Starting phenix.real_space_refine on Fri Jul 3 15:35:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m6o_23702/07_2026/7m6o_23702.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m6o_23702/07_2026/7m6o_23702.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7m6o_23702/07_2026/7m6o_23702.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m6o_23702/07_2026/7m6o_23702.cif" model { file = "/net/cci-nas-00/data/ceres_data/7m6o_23702/07_2026/7m6o_23702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m6o_23702/07_2026/7m6o_23702.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m6o_23702/07_2026/7m6o_23702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m6o_23702/07_2026/7m6o_23702.map" } resolution = 2.84 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 9555 2.51 5 N 2380 2.21 5 O 2635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14670 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2893 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 340} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2893 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 340} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2893 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 340} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2893 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 340} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2893 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 340} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {'NAG': 1, 'TCI': 1} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'NAG': 1, 'TCI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'NAG': 1, 'TCI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'NAG': 1, 'TCI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "E" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'NAG': 1, 'TCI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.29, per 1000 atoms: 0.22 Number of scatterers: 14670 At special positions: 0 Unit cell: (93.16, 91.8, 137.36, 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 2635 8.00 N 2380 7.00 C 9555 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 176 " distance=2.04 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 176 " distance=2.04 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 176 " distance=2.04 Simple disulfide: pdb=" SG CYS D 162 " - pdb=" SG CYS D 176 " distance=2.04 Simple disulfide: pdb=" SG CYS E 162 " - pdb=" SG CYS E 176 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 62 " " NAG B 802 " - " ASN B 62 " " NAG C 802 " - " ASN C 62 " " NAG D 802 " - " ASN D 62 " " NAG E 802 " - " ASN E 62 " Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 557.0 milliseconds 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 25 sheets defined 38.8% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 33 through 43 removed outlier: 3.789A pdb=" N PHE A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 removed outlier: 3.725A pdb=" N ILE A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 264 removed outlier: 3.972A pdb=" N VAL A 264 " --> pdb=" O ILE A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 295 removed outlier: 4.127A pdb=" N VAL A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 340 removed outlier: 3.679A pdb=" N LEU A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 442 Proline residue: A 419 - end of helix removed outlier: 3.878A pdb=" N HIS A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 43 removed outlier: 3.789A pdb=" N PHE B 37 " --> pdb=" O PRO B 33 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 251 removed outlier: 3.726A pdb=" N ILE B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 264 removed outlier: 3.972A pdb=" N VAL B 264 " --> pdb=" O ILE B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 295 removed outlier: 4.127A pdb=" N VAL B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 340 removed outlier: 3.679A pdb=" N LEU B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 442 Proline residue: B 419 - end of helix removed outlier: 3.878A pdb=" N HIS B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 43 removed outlier: 3.788A pdb=" N PHE C 37 " --> pdb=" O PRO C 33 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 251 removed outlier: 3.726A pdb=" N ILE C 249 " --> pdb=" O GLY C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 264 removed outlier: 3.972A pdb=" N VAL C 264 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 295 removed outlier: 4.127A pdb=" N VAL C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 340 removed outlier: 3.678A pdb=" N LEU C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 442 Proline residue: C 419 - end of helix removed outlier: 3.878A pdb=" N HIS C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 43 removed outlier: 3.788A pdb=" N PHE D 37 " --> pdb=" O PRO D 33 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 removed outlier: 3.725A pdb=" N ILE D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 264 removed outlier: 3.971A pdb=" N VAL D 264 " --> pdb=" O ILE D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 295 removed outlier: 4.126A pdb=" N VAL D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 340 removed outlier: 3.679A pdb=" N LEU D 322 " --> pdb=" O VAL D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 442 Proline residue: D 419 - end of helix removed outlier: 3.879A pdb=" N HIS D 442 " --> pdb=" O SER D 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 43 removed outlier: 3.788A pdb=" N PHE E 37 " --> pdb=" O PRO E 33 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 251 removed outlier: 3.725A pdb=" N ILE E 249 " --> pdb=" O GLY E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 264 removed outlier: 3.973A pdb=" N VAL E 264 " --> pdb=" O ILE E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 295 removed outlier: 4.126A pdb=" N VAL E 277 " --> pdb=" O ALA E 273 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG E 295 " --> pdb=" O SER E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 340 removed outlier: 3.679A pdb=" N LEU E 322 " --> pdb=" O VAL E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 442 Proline residue: E 419 - end of helix removed outlier: 3.879A 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: 7.439A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N VAL A 63 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 132 removed outlier: 3.522A pdb=" N ALA A 130 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N THR A 157 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE A 132 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ARG A 155 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 181 Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 181 removed outlier: 3.522A 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: 7.439A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL B 63 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 127 through 132 removed outlier: 3.523A pdb=" N ALA B 130 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N THR B 157 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE B 132 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ARG B 155 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 173 through 181 Processing sheet with id=AA9, first strand: chain 'B' and resid 173 through 181 removed outlier: 3.522A 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: 7.439A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL C 63 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 127 through 132 removed outlier: 3.522A pdb=" N ALA C 130 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N THR C 157 " --> pdb=" O ALA C 130 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE C 132 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ARG C 155 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 173 through 181 Processing sheet with id=AB5, first strand: chain 'C' and resid 173 through 181 removed outlier: 3.522A 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: 7.439A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL D 63 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 127 through 132 removed outlier: 3.522A pdb=" N ALA D 130 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N THR D 157 " --> pdb=" O ALA D 130 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE D 132 " --> pdb=" O ARG D 155 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ARG D 155 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 173 through 181 Processing sheet with id=AC1, first strand: chain 'D' and resid 173 through 181 removed outlier: 3.522A 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: 7.439A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL E 63 " --> pdb=" O GLU E 193 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 127 through 132 removed outlier: 3.523A pdb=" N ALA E 130 " --> pdb=" O THR E 157 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N THR E 157 " --> pdb=" O ALA E 130 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N PHE E 132 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ARG E 155 " --> pdb=" O PHE E 132 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 173 through 181 Processing sheet with id=AC6, first strand: chain 'E' and resid 173 through 181 removed outlier: 3.522A 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 225 845 hydrogen bonds defined for protein. 2520 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: 2.47 Time building geometry restraints manager: 1.43 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: 4325 1.34 - 1.46: 3271 1.46 - 1.58: 7264 1.58 - 1.70: 0 1.70 - 1.82: 170 Bond restraints: 15030 Sorted by residual: bond pdb=" SD MET B 287 " pdb=" CE MET B 287 " ideal model delta sigma weight residual 1.791 1.729 0.062 2.50e-02 1.60e+03 6.07e+00 bond pdb=" SD MET E 287 " pdb=" CE MET E 287 " ideal model delta sigma weight residual 1.791 1.730 0.061 2.50e-02 1.60e+03 6.03e+00 bond pdb=" SD MET D 287 " pdb=" CE MET D 287 " ideal model delta sigma weight residual 1.791 1.730 0.061 2.50e-02 1.60e+03 5.96e+00 bond pdb=" SD MET A 287 " pdb=" CE MET A 287 " ideal model delta sigma weight residual 1.791 1.730 0.061 2.50e-02 1.60e+03 5.92e+00 bond pdb=" SD MET C 287 " pdb=" CE MET C 287 " ideal model delta sigma weight residual 1.791 1.731 0.060 2.50e-02 1.60e+03 5.84e+00 ... (remaining 15025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 18932 2.48 - 4.97: 1243 4.97 - 7.45: 169 7.45 - 9.93: 36 9.93 - 12.42: 10 Bond angle restraints: 20390 Sorted by residual: angle pdb=" CA TRP E 263 " pdb=" CB TRP E 263 " pdb=" CG TRP E 263 " ideal model delta sigma weight residual 113.60 124.11 -10.51 1.90e+00 2.77e-01 3.06e+01 angle pdb=" CA TRP A 263 " pdb=" CB TRP A 263 " pdb=" CG TRP A 263 " ideal model delta sigma weight residual 113.60 124.08 -10.48 1.90e+00 2.77e-01 3.04e+01 angle pdb=" CA TRP B 263 " pdb=" CB TRP B 263 " pdb=" CG TRP B 263 " ideal model delta sigma weight residual 113.60 124.07 -10.47 1.90e+00 2.77e-01 3.04e+01 angle pdb=" CA TRP C 263 " pdb=" CB TRP C 263 " pdb=" CG TRP C 263 " ideal model delta sigma weight residual 113.60 124.06 -10.46 1.90e+00 2.77e-01 3.03e+01 angle pdb=" CA TRP D 263 " pdb=" CB TRP D 263 " pdb=" CG TRP D 263 " ideal model delta sigma weight residual 113.60 124.06 -10.46 1.90e+00 2.77e-01 3.03e+01 ... (remaining 20385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 8220 16.73 - 33.46: 580 33.46 - 50.19: 80 50.19 - 66.92: 25 66.92 - 83.65: 10 Dihedral angle restraints: 8915 sinusoidal: 3635 harmonic: 5280 Sorted by residual: dihedral pdb=" N PHE E 418 " pdb=" C PHE E 418 " pdb=" CA PHE E 418 " pdb=" CB PHE E 418 " ideal model delta harmonic sigma weight residual 122.80 132.07 -9.27 0 2.50e+00 1.60e-01 1.38e+01 dihedral pdb=" N PHE A 418 " pdb=" C PHE A 418 " pdb=" CA PHE A 418 " pdb=" CB PHE A 418 " ideal model delta harmonic sigma weight residual 122.80 132.06 -9.26 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" N PHE D 418 " pdb=" C PHE D 418 " pdb=" CA PHE D 418 " pdb=" CB PHE D 418 " ideal model delta harmonic sigma weight residual 122.80 132.05 -9.25 0 2.50e+00 1.60e-01 1.37e+01 ... (remaining 8912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1813 0.096 - 0.191: 406 0.191 - 0.287: 41 0.287 - 0.383: 20 0.383 - 0.478: 10 Chirality restraints: 2290 Sorted by residual: chirality pdb=" CB VAL D 264 " pdb=" CA VAL D 264 " pdb=" CG1 VAL D 264 " pdb=" CG2 VAL D 264 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CB VAL C 264 " pdb=" CA VAL C 264 " pdb=" CG1 VAL C 264 " pdb=" CG2 VAL C 264 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.65e+00 chirality pdb=" CB VAL E 264 " pdb=" CA VAL E 264 " pdb=" CG1 VAL E 264 " pdb=" CG2 VAL E 264 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.47 2.00e-01 2.50e+01 5.63e+00 ... (remaining 2287 not shown) Planarity restraints: 2540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 267 " 0.040 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" CG TRP C 267 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP C 267 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP C 267 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 267 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 267 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 267 " -0.025 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 267 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 267 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP C 267 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 267 " 0.040 2.00e-02 2.50e+03 2.33e-02 1.36e+01 pdb=" CG TRP D 267 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP D 267 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP D 267 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 267 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 267 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 267 " -0.025 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 267 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 267 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 267 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 267 " 0.040 2.00e-02 2.50e+03 2.33e-02 1.36e+01 pdb=" CG TRP E 267 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP E 267 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP E 267 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 267 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 267 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP E 267 " -0.025 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 267 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 267 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP E 267 " 0.015 2.00e-02 2.50e+03 ... (remaining 2537 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 594 2.72 - 3.26: 13746 3.26 - 3.81: 21821 3.81 - 4.35: 26910 4.35 - 4.90: 45528 Nonbonded interactions: 108599 Sorted by model distance: nonbonded pdb=" OD2 ASP D 110 " pdb=" OG SER D 112 " model vdw 2.171 3.040 nonbonded pdb=" OD2 ASP E 110 " pdb=" OG SER E 112 " model vdw 2.171 3.040 nonbonded pdb=" OD2 ASP B 110 " pdb=" OG SER B 112 " model vdw 2.172 3.040 nonbonded pdb=" OD2 ASP C 110 " pdb=" OG SER C 112 " model vdw 2.172 3.040 nonbonded pdb=" OD2 ASP A 110 " pdb=" OG SER A 112 " model vdw 2.172 3.040 ... (remaining 108594 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 32 through 442) selection = (chain 'B' and resid 32 through 442) selection = (chain 'C' and resid 32 through 442) selection = (chain 'D' and resid 32 through 442) selection = (chain 'E' and resid 32 through 442) } 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: 0.010 Normalize map: mean=0, sd=1: 4.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.540 Find NCS groups from input model: 0.330 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:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 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 0.117 15040 Z= 0.396 Angle : 1.377 12.416 20415 Z= 0.778 Chirality : 0.085 0.478 2290 Planarity : 0.009 0.076 2535 Dihedral : 11.922 83.653 5470 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % 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: -0.30 (0.19), residues: 1765 helix: 1.57 (0.19), residues: 625 sheet: 0.35 (0.27), residues: 370 loop : -2.07 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 295 TYR 0.050 0.005 TYR B 325 PHE 0.035 0.005 PHE C 72 TRP 0.053 0.005 TRP C 267 HIS 0.007 0.003 HIS B 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00882 / 0.40 (15030) covalent geometry : angle 1.37555 / 0.78 (20390) SS BOND : bond 0.01047 / 0.61 ( 5) SS BOND : angle 1.25325 / 0.64 ( 10) hydrogen bonds : bond 0.19438 / 12.92 ( 720) hydrogen bonds : angle 7.33821 / 5.15 ( 2520) link_NAG-ASN : bond 0.00418 / 0.26 ( 5) link_NAG-ASN : angle 2.76923 / 1.51 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.582 Fit side-chains REVERT: B 257 LEU cc_start: 0.9144 (tt) cc_final: 0.8923 (tp) REVERT: B 401 LYS cc_start: 0.8469 (mptt) cc_final: 0.7980 (mttp) REVERT: E 401 LYS cc_start: 0.8352 (mptt) cc_final: 0.8080 (tptt) outliers start: 0 outliers final: 1 residues processed: 266 average time/residue: 0.6254 time to fit residues: 179.4128 Evaluate side-chains 137 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 212 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.0010 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN B 85 ASN C 85 ASN D 85 ASN E 85 ASN E 201 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.095487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.067210 restraints weight = 35997.520| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.52 r_work: 0.2921 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15040 Z= 0.169 Angle : 0.731 7.614 20415 Z= 0.388 Chirality : 0.047 0.162 2290 Planarity : 0.005 0.056 2535 Dihedral : 6.374 69.135 1982 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.88 % Allowed : 13.42 % Favored : 84.70 % 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: 0.13 (0.19), residues: 1765 helix: 2.16 (0.19), residues: 645 sheet: 0.90 (0.26), residues: 375 loop : -2.39 (0.18), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 295 TYR 0.019 0.002 TYR E 433 PHE 0.021 0.002 PHE D 319 TRP 0.010 0.002 TRP A 310 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (15030) covalent geometry : angle 0.73015 / 0.39 (20390) SS BOND : bond 0.00598 / 0.35 ( 5) SS BOND : angle 0.44913 / 0.24 ( 10) hydrogen bonds : bond 0.06792 / 4.58 ( 720) hydrogen bonds : angle 5.22723 / 3.71 ( 2520) link_NAG-ASN : bond 0.00108 / 0.06 ( 5) link_NAG-ASN : angle 1.28436 / 0.71 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.592 Fit side-chains REVERT: A 286 THR cc_start: 0.9137 (t) cc_final: 0.8912 (p) REVERT: B 113 MET cc_start: 0.8145 (pp-130) cc_final: 0.7875 (ppp) REVERT: B 190 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8642 (tm) REVERT: B 244 MET cc_start: 0.8169 (mmm) cc_final: 0.7893 (mmm) REVERT: C 270 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7675 (mtp) outliers start: 30 outliers final: 17 residues processed: 170 average time/residue: 0.5809 time to fit residues: 108.6065 Evaluate side-chains 142 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 289 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 111 optimal weight: 0.0970 chunk 84 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 166 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 140 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 GLN B 290 GLN C 290 GLN D 290 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.096574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.068085 restraints weight = 36032.343| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.53 r_work: 0.2937 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15040 Z= 0.141 Angle : 0.624 10.991 20415 Z= 0.331 Chirality : 0.044 0.148 2290 Planarity : 0.004 0.043 2535 Dihedral : 5.998 74.045 1980 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.38 % Allowed : 14.17 % Favored : 83.45 % 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: 0.38 (0.19), residues: 1765 helix: 2.28 (0.20), residues: 645 sheet: 1.21 (0.26), residues: 375 loop : -2.29 (0.18), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 220 TYR 0.017 0.001 TYR E 433 PHE 0.016 0.001 PHE C 319 TRP 0.018 0.002 TRP C 263 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (15030) covalent geometry : angle 0.62410 / 0.33 (20390) SS BOND : bond 0.00483 / 0.28 ( 5) SS BOND : angle 0.33695 / 0.17 ( 10) hydrogen bonds : bond 0.05684 / 3.84 ( 720) hydrogen bonds : angle 4.66500 / 3.34 ( 2520) link_NAG-ASN : bond 0.00221 / 0.13 ( 5) link_NAG-ASN : angle 0.82363 / 0.47 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 0.602 Fit side-chains REVERT: A 77 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8367 (mm-30) REVERT: B 77 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8257 (mm-30) REVERT: B 113 MET cc_start: 0.8240 (pp-130) cc_final: 0.8034 (ppp) REVERT: B 190 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8646 (tm) REVERT: B 420 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8760 (pt) REVERT: C 77 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8348 (mm-30) REVERT: D 77 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8405 (mm-30) REVERT: D 190 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8597 (tm) REVERT: E 287 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8186 (ttm) outliers start: 38 outliers final: 14 residues processed: 156 average time/residue: 0.5771 time to fit residues: 99.1395 Evaluate side-chains 141 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 121 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 GLN B 290 GLN C 290 GLN D 290 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.089653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.059704 restraints weight = 35980.440| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.46 r_work: 0.2740 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.052 15040 Z= 0.384 Angle : 0.802 11.381 20415 Z= 0.431 Chirality : 0.051 0.178 2290 Planarity : 0.005 0.037 2535 Dihedral : 6.902 79.043 1980 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.58 % Allowed : 14.61 % Favored : 80.82 % 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: -0.01 (0.19), residues: 1765 helix: 1.99 (0.19), residues: 645 sheet: 0.52 (0.25), residues: 415 loop : -2.39 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 242 TYR 0.025 0.003 TYR B 221 PHE 0.032 0.003 PHE C 87 TRP 0.012 0.002 TRP B 92 HIS 0.005 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00928 / 0.38 (15030) covalent geometry : angle 0.79955 / 0.43 (20390) SS BOND : bond 0.00753 / 0.44 ( 5) SS BOND : angle 1.40348 / 0.72 ( 10) hydrogen bonds : bond 0.07181 / 4.83 ( 720) hydrogen bonds : angle 5.12969 / 3.61 ( 2520) link_NAG-ASN : bond 0.00529 / 0.31 ( 5) link_NAG-ASN : angle 2.11909 / 1.26 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 126 time to evaluate : 0.606 Fit side-chains REVERT: A 77 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8495 (mm-30) REVERT: A 113 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.7937 (pmm) REVERT: B 77 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8482 (mm-30) REVERT: B 113 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7733 (ppp) REVERT: B 285 LEU cc_start: 0.9258 (tt) cc_final: 0.8993 (tp) REVERT: D 77 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8551 (mm-30) REVERT: E 287 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8158 (tmm) outliers start: 73 outliers final: 30 residues processed: 183 average time/residue: 0.5599 time to fit residues: 113.0143 Evaluate side-chains 158 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 152 optimal weight: 0.8980 chunk 169 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 GLN B 290 GLN D 290 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.092130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.062696 restraints weight = 35574.940| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.46 r_work: 0.2808 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15040 Z= 0.159 Angle : 0.621 8.107 20415 Z= 0.333 Chirality : 0.045 0.149 2290 Planarity : 0.004 0.030 2535 Dihedral : 6.862 83.826 1980 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.45 % Allowed : 16.93 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.19), residues: 1765 helix: 2.24 (0.19), residues: 645 sheet: 0.73 (0.27), residues: 370 loop : -2.24 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 242 TYR 0.016 0.002 TYR E 429 PHE 0.014 0.002 PHE B 87 TRP 0.008 0.001 TRP B 92 HIS 0.004 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (15030) covalent geometry : angle 0.62054 / 0.33 (20390) SS BOND : bond 0.00466 / 0.27 ( 5) SS BOND : angle 0.64801 / 0.33 ( 10) hydrogen bonds : bond 0.05703 / 3.85 ( 720) hydrogen bonds : angle 4.60716 / 3.27 ( 2520) link_NAG-ASN : bond 0.00217 / 0.13 ( 5) link_NAG-ASN : angle 0.86659 / 0.49 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 125 time to evaluate : 0.510 Fit side-chains REVERT: A 113 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.7828 (pmm) REVERT: B 77 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8524 (mm-30) REVERT: B 113 MET cc_start: 0.8204 (pp-130) cc_final: 0.7817 (ppp) REVERT: B 190 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8840 (tm) REVERT: B 285 LEU cc_start: 0.9227 (tt) cc_final: 0.9008 (tp) REVERT: D 113 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.7955 (pmm) REVERT: D 190 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8805 (tm) REVERT: E 287 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8154 (ttm) outliers start: 55 outliers final: 21 residues processed: 167 average time/residue: 0.5934 time to fit residues: 108.6634 Evaluate side-chains 147 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 110 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 48 optimal weight: 0.0470 chunk 92 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 overall best weight: 1.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 GLN B 290 GLN D 290 GLN E 290 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.092272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.063009 restraints weight = 35474.011| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.46 r_work: 0.2814 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15040 Z= 0.152 Angle : 0.612 8.550 20415 Z= 0.330 Chirality : 0.044 0.151 2290 Planarity : 0.004 0.031 2535 Dihedral : 6.632 85.141 1980 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.39 % Allowed : 17.43 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.19), residues: 1765 helix: 2.28 (0.19), residues: 645 sheet: 0.77 (0.27), residues: 370 loop : -2.25 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 437 TYR 0.015 0.002 TYR A 433 PHE 0.014 0.002 PHE E 428 TRP 0.006 0.001 TRP C 310 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (15030) covalent geometry : angle 0.61210 / 0.33 (20390) SS BOND : bond 0.00407 / 0.24 ( 5) SS BOND : angle 0.52155 / 0.26 ( 10) hydrogen bonds : bond 0.05416 / 3.67 ( 720) hydrogen bonds : angle 4.50654 / 3.21 ( 2520) link_NAG-ASN : bond 0.00018 / 0.01 ( 5) link_NAG-ASN : angle 0.91516 / 0.55 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 122 time to evaluate : 0.584 Fit side-chains REVERT: A 113 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7797 (pmm) REVERT: B 77 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8575 (mm-30) REVERT: B 113 MET cc_start: 0.8220 (pp-130) cc_final: 0.7787 (ppp) REVERT: B 190 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8841 (tm) REVERT: B 285 LEU cc_start: 0.9218 (tt) cc_final: 0.8997 (tp) REVERT: D 113 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7814 (pmm) REVERT: D 190 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8802 (tm) outliers start: 54 outliers final: 29 residues processed: 162 average time/residue: 0.6124 time to fit residues: 108.7989 Evaluate side-chains 155 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 18 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 171 optimal weight: 10.0000 chunk 121 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 GLN B 290 GLN D 290 GLN E 290 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.091994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.062721 restraints weight = 35378.466| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.45 r_work: 0.2809 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15040 Z= 0.159 Angle : 0.609 8.124 20415 Z= 0.326 Chirality : 0.044 0.167 2290 Planarity : 0.004 0.033 2535 Dihedral : 6.482 86.441 1980 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.39 % Allowed : 17.43 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.19), residues: 1765 helix: 1.95 (0.19), residues: 680 sheet: 0.81 (0.27), residues: 370 loop : -2.17 (0.19), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 437 TYR 0.014 0.002 TYR D 433 PHE 0.015 0.002 PHE E 428 TRP 0.007 0.001 TRP D 92 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (15030) covalent geometry : angle 0.60858 / 0.33 (20390) SS BOND : bond 0.00400 / 0.23 ( 5) SS BOND : angle 0.61510 / 0.31 ( 10) hydrogen bonds : bond 0.05261 / 3.56 ( 720) hydrogen bonds : angle 4.44993 / 3.17 ( 2520) link_NAG-ASN : bond 0.00014 / 0.01 ( 5) link_NAG-ASN : angle 0.92756 / 0.56 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 122 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7837 (pmm) REVERT: B 77 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8586 (mm-30) REVERT: B 113 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7870 (ppp) REVERT: B 190 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8839 (tm) REVERT: B 285 LEU cc_start: 0.9200 (tt) cc_final: 0.8984 (tp) REVERT: D 113 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7922 (pmm) REVERT: D 190 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8812 (tm) REVERT: E 77 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8507 (mm-30) outliers start: 54 outliers final: 30 residues processed: 162 average time/residue: 0.6170 time to fit residues: 109.8763 Evaluate side-chains 157 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 120 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 75 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 89 optimal weight: 0.0040 chunk 53 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 GLN B 290 GLN D 290 GLN E 290 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.093114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.064162 restraints weight = 35522.292| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.46 r_work: 0.2840 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15040 Z= 0.127 Angle : 0.589 8.083 20415 Z= 0.313 Chirality : 0.044 0.167 2290 Planarity : 0.003 0.033 2535 Dihedral : 6.202 87.481 1980 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.51 % Allowed : 18.31 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.20), residues: 1765 helix: 2.03 (0.19), residues: 680 sheet: 0.93 (0.27), residues: 370 loop : -2.04 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 242 TYR 0.014 0.001 TYR D 325 PHE 0.017 0.001 PHE A 319 TRP 0.007 0.001 TRP D 310 HIS 0.002 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (15030) covalent geometry : angle 0.58890 / 0.31 (20390) SS BOND : bond 0.00356 / 0.21 ( 5) SS BOND : angle 0.35929 / 0.17 ( 10) hydrogen bonds : bond 0.04784 / 3.23 ( 720) hydrogen bonds : angle 4.30732 / 3.08 ( 2520) link_NAG-ASN : bond 0.00142 / 0.08 ( 5) link_NAG-ASN : angle 0.66349 / 0.39 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.563 Fit side-chains REVERT: B 113 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7874 (ppp) REVERT: B 190 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8825 (tm) REVERT: B 285 LEU cc_start: 0.9180 (tt) cc_final: 0.8976 (tp) REVERT: B 287 MET cc_start: 0.8884 (tpp) cc_final: 0.8596 (tpp) REVERT: D 113 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7797 (pmm) REVERT: D 190 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8776 (tm) REVERT: E 113 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.7959 (pmm) outliers start: 40 outliers final: 24 residues processed: 151 average time/residue: 0.6011 time to fit residues: 99.3428 Evaluate side-chains 149 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 5 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 148 optimal weight: 0.3980 chunk 119 optimal weight: 5.9990 chunk 159 optimal weight: 0.2980 chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 GLN B 201 GLN D 290 GLN E 290 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.091666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.061646 restraints weight = 35852.219| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.50 r_work: 0.2804 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15040 Z= 0.208 Angle : 0.654 8.330 20415 Z= 0.349 Chirality : 0.046 0.174 2290 Planarity : 0.004 0.034 2535 Dihedral : 6.269 87.188 1980 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.38 % Allowed : 18.81 % Favored : 78.81 % 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: 0.29 (0.20), residues: 1765 helix: 2.00 (0.19), residues: 680 sheet: 0.69 (0.25), residues: 410 loop : -2.15 (0.20), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 437 TYR 0.017 0.002 TYR A 433 PHE 0.021 0.002 PHE A 319 TRP 0.008 0.001 TRP E 263 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 (15030) covalent geometry : angle 0.65333 / 0.35 (20390) SS BOND : bond 0.00483 / 0.28 ( 5) SS BOND : angle 0.83246 / 0.42 ( 10) hydrogen bonds : bond 0.05370 / 3.63 ( 720) hydrogen bonds : angle 4.50465 / 3.20 ( 2520) link_NAG-ASN : bond 0.00177 / 0.10 ( 5) link_NAG-ASN : angle 1.24796 / 0.75 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 119 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 113 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.7835 (pmm) REVERT: B 113 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7823 (ppp) REVERT: B 190 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8880 (tm) REVERT: B 285 LEU cc_start: 0.9184 (tt) cc_final: 0.8981 (tp) REVERT: B 287 MET cc_start: 0.8912 (tpp) cc_final: 0.8539 (tpp) REVERT: C 244 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8992 (mmm) REVERT: D 113 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7954 (pmm) REVERT: E 77 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8544 (mm-30) REVERT: E 113 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8166 (pmm) outliers start: 38 outliers final: 27 residues processed: 150 average time/residue: 0.6231 time to fit residues: 102.4206 Evaluate side-chains 152 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 100 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 GLN ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 GLN E 290 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.093679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.064040 restraints weight = 35580.502| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.50 r_work: 0.2849 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15040 Z= 0.127 Angle : 0.603 8.251 20415 Z= 0.320 Chirality : 0.044 0.166 2290 Planarity : 0.003 0.032 2535 Dihedral : 6.084 89.079 1980 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.07 % Allowed : 19.25 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.20), residues: 1765 helix: 2.08 (0.19), residues: 675 sheet: 0.75 (0.27), residues: 380 loop : -1.90 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 437 TYR 0.015 0.001 TYR D 325 PHE 0.019 0.001 PHE A 319 TRP 0.008 0.001 TRP B 310 HIS 0.002 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (15030) covalent geometry : angle 0.60328 / 0.32 (20390) SS BOND : bond 0.00332 / 0.19 ( 5) SS BOND : angle 0.33377 / 0.16 ( 10) hydrogen bonds : bond 0.04638 / 3.14 ( 720) hydrogen bonds : angle 4.29784 / 3.07 ( 2520) link_NAG-ASN : bond 0.00224 / 0.13 ( 5) link_NAG-ASN : angle 0.55325 / 0.31 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7908 (ppp) REVERT: B 190 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8823 (tm) REVERT: B 287 MET cc_start: 0.8917 (tpp) cc_final: 0.8562 (tpp) REVERT: C 244 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8819 (mmm) REVERT: D 113 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7705 (pmm) REVERT: E 77 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8583 (mm-30) outliers start: 33 outliers final: 24 residues processed: 148 average time/residue: 0.6514 time to fit residues: 105.6160 Evaluate side-chains 151 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 121 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 145 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 chunk 19 optimal weight: 0.0570 chunk 74 optimal weight: 0.0270 chunk 50 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 GLN D 290 GLN E 290 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.093518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.063826 restraints weight = 35295.138| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.49 r_work: 0.2845 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15040 Z= 0.134 Angle : 0.605 9.421 20415 Z= 0.319 Chirality : 0.044 0.175 2290 Planarity : 0.003 0.033 2535 Dihedral : 6.018 89.936 1980 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.32 % Allowed : 18.93 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.19), residues: 1765 helix: 2.01 (0.19), residues: 670 sheet: 0.79 (0.27), residues: 380 loop : -1.90 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 437 TYR 0.015 0.001 TYR D 325 PHE 0.020 0.001 PHE A 319 TRP 0.007 0.001 TRP C 310 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (15030) covalent geometry : angle 0.60462 / 0.32 (20390) SS BOND : bond 0.00367 / 0.22 ( 5) SS BOND : angle 0.45044 / 0.22 ( 10) hydrogen bonds : bond 0.04632 / 3.14 ( 720) hydrogen bonds : angle 4.29066 / 3.07 ( 2520) link_NAG-ASN : bond 0.00084 / 0.05 ( 5) link_NAG-ASN : angle 0.72834 / 0.44 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4348.16 seconds wall clock time: 75 minutes 3.81 seconds (4503.81 seconds total)