Starting phenix.real_space_refine on Mon Apr 6 01:15:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m6o_23702/04_2026/7m6o_23702.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m6o_23702/04_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 { model { file = "/net/cci-nas-00/data/ceres_data/7m6o_23702/04_2026/7m6o_23702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m6o_23702/04_2026/7m6o_23702.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m6o_23702/04_2026/7m6o_23702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m6o_23702/04_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-2.1rc1-6017/lib/python3.9/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: 4 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: 4 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: 4 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: 4 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: 4 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.45, per 1000 atoms: 0.24 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: 1.06 Conformation dependent library (CDL) restraints added in 535.3 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: 0.50 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: 2.45 Time building geometry restraints manager: 1.47 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: 8385 16.73 - 33.46: 610 33.46 - 50.19: 90 50.19 - 66.92: 25 66.92 - 83.65: 10 Dihedral angle restraints: 9120 sinusoidal: 3840 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 9117 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: 0.000 Normalize map: mean=0, sd=1: 4.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.110 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 : 12.009 83.653 5675 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 covalent geometry : bond 0.00882 (15030) covalent geometry : angle 1.37555 (20390) SS BOND : bond 0.01047 ( 5) SS BOND : angle 1.25325 ( 10) hydrogen bonds : bond 0.19438 ( 720) hydrogen bonds : angle 7.33821 ( 2520) link_NAG-ASN : bond 0.00418 ( 5) link_NAG-ASN : angle 2.76923 ( 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 : 0.605 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: 0.7588 time to fit residues: 217.3127 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 : 0.409 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.095472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.067157 restraints weight = 36026.949| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.51 r_work: 0.2921 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15040 Z= 0.171 Angle : 0.726 7.567 20415 Z= 0.389 Chirality : 0.047 0.170 2290 Planarity : 0.005 0.056 2535 Dihedral : 6.519 71.604 2187 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.01 % Allowed : 12.92 % Favored : 85.08 % 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: 2.15 (0.19), residues: 645 sheet: 0.90 (0.26), residues: 375 loop : -2.40 (0.18), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 220 TYR 0.019 0.002 TYR E 433 PHE 0.021 0.002 PHE D 319 TRP 0.011 0.002 TRP C 267 HIS 0.004 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00370 (15030) covalent geometry : angle 0.72546 (20390) SS BOND : bond 0.00617 ( 5) SS BOND : angle 0.49850 ( 10) hydrogen bonds : bond 0.06856 ( 720) hydrogen bonds : angle 5.28030 ( 2520) link_NAG-ASN : bond 0.00093 ( 5) link_NAG-ASN : angle 1.47479 ( 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 180 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.590 Fit side-chains REVERT: A 286 THR cc_start: 0.9139 (t) cc_final: 0.8915 (p) REVERT: B 113 MET cc_start: 0.8138 (pp-130) cc_final: 0.7853 (ppp) REVERT: B 190 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8643 (tm) REVERT: B 244 MET cc_start: 0.8200 (mmm) cc_final: 0.7917 (mmm) REVERT: C 270 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7677 (mtp) REVERT: D 113 MET cc_start: 0.8041 (pp-130) cc_final: 0.7706 (ppp) outliers start: 32 outliers final: 17 residues processed: 172 average time/residue: 0.6198 time to fit residues: 116.8340 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 : 0.519 ------------------------------------------------------------------------------- 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: 0.6980 chunk 84 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 83 optimal weight: 0.3980 chunk 166 optimal weight: 0.0170 chunk 85 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 140 optimal weight: 7.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3652 r_free = 0.3652 target = 0.096560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.068201 restraints weight = 36072.789| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.52 r_work: 0.2950 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15040 Z= 0.137 Angle : 0.623 11.113 20415 Z= 0.331 Chirality : 0.044 0.162 2290 Planarity : 0.004 0.045 2535 Dihedral : 5.970 75.358 2185 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.32 % Allowed : 14.17 % Favored : 83.51 % 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 (0.19), residues: 1765 helix: 2.29 (0.20), residues: 645 sheet: 1.16 (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 0.013 0.001 TRP B 263 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00283 (15030) covalent geometry : angle 0.62247 (20390) SS BOND : bond 0.00472 ( 5) SS BOND : angle 0.30266 ( 10) hydrogen bonds : bond 0.05797 ( 720) hydrogen bonds : angle 4.71349 ( 2520) link_NAG-ASN : bond 0.00225 ( 5) link_NAG-ASN : angle 0.98295 ( 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 161 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 0.572 Fit side-chains REVERT: A 77 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8357 (mm-30) REVERT: B 77 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8231 (mm-30) REVERT: B 113 MET cc_start: 0.8192 (pp-130) cc_final: 0.7985 (ppp) REVERT: B 190 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8641 (tm) REVERT: C 77 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8439 (mm-30) REVERT: D 77 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8368 (mm-30) REVERT: D 190 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8571 (tm) REVERT: E 287 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8200 (ttm) outliers start: 37 outliers final: 13 residues processed: 152 average time/residue: 0.6526 time to fit residues: 108.4184 Evaluate side-chains 136 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 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 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: 6.9990 chunk 22 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3552 r_free = 0.3552 target = 0.091240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.061863 restraints weight = 35981.592| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.47 r_work: 0.2796 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 15040 Z= 0.293 Angle : 0.721 9.960 20415 Z= 0.386 Chirality : 0.047 0.144 2290 Planarity : 0.004 0.034 2535 Dihedral : 6.503 80.524 2185 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.82 % Allowed : 14.17 % Favored : 82.01 % 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: 0.14 (0.19), residues: 1765 helix: 2.16 (0.19), residues: 645 sheet: 0.77 (0.26), residues: 375 loop : -2.30 (0.19), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 220 TYR 0.019 0.002 TYR B 221 PHE 0.025 0.002 PHE E 87 TRP 0.011 0.001 TRP B 92 HIS 0.004 0.001 HIS E 239 Details of bonding type rmsd covalent geometry : bond 0.00705 (15030) covalent geometry : angle 0.71943 (20390) SS BOND : bond 0.00602 ( 5) SS BOND : angle 1.12052 ( 10) hydrogen bonds : bond 0.06486 ( 720) hydrogen bonds : angle 4.93632 ( 2520) link_NAG-ASN : bond 0.00264 ( 5) link_NAG-ASN : angle 1.72049 ( 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 182 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 121 time to evaluate : 0.559 Fit side-chains REVERT: B 113 MET cc_start: 0.8263 (pp-130) cc_final: 0.7728 (ppp) REVERT: B 285 LEU cc_start: 0.9246 (tt) cc_final: 0.9004 (tp) REVERT: E 77 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8385 (mm-30) REVERT: E 287 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8154 (ttm) outliers start: 61 outliers final: 29 residues processed: 171 average time/residue: 0.6451 time to fit residues: 120.6667 Evaluate side-chains 150 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 45 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 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 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 45 VAL Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 279 LEU 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: 2.9990 chunk 169 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 chunk 123 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 110 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN C 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 = 0.093268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.064066 restraints weight = 35750.574| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.48 r_work: 0.2846 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15040 Z= 0.135 Angle : 0.598 7.386 20415 Z= 0.321 Chirality : 0.044 0.149 2290 Planarity : 0.004 0.029 2535 Dihedral : 6.508 84.820 2185 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.45 % Allowed : 15.67 % Favored : 80.88 % 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: 0.33 (0.19), residues: 1765 helix: 2.33 (0.19), residues: 645 sheet: 0.89 (0.27), residues: 370 loop : -2.20 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 220 TYR 0.014 0.002 TYR D 325 PHE 0.017 0.001 PHE E 428 TRP 0.008 0.001 TRP A 310 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00298 (15030) covalent geometry : angle 0.59747 (20390) SS BOND : bond 0.00431 ( 5) SS BOND : angle 0.48864 ( 10) hydrogen bonds : bond 0.05436 ( 720) hydrogen bonds : angle 4.56558 ( 2520) link_NAG-ASN : bond 0.00208 ( 5) link_NAG-ASN : angle 0.95020 ( 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 182 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 127 time to evaluate : 0.588 Fit side-chains REVERT: A 113 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.7808 (pmm) REVERT: B 113 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7763 (ppp) REVERT: B 187 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8924 (mmm) REVERT: B 190 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8784 (tm) REVERT: B 285 LEU cc_start: 0.9226 (tt) cc_final: 0.8989 (tp) REVERT: D 190 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8692 (tm) REVERT: E 77 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8409 (mm-30) REVERT: E 113 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.7650 (pmm) outliers start: 55 outliers final: 26 residues processed: 163 average time/residue: 0.6138 time to fit residues: 109.8544 Evaluate side-chains 153 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 150 VAL 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 45 VAL 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 187 MET 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 115 ASP Chi-restraints excluded: chain C residue 150 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 150 VAL 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 45 VAL Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 150 VAL 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: 0.8980 chunk 48 optimal weight: 2.9990 chunk 92 optimal weight: 0.2980 chunk 4 optimal weight: 7.9990 chunk 116 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN C 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 = 0.3598 r_free = 0.3598 target = 0.093938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.064795 restraints weight = 35438.889| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.47 r_work: 0.2862 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3664 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= 0.130 Angle : 0.592 8.506 20415 Z= 0.318 Chirality : 0.044 0.156 2290 Planarity : 0.003 0.029 2535 Dihedral : 6.315 86.502 2185 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.70 % Allowed : 16.18 % Favored : 80.13 % 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: 0.39 (0.19), residues: 1765 helix: 2.37 (0.19), residues: 645 sheet: 0.94 (0.26), residues: 375 loop : -2.19 (0.19), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 437 TYR 0.015 0.001 TYR D 433 PHE 0.013 0.001 PHE E 428 TRP 0.007 0.001 TRP C 310 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00286 (15030) covalent geometry : angle 0.59137 (20390) SS BOND : bond 0.00370 ( 5) SS BOND : angle 0.38457 ( 10) hydrogen bonds : bond 0.05079 ( 720) hydrogen bonds : angle 4.41616 ( 2520) link_NAG-ASN : bond 0.00139 ( 5) link_NAG-ASN : angle 0.89770 ( 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 178 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 119 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.7781 (pmm) REVERT: A 197 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7676 (pmtt) REVERT: B 113 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7791 (ppp) REVERT: B 187 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8917 (mmm) REVERT: B 190 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8785 (tm) REVERT: B 285 LEU cc_start: 0.9197 (tt) cc_final: 0.8982 (tp) REVERT: C 113 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8291 (ppp) REVERT: D 113 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.7732 (pmm) REVERT: D 190 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8735 (tm) outliers start: 59 outliers final: 30 residues processed: 164 average time/residue: 0.6105 time to fit residues: 109.8547 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 : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 197 LYS 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 45 VAL 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 187 MET 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 113 MET Chi-restraints excluded: chain C residue 150 VAL 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 150 VAL 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 45 VAL Chi-restraints excluded: chain E residue 150 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 416 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 18 optimal weight: 0.0970 chunk 108 optimal weight: 4.9990 chunk 171 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 27 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3617 r_free = 0.3617 target = 0.095003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.066001 restraints weight = 35403.289| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.48 r_work: 0.2897 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3828 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= 0.118 Angle : 0.569 8.050 20415 Z= 0.304 Chirality : 0.043 0.158 2290 Planarity : 0.003 0.030 2535 Dihedral : 6.033 88.794 2185 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.32 % Allowed : 16.74 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.19), residues: 1765 helix: 2.46 (0.19), residues: 640 sheet: 0.99 (0.27), residues: 375 loop : -2.06 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 437 TYR 0.014 0.001 TYR D 325 PHE 0.013 0.001 PHE E 428 TRP 0.009 0.001 TRP A 310 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00250 (15030) covalent geometry : angle 0.56942 (20390) SS BOND : bond 0.00335 ( 5) SS BOND : angle 0.31999 ( 10) hydrogen bonds : bond 0.04603 ( 720) hydrogen bonds : angle 4.22348 ( 2520) link_NAG-ASN : bond 0.00228 ( 5) link_NAG-ASN : angle 0.75027 ( 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 181 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 128 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.7782 (pmm) REVERT: A 197 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7523 (pmtt) REVERT: B 113 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.8003 (ppp) REVERT: B 187 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8833 (mmm) REVERT: B 190 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8736 (tm) REVERT: B 285 LEU cc_start: 0.9192 (tt) cc_final: 0.8930 (tp) REVERT: B 287 MET cc_start: 0.8900 (mmm) cc_final: 0.8424 (tpp) REVERT: C 113 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7896 (ppp) REVERT: C 286 THR cc_start: 0.9163 (t) cc_final: 0.8928 (p) REVERT: D 113 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7678 (pmm) REVERT: D 190 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8657 (tm) outliers start: 53 outliers final: 25 residues processed: 164 average time/residue: 0.6042 time to fit residues: 108.8877 Evaluate side-chains 154 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 187 MET Chi-restraints excluded: chain A residue 197 LYS 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 B residue 45 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 187 MET 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 113 MET Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 156 ILE 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 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 45 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 75 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 89 optimal weight: 0.0370 chunk 53 optimal weight: 4.9990 chunk 156 optimal weight: 0.5980 chunk 153 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3615 r_free = 0.3615 target = 0.094741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.065682 restraints weight = 35624.847| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.49 r_work: 0.2882 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3910 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= 0.122 Angle : 0.585 9.953 20415 Z= 0.305 Chirality : 0.043 0.166 2290 Planarity : 0.003 0.030 2535 Dihedral : 5.875 89.208 2185 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.95 % Allowed : 17.68 % Favored : 79.37 % 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: 0.50 (0.19), residues: 1765 helix: 2.43 (0.19), residues: 640 sheet: 1.00 (0.27), residues: 375 loop : -2.06 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 437 TYR 0.015 0.001 TYR B 433 PHE 0.013 0.001 PHE E 428 TRP 0.007 0.001 TRP A 310 HIS 0.002 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00270 (15030) covalent geometry : angle 0.58524 (20390) SS BOND : bond 0.00339 ( 5) SS BOND : angle 0.37148 ( 10) hydrogen bonds : bond 0.04515 ( 720) hydrogen bonds : angle 4.21618 ( 2520) link_NAG-ASN : bond 0.00133 ( 5) link_NAG-ASN : angle 0.85918 ( 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 173 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 126 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8697 (tm) REVERT: A 197 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7542 (pmtt) REVERT: B 113 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7897 (ppp) REVERT: B 187 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8872 (mmm) REVERT: B 190 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8755 (tm) REVERT: B 285 LEU cc_start: 0.9196 (tt) cc_final: 0.8944 (tp) REVERT: C 113 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7940 (ppp) REVERT: C 286 THR cc_start: 0.9154 (t) cc_final: 0.8923 (p) REVERT: D 113 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.7670 (pmm) REVERT: D 190 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8717 (tm) REVERT: D 221 TYR cc_start: 0.8261 (OUTLIER) cc_final: 0.7991 (p90) outliers start: 47 outliers final: 28 residues processed: 159 average time/residue: 0.6191 time to fit residues: 107.7764 Evaluate side-chains 158 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 197 LYS 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 B residue 113 MET Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 187 MET 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 113 MET Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 156 ILE 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 150 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 190 LEU 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: 3.9990 chunk 26 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 148 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3568 r_free = 0.3568 target = 0.092038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.062602 restraints weight = 35795.752| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.47 r_work: 0.2807 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4010 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= 0.198 Angle : 0.660 10.049 20415 Z= 0.347 Chirality : 0.046 0.170 2290 Planarity : 0.004 0.030 2535 Dihedral : 6.025 88.793 2185 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.26 % Allowed : 18.12 % Favored : 78.62 % 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: 0.32 (0.19), residues: 1765 helix: 2.08 (0.19), residues: 675 sheet: 0.85 (0.27), residues: 370 loop : -2.11 (0.19), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 437 TYR 0.016 0.002 TYR A 433 PHE 0.018 0.002 PHE A 87 TRP 0.008 0.001 TRP A 263 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00470 (15030) covalent geometry : angle 0.65888 (20390) SS BOND : bond 0.00462 ( 5) SS BOND : angle 0.79708 ( 10) hydrogen bonds : bond 0.05207 ( 720) hydrogen bonds : angle 4.45990 ( 2520) link_NAG-ASN : bond 0.00131 ( 5) link_NAG-ASN : angle 1.43553 ( 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 173 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 121 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.7788 (pmm) REVERT: A 244 MET cc_start: 0.8777 (mmm) cc_final: 0.8515 (mmt) REVERT: B 113 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7856 (ppp) REVERT: B 190 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8857 (tm) REVERT: B 285 LEU cc_start: 0.9189 (tt) cc_final: 0.8987 (tp) REVERT: B 287 MET cc_start: 0.8832 (tpp) cc_final: 0.8546 (tpp) REVERT: C 113 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7926 (ppp) REVERT: D 113 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.7775 (pmm) outliers start: 52 outliers final: 31 residues processed: 160 average time/residue: 0.5846 time to fit residues: 102.9129 Evaluate side-chains 156 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 150 VAL 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 113 MET Chi-restraints excluded: chain B residue 150 VAL 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 113 MET Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 156 ILE 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 150 VAL 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 150 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 100 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 chunk 88 optimal weight: 0.2980 chunk 70 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3594 r_free = 0.3594 target = 0.093564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.064308 restraints weight = 35591.839| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.49 r_work: 0.2846 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15040 Z= 0.128 Angle : 0.613 8.750 20415 Z= 0.320 Chirality : 0.044 0.168 2290 Planarity : 0.003 0.031 2535 Dihedral : 5.871 89.867 2185 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.01 % Allowed : 19.37 % Favored : 78.62 % 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: 0.42 (0.19), residues: 1765 helix: 2.12 (0.19), residues: 675 sheet: 0.92 (0.27), residues: 370 loop : -2.00 (0.19), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 437 TYR 0.015 0.001 TYR B 433 PHE 0.013 0.001 PHE A 319 TRP 0.008 0.001 TRP A 263 HIS 0.002 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00289 (15030) covalent geometry : angle 0.61331 (20390) SS BOND : bond 0.00356 ( 5) SS BOND : angle 0.38664 ( 10) hydrogen bonds : bond 0.04633 ( 720) hydrogen bonds : angle 4.29204 ( 2520) link_NAG-ASN : bond 0.00197 ( 5) link_NAG-ASN : angle 0.85959 ( 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 154 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7964 (ppp) REVERT: B 190 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8818 (tm) REVERT: B 287 MET cc_start: 0.8845 (tpp) cc_final: 0.8489 (tpp) REVERT: C 113 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7923 (ppp) REVERT: D 113 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7705 (pmm) REVERT: D 190 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8762 (tm) outliers start: 32 outliers final: 26 residues processed: 148 average time/residue: 0.6371 time to fit residues: 103.1823 Evaluate side-chains 150 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL 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 150 VAL 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 113 MET Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 150 VAL 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 150 VAL Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 244 MET 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: 3.9990 chunk 100 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 74 optimal weight: 0.0670 chunk 50 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 37 optimal weight: 0.0170 overall best weight: 1.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3594 r_free = 0.3594 target = 0.093619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.064347 restraints weight = 35335.247| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.47 r_work: 0.2848 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4129 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= 0.132 Angle : 0.610 8.687 20415 Z= 0.317 Chirality : 0.044 0.171 2290 Planarity : 0.003 0.031 2535 Dihedral : 5.780 89.485 2185 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.32 % Allowed : 19.25 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.19), residues: 1765 helix: 2.06 (0.19), residues: 670 sheet: 1.01 (0.27), residues: 370 loop : -1.98 (0.19), residues: 725 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 0.011 0.001 PHE A 87 TRP 0.009 0.001 TRP A 263 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00303 (15030) covalent geometry : angle 0.60960 (20390) SS BOND : bond 0.00365 ( 5) SS BOND : angle 0.43769 ( 10) hydrogen bonds : bond 0.04561 ( 720) hydrogen bonds : angle 4.25498 ( 2520) link_NAG-ASN : bond 0.00109 ( 5) link_NAG-ASN : angle 0.94433 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4701.80 seconds wall clock time: 80 minutes 56.43 seconds (4856.43 seconds total)