dihedral : 6.994 97.871 1995 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.45 % Allowed : 17.12 % Favored : 80.44 % 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: 0.83 (0.19), residues: 1775 helix: 3.02 (0.19), residues: 620 sheet: 0.71 (0.25), residues: 400 loop : -1.80 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 242 TYR 0.016 0.001 TYR A 433 PHE 0.014 0.001 PHE D 266 TRP 0.033 0.001 TRP D 263 HIS 0.002 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (15085) covalent geometry : angle 0.61411 / 0.31 (20465) SS BOND : bond 0.00312 / 0.18 ( 5) SS BOND : angle 0.28937 / 0.14 ( 10) hydrogen bonds : bond 0.04606 / 3.06 ( 720) hydrogen bonds : angle 3.62953 / 2.49 ( 2505) link_NAG-ASN : bond 0.00132 / 0.08 ( 5) link_NAG-ASN : angle 0.77671 / 0.43 ( 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 179 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 140 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 113 MET cc_start: 0.8617 (ppp) cc_final: 0.8195 (ppp) REVERT: A 181 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8145 (tm-30) REVERT: A 196 GLU cc_start: 0.8325 (pm20) cc_final: 0.7752 (pm20) REVERT: A 197 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8183 (pmtt) REVERT: A 221 TYR cc_start: 0.8466 (OUTLIER) cc_final: 0.7952 (p90) REVERT: A 263 TRP cc_start: 0.7680 (m-10) cc_final: 0.7393 (m-10) REVERT: A 428 PHE cc_start: 0.8781 (t80) cc_final: 0.8125 (t80) REVERT: B 181 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8560 (pp20) REVERT: B 333 ARG cc_start: 0.8364 (tpp80) cc_final: 0.8106 (tpp-160) REVERT: B 428 PHE cc_start: 0.8752 (t80) cc_final: 0.8125 (t80) REVERT: C 181 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8268 (pp20) REVERT: C 196 GLU cc_start: 0.8286 (pm20) cc_final: 0.7568 (pm20) REVERT: C 197 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8004 (pmtt) REVERT: C 221 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.7903 (p90) REVERT: C 266 PHE cc_start: 0.7113 (m-10) cc_final: 0.6814 (m-10) REVERT: C 426 ASN cc_start: 0.8616 (t0) cc_final: 0.8369 (t0) REVERT: C 428 PHE cc_start: 0.8874 (t80) cc_final: 0.8439 (t80) REVERT: D 113 MET cc_start: 0.8482 (ppp) cc_final: 0.8151 (ppp) REVERT: D 221 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.8172 (p90) REVERT: D 428 PHE cc_start: 0.8782 (t80) cc_final: 0.8193 (t80) REVERT: E 79 THR cc_start: 0.8962 (m) cc_final: 0.8707 (p) REVERT: E 113 MET cc_start: 0.8406 (pmm) cc_final: 0.8154 (ppp) REVERT: E 221 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.8109 (p90) REVERT: E 263 TRP cc_start: 0.7987 (m-10) cc_final: 0.7520 (m-10) REVERT: E 308 ASP cc_start: 0.8992 (m-30) cc_final: 0.8769 (m-30) REVERT: E 428 PHE cc_start: 0.8844 (t80) cc_final: 0.8249 (t80) outliers start: 39 outliers final: 23 residues processed: 164 average time/residue: 0.4785 time to fit residues: 86.7094 Evaluate side-chains 166 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 63 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 72 optimal weight: 0.0870 chunk 103 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.092908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.067981 restraints weight = 32184.554| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.45 r_work: 0.2864 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15095 Z= 0.126 Angle : 0.607 10.294 20490 Z= 0.309 Chirality : 0.043 0.145 2300 Planarity : 0.003 0.032 2545 Dihedral : 6.926 97.430 1995 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.19 % Allowed : 17.87 % Favored : 79.94 % 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: 0.85 (0.19), residues: 1775 helix: 3.04 (0.19), residues: 620 sheet: 0.84 (0.25), residues: 380 loop : -1.81 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 242 TYR 0.018 0.001 TYR E 433 PHE 0.015 0.001 PHE D 266 TRP 0.048 0.001 TRP D 263 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (15085) covalent geometry : angle 0.60694 / 0.31 (20465) SS BOND : bond 0.00308 / 0.18 ( 5) SS BOND : angle 0.28060 / 0.14 ( 10) hydrogen bonds : bond 0.04494 / 2.99 ( 720) hydrogen bonds : angle 3.59667 / 2.47 ( 2505) link_NAG-ASN : bond 0.00148 / 0.09 ( 5) link_NAG-ASN : angle 0.74387 / 0.41 ( 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 173 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: A 113 MET cc_start: 0.8645 (ppp) cc_final: 0.8175 (ppp) REVERT: A 181 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8183 (tm-30) REVERT: A 196 GLU cc_start: 0.8332 (pm20) cc_final: 0.7760 (pm20) REVERT: A 197 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8161 (pmtt) REVERT: A 221 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.7922 (p90) REVERT: A 263 TRP cc_start: 0.7675 (m-10) cc_final: 0.7330 (m-10) REVERT: A 428 PHE cc_start: 0.8784 (t80) cc_final: 0.8132 (t80) REVERT: B 181 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8546 (pp20) REVERT: B 428 PHE cc_start: 0.8748 (t80) cc_final: 0.8106 (t80) REVERT: C 181 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8274 (pp20) REVERT: C 221 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.7861 (p90) REVERT: C 263 TRP cc_start: 0.7870 (m-10) cc_final: 0.7504 (m-10) REVERT: C 426 ASN cc_start: 0.8623 (t0) cc_final: 0.8353 (t0) REVERT: C 428 PHE cc_start: 0.8881 (t80) cc_final: 0.8456 (t80) REVERT: D 113 MET cc_start: 0.8489 (ppp) cc_final: 0.8147 (ppp) REVERT: D 221 TYR cc_start: 0.8348 (OUTLIER) cc_final: 0.8088 (p90) REVERT: D 428 PHE cc_start: 0.8770 (t80) cc_final: 0.8184 (t80) REVERT: E 79 THR cc_start: 0.8960 (m) cc_final: 0.8694 (p) REVERT: E 113 MET cc_start: 0.8413 (pmm) cc_final: 0.8142 (ppp) REVERT: E 181 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8389 (pp20) REVERT: E 187 MET cc_start: 0.8846 (tpt) cc_final: 0.8417 (tpp) REVERT: E 196 GLU cc_start: 0.8400 (pm20) cc_final: 0.8167 (pm20) REVERT: E 221 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.8058 (p90) REVERT: E 263 TRP cc_start: 0.7956 (m-10) cc_final: 0.7502 (m-10) REVERT: E 308 ASP cc_start: 0.8986 (m-30) cc_final: 0.8762 (m-30) REVERT: E 428 PHE cc_start: 0.8857 (t80) cc_final: 0.8287 (t80) outliers start: 35 outliers final: 26 residues processed: 158 average time/residue: 0.5154 time to fit residues: 90.0268 Evaluate side-chains 168 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 129 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 107 optimal weight: 0.0170 chunk 146 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.092779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.067925 restraints weight = 32109.745| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.44 r_work: 0.2864 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15095 Z= 0.129 Angle : 0.624 11.017 20490 Z= 0.313 Chirality : 0.043 0.145 2300 Planarity : 0.003 0.032 2545 Dihedral : 6.908 97.220 1995 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.45 % Allowed : 17.87 % Favored : 79.69 % 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: 0.85 (0.19), residues: 1775 helix: 3.04 (0.19), residues: 620 sheet: 0.84 (0.25), residues: 380 loop : -1.81 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 333 TYR 0.015 0.001 TYR A 433 PHE 0.015 0.001 PHE D 266 TRP 0.040 0.001 TRP D 263 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (15085) covalent geometry : angle 0.62359 / 0.31 (20465) SS BOND : bond 0.00306 / 0.18 ( 5) SS BOND : angle 0.29129 / 0.14 ( 10) hydrogen bonds : bond 0.04463 / 2.96 ( 720) hydrogen bonds : angle 3.59829 / 2.47 ( 2505) link_NAG-ASN : bond 0.00144 / 0.09 ( 5) link_NAG-ASN : angle 0.74351 / 0.41 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3265.33 seconds wall clock time: 56 minutes 36.77 seconds (3396.77 seconds total)