Starting phenix.real_space_refine on Thu Feb 5 04:04:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m6q_23704/02_2026/7m6q_23704.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m6q_23704/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7m6q_23704/02_2026/7m6q_23704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m6q_23704/02_2026/7m6q_23704.map" model { file = "/net/cci-nas-00/data/ceres_data/7m6q_23704/02_2026/7m6q_23704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m6q_23704/02_2026/7m6q_23704.cif" } 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-2.0-5952/lib/python3.9/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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.80, per 1000 atoms: 0.19 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: 1.27 Conformation dependent library (CDL) restraints added in 462.6 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: 0.46 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: 2.10 Time building geometry restraints manager: 1.68 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 - 35.91: 8960 35.91 - 71.82: 170 71.82 - 107.74: 15 107.74 - 143.65: 0 143.65 - 179.56: 10 Dihedral angle restraints: 9155 sinusoidal: 3845 harmonic: 5310 Sorted by residual: dihedral pdb=" C11 TCI D 803 " pdb=" C12 TCI D 803 " pdb=" C13 TCI D 803 " pdb=" C15 TCI D 803 " ideal model delta sinusoidal sigma weight residual 64.70 -114.86 179.56 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C11 TCI A 803 " pdb=" C12 TCI A 803 " pdb=" C13 TCI A 803 " pdb=" C15 TCI A 803 " ideal model delta sinusoidal sigma weight residual 64.70 -114.84 179.54 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C11 TCI E 502 " pdb=" C12 TCI E 502 " pdb=" C13 TCI E 502 " pdb=" C15 TCI E 502 " ideal model delta sinusoidal sigma weight residual 64.70 -114.84 179.54 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 9152 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.600 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 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:6.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 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 : 15.900 179.560 5690 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 covalent geometry : bond 0.00853 (15085) covalent geometry : angle 1.15894 (20465) SS BOND : bond 0.01046 ( 5) SS BOND : angle 1.15600 ( 10) hydrogen bonds : bond 0.19442 ( 720) hydrogen bonds : angle 6.80224 ( 2505) link_NAG-ASN : bond 0.00417 ( 5) link_NAG-ASN : angle 2.56188 ( 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 : 0.575 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: 0.5674 time to fit residues: 143.4011 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 : 0.532 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3529 r_free = 0.3529 target = 0.094138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.070485 restraints weight = 32721.895| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.57 r_work: 0.2918 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15095 Z= 0.159 Angle : 0.705 9.803 20490 Z= 0.366 Chirality : 0.046 0.167 2300 Planarity : 0.004 0.047 2545 Dihedral : 16.648 179.120 2212 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.61 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 0.008 0.001 ARG D 415 TYR 0.022 0.002 TYR E 325 PHE 0.011 0.001 PHE D 87 TRP 0.023 0.002 TRP E 267 HIS 0.004 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00332 (15085) covalent geometry : angle 0.70530 (20465) SS BOND : bond 0.00517 ( 5) SS BOND : angle 0.17128 ( 10) hydrogen bonds : bond 0.07191 ( 720) hydrogen bonds : angle 5.00327 ( 2505) link_NAG-ASN : bond 0.00283 ( 5) link_NAG-ASN : angle 1.04792 ( 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 189 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 0.558 Fit side-chains REVERT: A 171 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8416 (mpp) REVERT: A 267 TRP cc_start: 0.6626 (t-100) cc_final: 0.6167 (t-100) REVERT: A 426 ASN cc_start: 0.8608 (t0) cc_final: 0.8394 (t0) REVERT: A 428 PHE cc_start: 0.8730 (t80) cc_final: 0.8306 (m-80) REVERT: A 437 ARG cc_start: 0.7239 (mtp180) cc_final: 0.6081 (mtm180) REVERT: B 79 THR cc_start: 0.8934 (m) cc_final: 0.8351 (p) REVERT: B 81 ASP cc_start: 0.8491 (p0) cc_final: 0.8108 (p0) REVERT: B 196 GLU cc_start: 0.8595 (pm20) cc_final: 0.8348 (pm20) REVERT: B 266 PHE cc_start: 0.6208 (m-10) cc_final: 0.5751 (m-10) REVERT: B 428 PHE cc_start: 0.8777 (t80) cc_final: 0.8195 (t80) REVERT: B 437 ARG cc_start: 0.7074 (mtp180) cc_final: 0.6166 (mtt180) REVERT: C 308 ASP cc_start: 0.8868 (m-30) cc_final: 0.8583 (m-30) REVERT: C 428 PHE cc_start: 0.8810 (t80) cc_final: 0.8112 (t80) REVERT: C 437 ARG cc_start: 0.7049 (mtp180) cc_final: 0.6057 (mtt180) REVERT: D 79 THR cc_start: 0.8961 (m) cc_final: 0.8402 (p) REVERT: D 81 ASP cc_start: 0.8560 (p0) cc_final: 0.8299 (p0) REVERT: D 113 MET cc_start: 0.8333 (ppp) cc_final: 0.7988 (ppp) REVERT: D 243 GLN cc_start: 0.9081 (mm-40) cc_final: 0.8856 (mt0) REVERT: D 428 PHE cc_start: 0.8879 (t80) cc_final: 0.8307 (t80) REVERT: D 437 ARG cc_start: 0.7099 (mtp180) cc_final: 0.6209 (mtt180) REVERT: E 79 THR cc_start: 0.9041 (m) cc_final: 0.8583 (p) REVERT: E 81 ASP cc_start: 0.8462 (p0) cc_final: 0.8206 (p0) REVERT: E 113 MET cc_start: 0.8623 (pmm) cc_final: 0.8080 (ppp) REVERT: E 187 MET cc_start: 0.8660 (mmm) cc_final: 0.8422 (tpp) REVERT: E 308 ASP cc_start: 0.9068 (m-30) cc_final: 0.8728 (m-30) REVERT: E 428 PHE cc_start: 0.8843 (t80) cc_final: 0.8264 (t80) REVERT: E 437 ARG cc_start: 0.7202 (mtp180) cc_final: 0.6201 (mtm180) outliers start: 38 outliers final: 14 residues processed: 175 average time/residue: 0.5558 time to fit residues: 107.1652 Evaluate side-chains 149 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 143 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 36 optimal weight: 0.0370 chunk 121 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 chunk 82 optimal weight: 2.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.092569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.068416 restraints weight = 33185.934| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.59 r_work: 0.2869 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2155 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= 0.151 Angle : 0.651 7.590 20490 Z= 0.333 Chirality : 0.045 0.155 2300 Planarity : 0.004 0.041 2545 Dihedral : 15.999 179.896 2206 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.76 % Allowed : 11.47 % Favored : 85.77 % 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: 0.47 (0.19), residues: 1775 helix: 2.42 (0.19), residues: 645 sheet: 1.00 (0.25), residues: 380 loop : -2.12 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 155 TYR 0.019 0.002 TYR B 325 PHE 0.013 0.001 PHE D 87 TRP 0.014 0.001 TRP E 267 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00340 (15085) covalent geometry : angle 0.65071 (20465) SS BOND : bond 0.00451 ( 5) SS BOND : angle 0.39211 ( 10) hydrogen bonds : bond 0.06098 ( 720) hydrogen bonds : angle 4.40421 ( 2505) link_NAG-ASN : bond 0.00142 ( 5) link_NAG-ASN : angle 1.04114 ( 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 193 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 428 PHE cc_start: 0.8795 (t80) cc_final: 0.8061 (t80) REVERT: A 437 ARG cc_start: 0.7260 (mtp180) cc_final: 0.6110 (mtm180) REVERT: B 79 THR cc_start: 0.8952 (m) cc_final: 0.8629 (p) REVERT: B 266 PHE cc_start: 0.6562 (m-10) cc_final: 0.6122 (m-10) REVERT: B 428 PHE cc_start: 0.8787 (t80) cc_final: 0.8180 (t80) REVERT: C 428 PHE cc_start: 0.8822 (t80) cc_final: 0.8131 (t80) REVERT: C 437 ARG cc_start: 0.6916 (mtp180) cc_final: 0.5821 (mtm180) REVERT: D 113 MET cc_start: 0.8439 (ppp) cc_final: 0.8072 (ppp) REVERT: D 244 MET cc_start: 0.9136 (mmm) cc_final: 0.8923 (tpp) REVERT: D 428 PHE cc_start: 0.8844 (t80) cc_final: 0.8283 (t80) REVERT: D 437 ARG cc_start: 0.7072 (mtp180) cc_final: 0.6149 (mtm180) REVERT: E 79 THR cc_start: 0.8999 (m) cc_final: 0.8674 (p) REVERT: E 113 MET cc_start: 0.8563 (pmm) cc_final: 0.8105 (ppp) REVERT: E 308 ASP cc_start: 0.9054 (m-30) cc_final: 0.8798 (m-30) REVERT: E 428 PHE cc_start: 0.8847 (t80) cc_final: 0.8272 (t80) REVERT: E 437 ARG cc_start: 0.7066 (mtp180) cc_final: 0.6020 (mtm180) outliers start: 44 outliers final: 15 residues processed: 177 average time/residue: 0.5391 time to fit residues: 105.6866 Evaluate side-chains 147 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 244 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 298 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 244 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: 2.9990 chunk 20 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 84 optimal weight: 0.2980 chunk 87 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 19 optimal weight: 0.0970 chunk 117 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.093443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.069226 restraints weight = 32822.590| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 3.58 r_work: 0.2886 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2469 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= 0.128 Angle : 0.618 8.267 20490 Z= 0.315 Chirality : 0.043 0.145 2300 Planarity : 0.003 0.037 2545 Dihedral : 15.859 179.165 2202 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.76 % Allowed : 12.79 % Favored : 84.45 % 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: 0.61 (0.19), residues: 1775 helix: 2.52 (0.19), residues: 645 sheet: 1.02 (0.25), residues: 375 loop : -1.97 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 333 TYR 0.017 0.001 TYR D 325 PHE 0.011 0.001 PHE C 87 TRP 0.013 0.001 TRP E 267 HIS 0.003 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00282 (15085) covalent geometry : angle 0.61800 (20465) SS BOND : bond 0.00330 ( 5) SS BOND : angle 0.17839 ( 10) hydrogen bonds : bond 0.05390 ( 720) hydrogen bonds : angle 4.12515 ( 2505) link_NAG-ASN : bond 0.00209 ( 5) link_NAG-ASN : angle 0.78525 ( 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 183 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 139 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 428 PHE cc_start: 0.8757 (t80) cc_final: 0.8081 (t80) REVERT: A 437 ARG cc_start: 0.7135 (mtp180) cc_final: 0.6009 (mtm180) REVERT: B 79 THR cc_start: 0.8881 (m) cc_final: 0.8536 (p) REVERT: B 196 GLU cc_start: 0.8541 (pm20) cc_final: 0.8221 (pm20) REVERT: B 215 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8406 (tm-30) REVERT: B 266 PHE cc_start: 0.6480 (m-10) cc_final: 0.6189 (m-10) REVERT: B 428 PHE cc_start: 0.8772 (t80) cc_final: 0.8175 (t80) REVERT: C 428 PHE cc_start: 0.8818 (t80) cc_final: 0.8133 (t80) REVERT: D 113 MET cc_start: 0.8402 (ppp) cc_final: 0.8107 (ppp) REVERT: D 244 MET cc_start: 0.9105 (mmm) cc_final: 0.8886 (tpp) REVERT: D 428 PHE cc_start: 0.8833 (t80) cc_final: 0.8271 (t80) REVERT: D 437 ARG cc_start: 0.6984 (mtp180) cc_final: 0.6201 (mtm180) REVERT: E 79 THR cc_start: 0.8943 (m) cc_final: 0.8603 (p) REVERT: E 113 MET cc_start: 0.8538 (pmm) cc_final: 0.8033 (ppp) REVERT: E 308 ASP cc_start: 0.9039 (m-30) cc_final: 0.8787 (m-30) REVERT: E 428 PHE cc_start: 0.8836 (t80) cc_final: 0.8267 (t80) REVERT: E 437 ARG cc_start: 0.7040 (mtp180) cc_final: 0.6057 (mtm180) outliers start: 44 outliers final: 20 residues processed: 164 average time/residue: 0.5414 time to fit residues: 97.7549 Evaluate side-chains 148 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 B residue 154 ILE Chi-restraints excluded: chain B residue 244 MET 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 164 MET Chi-restraints excluded: chain D residue 264 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 48 optimal weight: 0.2980 chunk 164 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 154 optimal weight: 5.9990 chunk 145 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3497 r_free = 0.3497 target = 0.093007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.068553 restraints weight = 32995.704| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.60 r_work: 0.2868 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2722 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= 0.130 Angle : 0.605 8.942 20490 Z= 0.308 Chirality : 0.043 0.151 2300 Planarity : 0.003 0.034 2545 Dihedral : 15.783 179.574 2202 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.76 % Allowed : 14.04 % Favored : 83.20 % 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: 0.69 (0.19), residues: 1775 helix: 2.62 (0.19), residues: 645 sheet: 1.04 (0.25), residues: 385 loop : -1.98 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 333 TYR 0.016 0.001 TYR B 325 PHE 0.011 0.001 PHE C 87 TRP 0.017 0.001 TRP B 267 HIS 0.003 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00291 (15085) covalent geometry : angle 0.60469 (20465) SS BOND : bond 0.00306 ( 5) SS BOND : angle 0.25559 ( 10) hydrogen bonds : bond 0.05023 ( 720) hydrogen bonds : angle 3.94914 ( 2505) link_NAG-ASN : bond 0.00160 ( 5) link_NAG-ASN : angle 0.83462 ( 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 181 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 137 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 428 PHE cc_start: 0.8753 (t80) cc_final: 0.8086 (t80) REVERT: B 79 THR cc_start: 0.8835 (m) cc_final: 0.8449 (p) REVERT: B 196 GLU cc_start: 0.8542 (pm20) cc_final: 0.8320 (pm20) REVERT: B 215 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8433 (tm-30) REVERT: B 428 PHE cc_start: 0.8752 (t80) cc_final: 0.8139 (t80) REVERT: C 196 GLU cc_start: 0.8381 (pm20) cc_final: 0.7524 (pm20) REVERT: C 197 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.7966 (pmtt) REVERT: C 221 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.8204 (p90) REVERT: C 266 PHE cc_start: 0.7014 (m-10) cc_final: 0.6810 (m-10) REVERT: C 428 PHE cc_start: 0.8860 (t80) cc_final: 0.8411 (t80) REVERT: D 113 MET cc_start: 0.8406 (ppp) cc_final: 0.8038 (ppp) REVERT: D 428 PHE cc_start: 0.8787 (t80) cc_final: 0.8233 (t80) REVERT: E 79 THR cc_start: 0.8887 (m) cc_final: 0.8510 (p) REVERT: E 113 MET cc_start: 0.8493 (pmm) cc_final: 0.8111 (ppp) REVERT: E 187 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8576 (tpp) REVERT: E 308 ASP cc_start: 0.9015 (m-30) cc_final: 0.8779 (m-30) REVERT: E 428 PHE cc_start: 0.8815 (t80) cc_final: 0.8268 (t80) outliers start: 44 outliers final: 19 residues processed: 164 average time/residue: 0.5008 time to fit residues: 90.7484 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 115 ASP 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 B residue 154 ILE Chi-restraints excluded: chain B residue 244 MET 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 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 264 VAL Chi-restraints excluded: chain E residue 187 MET 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: 0.3980 chunk 5 optimal weight: 0.7980 chunk 150 optimal weight: 0.0570 chunk 75 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 101 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.6502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN C 179 GLN D 179 GLN E 85 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.093181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.068686 restraints weight = 32717.713| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.61 r_work: 0.2869 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15095 Z= 0.126 Angle : 0.611 9.555 20490 Z= 0.310 Chirality : 0.043 0.146 2300 Planarity : 0.003 0.032 2545 Dihedral : 15.726 179.923 2202 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.13 % Allowed : 15.11 % Favored : 82.76 % 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: 0.74 (0.19), residues: 1775 helix: 2.83 (0.19), residues: 620 sheet: 1.08 (0.26), residues: 375 loop : -1.91 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 333 TYR 0.015 0.001 TYR A 325 PHE 0.011 0.001 PHE B 266 TRP 0.019 0.001 TRP A 263 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00286 (15085) covalent geometry : angle 0.61118 (20465) SS BOND : bond 0.00286 ( 5) SS BOND : angle 0.21830 ( 10) hydrogen bonds : bond 0.04789 ( 720) hydrogen bonds : angle 3.75292 ( 2505) link_NAG-ASN : bond 0.00196 ( 5) link_NAG-ASN : angle 0.77197 ( 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 165 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8358 (pm20) cc_final: 0.7838 (pm20) REVERT: A 197 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8172 (pmtt) REVERT: A 428 PHE cc_start: 0.8725 (t80) cc_final: 0.8065 (t80) REVERT: B 215 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8397 (tm-30) REVERT: B 221 TYR cc_start: 0.8645 (OUTLIER) cc_final: 0.8223 (p90) REVERT: B 428 PHE cc_start: 0.8756 (t80) cc_final: 0.8152 (t80) REVERT: C 221 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.8138 (p90) REVERT: C 266 PHE cc_start: 0.6975 (m-10) cc_final: 0.6751 (m-80) REVERT: C 428 PHE cc_start: 0.8860 (t80) cc_final: 0.8404 (t80) REVERT: D 113 MET cc_start: 0.8491 (ppp) cc_final: 0.8136 (ppp) REVERT: D 428 PHE cc_start: 0.8782 (t80) cc_final: 0.8225 (t80) REVERT: E 79 THR cc_start: 0.8903 (m) cc_final: 0.8526 (p) REVERT: E 113 MET cc_start: 0.8484 (pmm) cc_final: 0.8088 (ppp) REVERT: E 187 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8559 (tpp) REVERT: E 308 ASP cc_start: 0.9016 (m-30) cc_final: 0.8783 (m-30) REVERT: E 428 PHE cc_start: 0.8808 (t80) cc_final: 0.8256 (t80) outliers start: 34 outliers final: 17 residues processed: 150 average time/residue: 0.5123 time to fit residues: 85.0286 Evaluate side-chains 152 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 164 MET 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 D residue 416 VAL Chi-restraints excluded: chain E residue 187 MET 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: 1.9990 chunk 121 optimal weight: 0.5980 chunk 101 optimal weight: 20.0000 chunk 137 optimal weight: 5.9990 chunk 6 optimal weight: 0.0370 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3454 r_free = 0.3454 target = 0.090617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.065811 restraints weight = 32790.450| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.59 r_work: 0.2808 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15095 Z= 0.165 Angle : 0.630 9.544 20490 Z= 0.322 Chirality : 0.044 0.137 2300 Planarity : 0.003 0.034 2545 Dihedral : 15.803 179.750 2202 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.88 % Allowed : 15.36 % 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: 0.75 (0.19), residues: 1775 helix: 2.74 (0.19), residues: 645 sheet: 0.78 (0.24), residues: 410 loop : -1.92 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 333 TYR 0.018 0.002 TYR D 429 PHE 0.015 0.001 PHE A 87 TRP 0.024 0.001 TRP A 263 HIS 0.003 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00390 (15085) covalent geometry : angle 0.62981 (20465) SS BOND : bond 0.00373 ( 5) SS BOND : angle 0.48671 ( 10) hydrogen bonds : bond 0.05159 ( 720) hydrogen bonds : angle 3.80200 ( 2505) link_NAG-ASN : bond 0.00036 ( 5) link_NAG-ASN : angle 1.11210 ( 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 181 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 135 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8228 (tm-30) REVERT: A 428 PHE cc_start: 0.8770 (t80) cc_final: 0.8118 (t80) REVERT: B 79 THR cc_start: 0.8872 (m) cc_final: 0.8480 (p) REVERT: B 181 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8307 (pp20) REVERT: B 215 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8443 (tm-30) REVERT: B 221 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.8234 (p90) REVERT: B 244 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8804 (tpp) REVERT: B 428 PHE cc_start: 0.8762 (t80) cc_final: 0.8140 (t80) REVERT: C 196 GLU cc_start: 0.8341 (pm20) cc_final: 0.7647 (pm20) REVERT: C 197 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8106 (pmtt) REVERT: C 221 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.7947 (p90) REVERT: C 266 PHE cc_start: 0.7051 (m-10) cc_final: 0.6735 (m-10) REVERT: C 428 PHE cc_start: 0.8877 (t80) cc_final: 0.8434 (t80) REVERT: D 113 MET cc_start: 0.8443 (ppp) cc_final: 0.8101 (ppp) REVERT: D 428 PHE cc_start: 0.8827 (t80) cc_final: 0.8283 (t80) REVERT: E 79 THR cc_start: 0.8891 (m) cc_final: 0.8638 (p) REVERT: E 113 MET cc_start: 0.8461 (pmm) cc_final: 0.8106 (ppp) REVERT: E 221 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.8192 (p90) REVERT: E 308 ASP cc_start: 0.9049 (m-30) cc_final: 0.8810 (m-30) REVERT: E 428 PHE cc_start: 0.8829 (t80) cc_final: 0.8212 (t80) outliers start: 46 outliers final: 21 residues processed: 160 average time/residue: 0.5219 time to fit residues: 92.7003 Evaluate side-chains 159 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 264 VAL 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 204 ASP Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 244 MET 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 164 MET 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 D residue 416 VAL Chi-restraints excluded: chain E residue 115 ASP 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: 3.9990 chunk 69 optimal weight: 3.9990 chunk 19 optimal weight: 0.0020 chunk 71 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 97 optimal weight: 0.0870 chunk 18 optimal weight: 0.0470 chunk 148 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3497 r_free = 0.3497 target = 0.093213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.068417 restraints weight = 32688.555| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.60 r_work: 0.2862 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3229 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= 0.117 Angle : 0.615 10.552 20490 Z= 0.308 Chirality : 0.043 0.149 2300 Planarity : 0.003 0.031 2545 Dihedral : 15.595 179.833 2200 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.63 % Allowed : 17.12 % Favored : 81.25 % 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: 0.82 (0.19), residues: 1775 helix: 2.89 (0.19), residues: 625 sheet: 0.99 (0.26), residues: 370 loop : -1.80 (0.19), residues: 780 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 0.010 0.001 PHE D 266 TRP 0.031 0.001 TRP A 263 HIS 0.002 0.000 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00256 (15085) covalent geometry : angle 0.61522 (20465) SS BOND : bond 0.00255 ( 5) SS BOND : angle 0.12776 ( 10) hydrogen bonds : bond 0.04449 ( 720) hydrogen bonds : angle 3.59697 ( 2505) link_NAG-ASN : bond 0.00304 ( 5) link_NAG-ASN : angle 0.67468 ( 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 166 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8265 (tm-30) REVERT: A 428 PHE cc_start: 0.8723 (t80) cc_final: 0.8080 (t80) REVERT: B 79 THR cc_start: 0.8802 (m) cc_final: 0.8453 (p) REVERT: B 80 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8422 (tpt) REVERT: B 181 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8547 (pp20) REVERT: B 215 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8387 (tm-30) REVERT: B 221 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.8195 (p90) REVERT: B 244 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8743 (tpp) REVERT: B 428 PHE cc_start: 0.8743 (t80) cc_final: 0.8129 (t80) REVERT: C 187 MET cc_start: 0.8484 (tpp) cc_final: 0.8235 (mmp) REVERT: C 221 TYR cc_start: 0.8473 (OUTLIER) cc_final: 0.7974 (p90) REVERT: C 263 TRP cc_start: 0.7900 (m-10) cc_final: 0.7498 (m-10) REVERT: C 426 ASN cc_start: 0.8538 (t0) cc_final: 0.8312 (t0) REVERT: C 428 PHE cc_start: 0.8847 (t80) cc_final: 0.8437 (t80) REVERT: D 113 MET cc_start: 0.8453 (ppp) cc_final: 0.8080 (ppp) REVERT: D 263 TRP cc_start: 0.7401 (m-10) cc_final: 0.7089 (m-10) REVERT: D 428 PHE cc_start: 0.8795 (t80) cc_final: 0.8248 (t80) REVERT: E 79 THR cc_start: 0.8862 (m) cc_final: 0.8616 (p) REVERT: E 113 MET cc_start: 0.8364 (pmm) cc_final: 0.8061 (ppp) REVERT: E 263 TRP cc_start: 0.7941 (m-10) cc_final: 0.7479 (m-10) REVERT: E 308 ASP cc_start: 0.9016 (m-30) cc_final: 0.8782 (m-30) REVERT: E 428 PHE cc_start: 0.8833 (t80) cc_final: 0.8241 (t80) outliers start: 26 outliers final: 16 residues processed: 150 average time/residue: 0.5348 time to fit residues: 88.9620 Evaluate side-chains 157 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 244 MET 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 164 MET 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 264 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 138 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 0.0170 chunk 76 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 87 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.6622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3492 r_free = 0.3492 target = 0.092860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.068085 restraints weight = 32709.275| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.59 r_work: 0.2853 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15095 Z= 0.123 Angle : 0.606 9.773 20490 Z= 0.305 Chirality : 0.043 0.160 2300 Planarity : 0.003 0.032 2545 Dihedral : 15.442 178.627 2200 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.94 % Allowed : 17.49 % Favored : 80.56 % 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: 2.89 (0.19), residues: 625 sheet: 0.95 (0.25), residues: 380 loop : -1.79 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 415 TYR 0.016 0.001 TYR A 433 PHE 0.010 0.001 PHE A 87 TRP 0.044 0.001 TRP A 263 HIS 0.002 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00281 (15085) covalent geometry : angle 0.60546 (20465) SS BOND : bond 0.00282 ( 5) SS BOND : angle 0.24905 ( 10) hydrogen bonds : bond 0.04401 ( 720) hydrogen bonds : angle 3.57885 ( 2505) link_NAG-ASN : bond 0.00160 ( 5) link_NAG-ASN : angle 0.81553 ( 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 165 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8233 (tm-30) REVERT: A 221 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.7926 (p90) REVERT: A 428 PHE cc_start: 0.8748 (t80) cc_final: 0.8077 (t80) REVERT: B 79 THR cc_start: 0.8821 (m) cc_final: 0.8456 (p) REVERT: B 181 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8513 (pp20) REVERT: B 215 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8414 (tm-30) REVERT: B 221 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.8258 (p90) REVERT: B 244 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8758 (tpp) REVERT: B 270 MET cc_start: 0.4090 (pmm) cc_final: 0.3667 (mmm) REVERT: B 428 PHE cc_start: 0.8742 (t80) cc_final: 0.8124 (t80) REVERT: C 221 TYR cc_start: 0.8451 (OUTLIER) cc_final: 0.7933 (p90) REVERT: C 263 TRP cc_start: 0.7830 (m-10) cc_final: 0.7490 (m-10) REVERT: C 266 PHE cc_start: 0.7121 (m-80) cc_final: 0.6736 (m-80) REVERT: C 428 PHE cc_start: 0.8846 (t80) cc_final: 0.8422 (t80) REVERT: D 113 MET cc_start: 0.8441 (ppp) cc_final: 0.8074 (ppp) REVERT: D 221 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.8203 (p90) REVERT: D 263 TRP cc_start: 0.7384 (m-10) cc_final: 0.7126 (m-10) REVERT: D 428 PHE cc_start: 0.8797 (t80) cc_final: 0.8248 (t80) REVERT: E 79 THR cc_start: 0.8874 (m) cc_final: 0.8616 (p) REVERT: E 113 MET cc_start: 0.8338 (pmm) cc_final: 0.8052 (ppp) REVERT: E 221 TYR cc_start: 0.8466 (OUTLIER) cc_final: 0.8194 (p90) REVERT: E 263 TRP cc_start: 0.7908 (m-10) cc_final: 0.7462 (m-10) REVERT: E 308 ASP cc_start: 0.9021 (m-30) cc_final: 0.8785 (m-30) REVERT: E 428 PHE cc_start: 0.8835 (t80) cc_final: 0.8285 (t80) outliers start: 31 outliers final: 16 residues processed: 145 average time/residue: 0.5306 time to fit residues: 84.9572 Evaluate side-chains 158 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 244 MET 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 221 TYR 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 221 TYR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 416 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 63 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 151 optimal weight: 0.0970 chunk 7 optimal weight: 7.9990 chunk 127 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 72 optimal weight: 0.0670 chunk 103 optimal weight: 0.0980 chunk 43 optimal weight: 0.0970 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.1914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3551 r_free = 0.3551 target = 0.095960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.070997 restraints weight = 32254.989| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.48 r_work: 0.2928 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15095 Z= 0.112 Angle : 0.607 10.485 20490 Z= 0.303 Chirality : 0.043 0.155 2300 Planarity : 0.003 0.034 2545 Dihedral : 15.163 176.644 2200 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.38 % Allowed : 18.37 % Favored : 80.25 % 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: 0.86 (0.19), residues: 1775 helix: 2.85 (0.19), residues: 630 sheet: 0.97 (0.26), residues: 370 loop : -1.72 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 242 TYR 0.015 0.001 TYR A 433 PHE 0.012 0.001 PHE D 266 TRP 0.034 0.001 TRP A 263 HIS 0.002 0.000 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00242 (15085) covalent geometry : angle 0.60728 (20465) SS BOND : bond 0.00225 ( 5) SS BOND : angle 0.11226 ( 10) hydrogen bonds : bond 0.03968 ( 720) hydrogen bonds : angle 3.47243 ( 2505) link_NAG-ASN : bond 0.00318 ( 5) link_NAG-ASN : angle 0.53743 ( 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 161 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8283 (tm-30) REVERT: A 428 PHE cc_start: 0.8737 (t80) cc_final: 0.8112 (t80) REVERT: B 79 THR cc_start: 0.8809 (m) cc_final: 0.8450 (p) REVERT: B 181 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8451 (pp20) REVERT: B 215 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8353 (tm-30) REVERT: B 263 TRP cc_start: 0.7563 (m-10) cc_final: 0.6894 (m-10) REVERT: B 333 ARG cc_start: 0.8129 (tpp80) cc_final: 0.7807 (ttp80) REVERT: B 428 PHE cc_start: 0.8749 (t80) cc_final: 0.8136 (t80) REVERT: C 187 MET cc_start: 0.8338 (tpp) cc_final: 0.8102 (mmp) REVERT: C 196 GLU cc_start: 0.8313 (pm20) cc_final: 0.7637 (pm20) REVERT: C 221 TYR cc_start: 0.8458 (OUTLIER) cc_final: 0.7936 (p90) REVERT: C 263 TRP cc_start: 0.7732 (m-10) cc_final: 0.7412 (m-10) REVERT: C 426 ASN cc_start: 0.8649 (t0) cc_final: 0.8413 (t0) REVERT: C 428 PHE cc_start: 0.8863 (t80) cc_final: 0.8457 (t80) REVERT: D 113 MET cc_start: 0.8513 (ppp) cc_final: 0.8137 (ppp) REVERT: D 270 MET cc_start: 0.3989 (pmm) cc_final: 0.3578 (mmm) REVERT: D 428 PHE cc_start: 0.8785 (t80) cc_final: 0.8239 (t80) REVERT: E 79 THR cc_start: 0.8923 (m) cc_final: 0.8670 (p) REVERT: E 113 MET cc_start: 0.8330 (pmm) cc_final: 0.8113 (ppp) REVERT: E 196 GLU cc_start: 0.8508 (pm20) cc_final: 0.8300 (pm20) REVERT: E 263 TRP cc_start: 0.7813 (m-10) cc_final: 0.7452 (m-10) REVERT: E 308 ASP cc_start: 0.8952 (m-30) cc_final: 0.8737 (m-30) REVERT: E 428 PHE cc_start: 0.8837 (t80) cc_final: 0.8312 (t80) outliers start: 22 outliers final: 12 residues processed: 153 average time/residue: 0.5109 time to fit residues: 86.6810 Evaluate side-chains 150 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 181 GLU 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 221 TYR Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 277 VAL 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 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: 0.9980 chunk 172 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 107 optimal weight: 0.0030 chunk 146 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 132 optimal weight: 0.0670 chunk 82 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 overall best weight: 0.4528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.095343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.070508 restraints weight = 32126.426| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.46 r_work: 0.2918 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3507 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= 0.114 Angle : 0.615 10.274 20490 Z= 0.304 Chirality : 0.043 0.157 2300 Planarity : 0.003 0.031 2545 Dihedral : 14.979 174.189 2200 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.63 % Allowed : 18.56 % Favored : 79.81 % 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: 0.89 (0.19), residues: 1775 helix: 2.86 (0.19), residues: 630 sheet: 0.96 (0.26), residues: 370 loop : -1.68 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 333 TYR 0.015 0.001 TYR A 433 PHE 0.012 0.001 PHE D 266 TRP 0.032 0.001 TRP A 263 HIS 0.003 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00258 (15085) covalent geometry : angle 0.61546 (20465) SS BOND : bond 0.00249 ( 5) SS BOND : angle 0.23570 ( 10) hydrogen bonds : bond 0.03976 ( 720) hydrogen bonds : angle 3.48152 ( 2505) link_NAG-ASN : bond 0.00186 ( 5) link_NAG-ASN : angle 0.73502 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3598.73 seconds wall clock time: 62 minutes 23.60 seconds (3743.60 seconds total)