Starting phenix.real_space_refine on Sat Mar 16 12:16:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6p_23703/03_2024/7m6p_23703.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6p_23703/03_2024/7m6p_23703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6p_23703/03_2024/7m6p_23703.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6p_23703/03_2024/7m6p_23703.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6p_23703/03_2024/7m6p_23703.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6p_23703/03_2024/7m6p_23703.pdb" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9510 2.51 5 N 2400 2.21 5 O 2640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14650 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2911 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2911 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2911 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2911 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2911 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.66, per 1000 atoms: 0.52 Number of scatterers: 14650 At special positions: 0 Unit cell: (96.8, 95.7, 137.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2640 8.00 N 2400 7.00 C 9510 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 176 " distance=2.04 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 176 " distance=2.04 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 176 " distance=2.04 Simple disulfide: pdb=" SG CYS D 162 " - pdb=" SG CYS D 176 " distance=2.04 Simple disulfide: pdb=" SG CYS E 162 " - pdb=" SG CYS E 176 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 5.53 Conformation dependent library (CDL) restraints added in 3.3 seconds 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3450 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 25 sheets defined 39.7% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 33 through 42 removed outlier: 3.753A pdb=" N PHE A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 removed outlier: 3.525A pdb=" N ILE A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 268 removed outlier: 3.788A pdb=" N TRP A 267 " --> pdb=" O TRP A 263 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 295 removed outlier: 4.064A pdb=" N VAL A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 281 " --> pdb=" O VAL A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 339 Processing helix chain 'A' and resid 396 through 444 removed outlier: 3.728A pdb=" N LEU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) Proline residue: A 419 - end of helix removed outlier: 3.656A pdb=" N THR A 432 " --> pdb=" O PHE A 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 42 removed outlier: 3.753A pdb=" N PHE B 37 " --> pdb=" O PRO B 33 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 251 removed outlier: 3.526A pdb=" N ILE B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 268 removed outlier: 3.789A pdb=" N TRP B 267 " --> pdb=" O TRP B 263 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 295 removed outlier: 4.063A pdb=" N VAL B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 281 " --> pdb=" O VAL B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 339 Processing helix chain 'B' and resid 396 through 444 removed outlier: 3.727A pdb=" N LEU B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG B 406 " --> pdb=" O LEU B 402 " (cutoff:3.500A) Proline residue: B 419 - end of helix removed outlier: 3.656A pdb=" N THR B 432 " --> pdb=" O PHE B 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 42 removed outlier: 3.753A pdb=" N PHE C 37 " --> pdb=" O PRO C 33 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 251 removed outlier: 3.526A pdb=" N ILE C 249 " --> pdb=" O GLY C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 268 removed outlier: 3.788A pdb=" N TRP C 267 " --> pdb=" O TRP C 263 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE C 268 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 295 removed outlier: 4.063A pdb=" N VAL C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY C 280 " --> pdb=" O ARG C 276 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE C 281 " --> pdb=" O VAL C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 339 Processing helix chain 'C' and resid 396 through 444 removed outlier: 3.728A pdb=" N LEU C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG C 406 " --> pdb=" O LEU C 402 " (cutoff:3.500A) Proline residue: C 419 - end of helix removed outlier: 3.657A pdb=" N THR C 432 " --> pdb=" O PHE C 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 42 removed outlier: 3.754A pdb=" N PHE D 37 " --> pdb=" O PRO D 33 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 removed outlier: 3.526A pdb=" N ILE D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 268 removed outlier: 3.788A pdb=" N TRP D 267 " --> pdb=" O TRP D 263 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE D 268 " --> pdb=" O VAL D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 295 removed outlier: 4.065A pdb=" N VAL D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY D 280 " --> pdb=" O ARG D 276 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE D 281 " --> pdb=" O VAL D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 339 Processing helix chain 'D' and resid 396 through 444 removed outlier: 3.728A pdb=" N LEU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG D 406 " --> pdb=" O LEU D 402 " (cutoff:3.500A) Proline residue: D 419 - end of helix removed outlier: 3.656A pdb=" N THR D 432 " --> pdb=" O PHE D 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 42 removed outlier: 3.753A pdb=" N PHE E 37 " --> pdb=" O PRO E 33 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 251 removed outlier: 3.526A pdb=" N ILE E 249 " --> pdb=" O GLY E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 268 removed outlier: 3.788A pdb=" N TRP E 267 " --> pdb=" O TRP E 263 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE E 268 " --> pdb=" O VAL E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 295 removed outlier: 4.064A pdb=" N VAL E 277 " --> pdb=" O ALA E 273 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY E 280 " --> pdb=" O ARG E 276 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE E 281 " --> pdb=" O VAL E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 339 Processing helix chain 'E' and resid 396 through 444 removed outlier: 3.727A pdb=" N LEU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG E 406 " --> pdb=" O LEU E 402 " (cutoff:3.500A) Proline residue: E 419 - end of helix removed outlier: 3.656A pdb=" N THR E 432 " --> pdb=" O PHE E 428 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 108 removed outlier: 4.046A pdb=" N TRP A 92 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL A 63 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 128 removed outlier: 3.744A pdb=" N VAL A 159 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TRP A 92 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 123 through 124 Processing sheet with id=AA4, first strand: chain 'A' and resid 123 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 108 removed outlier: 4.045A pdb=" N TRP B 92 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL B 63 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 127 through 128 removed outlier: 3.744A pdb=" N VAL B 159 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TRP B 92 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AA9, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AB1, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AB2, first strand: chain 'C' and resid 107 through 108 removed outlier: 4.047A pdb=" N TRP C 92 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N VAL C 63 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 127 through 128 removed outlier: 3.743A pdb=" N VAL C 159 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TRP C 92 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 123 through 124 Processing sheet with id=AB5, first strand: chain 'C' and resid 123 through 124 Processing sheet with id=AB6, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AB7, first strand: chain 'D' and resid 107 through 108 removed outlier: 4.046A pdb=" N TRP D 92 " --> pdb=" O VAL D 150 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL D 63 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 127 through 128 removed outlier: 3.743A pdb=" N VAL D 159 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TRP D 92 " --> pdb=" O VAL D 150 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 123 through 124 Processing sheet with id=AC1, first strand: chain 'D' and resid 123 through 124 Processing sheet with id=AC2, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AC3, first strand: chain 'E' and resid 107 through 108 removed outlier: 4.046A pdb=" N TRP E 92 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASP E 81 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER E 74 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL E 63 " --> pdb=" O GLU E 193 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 127 through 128 removed outlier: 3.744A pdb=" N VAL E 159 " --> pdb=" O LYS E 128 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TRP E 92 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASP E 81 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER E 74 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 123 through 124 Processing sheet with id=AC6, first strand: chain 'E' and resid 123 through 124 Processing sheet with id=AC7, first strand: chain 'E' and resid 224 through 225 890 hydrogen bonds defined for protein. 2565 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.73 Time building geometry restraints manager: 6.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4273 1.34 - 1.46: 3791 1.46 - 1.58: 6766 1.58 - 1.71: 0 1.71 - 1.83: 170 Bond restraints: 15000 Sorted by residual: bond pdb=" CB MET C 187 " pdb=" CG MET C 187 " ideal model delta sigma weight residual 1.520 1.447 0.073 3.00e-02 1.11e+03 5.85e+00 bond pdb=" CB MET E 187 " pdb=" CG MET E 187 " ideal model delta sigma weight residual 1.520 1.448 0.072 3.00e-02 1.11e+03 5.81e+00 bond pdb=" CB MET B 187 " pdb=" CG MET B 187 " ideal model delta sigma weight residual 1.520 1.448 0.072 3.00e-02 1.11e+03 5.81e+00 bond pdb=" CB MET D 187 " pdb=" CG MET D 187 " ideal model delta sigma weight residual 1.520 1.448 0.072 3.00e-02 1.11e+03 5.79e+00 bond pdb=" CB MET A 187 " pdb=" CG MET A 187 " ideal model delta sigma weight residual 1.520 1.448 0.072 3.00e-02 1.11e+03 5.76e+00 ... (remaining 14995 not shown) Histogram of bond angle deviations from ideal: 98.50 - 105.64: 375 105.64 - 112.79: 7610 112.79 - 119.93: 5333 119.93 - 127.07: 6800 127.07 - 134.21: 207 Bond angle restraints: 20325 Sorted by residual: angle pdb=" C VAL A 135 " pdb=" N THR A 136 " pdb=" CA THR A 136 " ideal model delta sigma weight residual 121.54 131.59 -10.05 1.91e+00 2.74e-01 2.77e+01 angle pdb=" C VAL E 135 " pdb=" N THR E 136 " pdb=" CA THR E 136 " ideal model delta sigma weight residual 121.54 131.58 -10.04 1.91e+00 2.74e-01 2.76e+01 angle pdb=" C VAL B 135 " pdb=" N THR B 136 " pdb=" CA THR B 136 " ideal model delta sigma weight residual 121.54 131.57 -10.03 1.91e+00 2.74e-01 2.76e+01 angle pdb=" C VAL D 135 " pdb=" N THR D 136 " pdb=" CA THR D 136 " ideal model delta sigma weight residual 121.54 131.56 -10.02 1.91e+00 2.74e-01 2.75e+01 angle pdb=" C VAL C 135 " pdb=" N THR C 136 " pdb=" CA THR C 136 " ideal model delta sigma weight residual 121.54 131.53 -9.99 1.91e+00 2.74e-01 2.73e+01 ... (remaining 20320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 8329 17.22 - 34.44: 579 34.44 - 51.66: 112 51.66 - 68.88: 20 68.88 - 86.11: 10 Dihedral angle restraints: 9050 sinusoidal: 3740 harmonic: 5310 Sorted by residual: dihedral pdb=" N PHE B 266 " pdb=" C PHE B 266 " pdb=" CA PHE B 266 " pdb=" CB PHE B 266 " ideal model delta harmonic sigma weight residual 122.80 135.86 -13.06 0 2.50e+00 1.60e-01 2.73e+01 dihedral pdb=" N PHE D 266 " pdb=" C PHE D 266 " pdb=" CA PHE D 266 " pdb=" CB PHE D 266 " ideal model delta harmonic sigma weight residual 122.80 135.85 -13.05 0 2.50e+00 1.60e-01 2.72e+01 dihedral pdb=" N PHE E 266 " pdb=" C PHE E 266 " pdb=" CA PHE E 266 " pdb=" CB PHE E 266 " ideal model delta harmonic sigma weight residual 122.80 135.84 -13.04 0 2.50e+00 1.60e-01 2.72e+01 ... (remaining 9047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1942 0.096 - 0.191: 283 0.191 - 0.287: 56 0.287 - 0.383: 4 0.383 - 0.478: 5 Chirality restraints: 2290 Sorted by residual: chirality pdb=" CA PHE B 266 " pdb=" N PHE B 266 " pdb=" C PHE B 266 " pdb=" CB PHE B 266 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CA PHE D 266 " pdb=" N PHE D 266 " pdb=" C PHE D 266 " pdb=" CB PHE D 266 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.71e+00 chirality pdb=" CA PHE E 266 " pdb=" N PHE E 266 " pdb=" C PHE E 266 " pdb=" CB PHE E 266 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.69e+00 ... (remaining 2287 not shown) Planarity restraints: 2550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 266 " 0.026 2.00e-02 2.50e+03 2.86e-02 1.43e+01 pdb=" CG PHE A 266 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE A 266 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 266 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE A 266 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 PHE A 266 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 266 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 266 " 0.026 2.00e-02 2.50e+03 2.86e-02 1.43e+01 pdb=" CG PHE E 266 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE E 266 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE E 266 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE E 266 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE E 266 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 266 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 266 " -0.026 2.00e-02 2.50e+03 2.85e-02 1.42e+01 pdb=" CG PHE D 266 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE D 266 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE D 266 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE D 266 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE D 266 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 266 " 0.007 2.00e-02 2.50e+03 ... (remaining 2547 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3865 2.81 - 3.34: 13546 3.34 - 3.86: 23842 3.86 - 4.38: 26471 4.38 - 4.90: 46987 Nonbonded interactions: 114711 Sorted by model distance: nonbonded pdb=" OD2 ASP D 110 " pdb=" OG SER D 112 " model vdw 2.293 2.440 nonbonded pdb=" OD2 ASP B 110 " pdb=" OG SER B 112 " model vdw 2.293 2.440 nonbonded pdb=" OD2 ASP C 110 " pdb=" OG SER C 112 " model vdw 2.293 2.440 nonbonded pdb=" OD2 ASP E 110 " pdb=" OG SER E 112 " model vdw 2.293 2.440 nonbonded pdb=" OD2 ASP A 110 " pdb=" OG SER A 112 " model vdw 2.294 2.440 ... (remaining 114706 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 32 through 444) selection = (chain 'B' and resid 32 through 444) selection = (chain 'C' and resid 32 through 444) selection = (chain 'D' and resid 32 through 444) selection = (chain 'E' and resid 32 through 444) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 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: 6.450 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 39.050 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.070 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 15000 Z= 0.532 Angle : 1.270 12.840 20325 Z= 0.725 Chirality : 0.075 0.478 2290 Planarity : 0.008 0.060 2545 Dihedral : 12.688 86.106 5585 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.20), residues: 1775 helix: 2.34 (0.19), residues: 650 sheet: 0.19 (0.29), residues: 370 loop : -1.90 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 267 HIS 0.008 0.003 HIS B 335 PHE 0.065 0.005 PHE A 266 TYR 0.028 0.003 TYR A 325 ARG 0.004 0.001 ARG E 400 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 562 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 THR cc_start: 0.9152 (p) cc_final: 0.8767 (p) REVERT: A 105 ASP cc_start: 0.7674 (p0) cc_final: 0.7290 (p0) REVERT: A 138 ASP cc_start: 0.7084 (p0) cc_final: 0.6520 (p0) REVERT: A 263 TRP cc_start: 0.6830 (m-10) cc_final: 0.6521 (m-10) REVERT: A 287 MET cc_start: 0.9284 (mmm) cc_final: 0.9051 (mmm) REVERT: B 115 ASP cc_start: 0.7564 (p0) cc_final: 0.7143 (p0) REVERT: B 138 ASP cc_start: 0.6447 (p0) cc_final: 0.6212 (p0) REVERT: B 287 MET cc_start: 0.9395 (mmm) cc_final: 0.9101 (mmp) REVERT: B 408 LYS cc_start: 0.8732 (mmtm) cc_final: 0.8313 (ptpt) REVERT: B 420 LEU cc_start: 0.8881 (tp) cc_final: 0.8644 (tp) REVERT: B 423 LEU cc_start: 0.9260 (tp) cc_final: 0.9025 (tt) REVERT: C 138 ASP cc_start: 0.7296 (p0) cc_final: 0.7089 (p0) REVERT: C 140 LYS cc_start: 0.8699 (mttp) cc_final: 0.8450 (mttp) REVERT: C 287 MET cc_start: 0.9286 (mmm) cc_final: 0.8913 (mmp) REVERT: C 426 ASN cc_start: 0.8587 (m-40) cc_final: 0.7560 (m-40) REVERT: D 78 THR cc_start: 0.9127 (p) cc_final: 0.8791 (p) REVERT: D 153 SER cc_start: 0.8547 (t) cc_final: 0.8314 (p) REVERT: D 164 MET cc_start: 0.8681 (ptp) cc_final: 0.8421 (ptp) REVERT: D 287 MET cc_start: 0.9371 (mmm) cc_final: 0.9036 (mmp) REVERT: D 311 MET cc_start: 0.8855 (mmt) cc_final: 0.8499 (mmm) REVERT: E 78 THR cc_start: 0.9082 (p) cc_final: 0.8721 (p) REVERT: E 138 ASP cc_start: 0.7178 (p0) cc_final: 0.6971 (p0) REVERT: E 287 MET cc_start: 0.9307 (mmm) cc_final: 0.9030 (mmp) REVERT: E 426 ASN cc_start: 0.8696 (m-40) cc_final: 0.8154 (m-40) outliers start: 0 outliers final: 0 residues processed: 562 average time/residue: 0.2441 time to fit residues: 202.7150 Evaluate side-chains 361 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 83 optimal weight: 0.0020 chunk 102 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 239 HIS A 250 GLN A 426 ASN B 85 ASN B 239 HIS B 334 GLN C 179 GLN C 210 GLN C 239 HIS C 269 ASN C 329 ASN ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN D 239 HIS D 290 GLN D 426 ASN E 85 ASN E 179 GLN ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 HIS E 250 GLN E 290 GLN E 334 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15000 Z= 0.234 Angle : 0.734 9.138 20325 Z= 0.388 Chirality : 0.048 0.207 2290 Planarity : 0.005 0.050 2545 Dihedral : 5.116 24.015 2060 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.37 % Allowed : 14.27 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.19), residues: 1775 helix: 2.02 (0.18), residues: 675 sheet: 0.86 (0.27), residues: 375 loop : -1.99 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 267 HIS 0.003 0.001 HIS E 239 PHE 0.034 0.002 PHE B 266 TYR 0.018 0.002 TYR B 433 ARG 0.008 0.001 ARG D 400 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 417 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.7326 (p0) REVERT: A 174 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7812 (mm110) REVERT: B 105 ASP cc_start: 0.7830 (p0) cc_final: 0.7589 (p0) REVERT: B 177 ILE cc_start: 0.9156 (mm) cc_final: 0.8674 (mm) REVERT: B 201 GLN cc_start: 0.7522 (mp10) cc_final: 0.7208 (mp10) REVERT: B 423 LEU cc_start: 0.9204 (tp) cc_final: 0.9002 (tt) REVERT: B 439 GLU cc_start: 0.6679 (tm-30) cc_final: 0.6418 (tm-30) REVERT: C 39 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7517 (p0) REVERT: D 138 ASP cc_start: 0.6724 (p0) cc_final: 0.6387 (p0) REVERT: D 140 LYS cc_start: 0.8888 (mtpp) cc_final: 0.8583 (mtmm) REVERT: D 426 ASN cc_start: 0.8644 (m-40) cc_final: 0.8271 (m110) REVERT: E 39 ASP cc_start: 0.7545 (OUTLIER) cc_final: 0.7337 (p0) REVERT: E 158 LEU cc_start: 0.8750 (mt) cc_final: 0.8492 (mp) outliers start: 38 outliers final: 16 residues processed: 442 average time/residue: 0.2258 time to fit residues: 151.3271 Evaluate side-chains 390 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 370 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 290 GLN Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 269 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 141 optimal weight: 0.0470 chunk 157 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15000 Z= 0.213 Angle : 0.677 9.802 20325 Z= 0.351 Chirality : 0.046 0.178 2290 Planarity : 0.004 0.060 2545 Dihedral : 4.853 26.195 2060 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.55 % Allowed : 16.82 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.19), residues: 1775 helix: 2.16 (0.19), residues: 670 sheet: 0.97 (0.27), residues: 375 loop : -1.99 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP A 267 HIS 0.002 0.001 HIS A 335 PHE 0.030 0.002 PHE C 266 TYR 0.020 0.002 TYR A 246 ARG 0.005 0.000 ARG D 400 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 387 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7565 (p0) cc_final: 0.7318 (p0) REVERT: A 140 LYS cc_start: 0.8676 (mtmm) cc_final: 0.8382 (mtmm) REVERT: A 174 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7771 (mm110) REVERT: B 105 ASP cc_start: 0.7892 (p0) cc_final: 0.7555 (p0) REVERT: B 177 ILE cc_start: 0.9146 (mm) cc_final: 0.8458 (mm) REVERT: B 201 GLN cc_start: 0.7443 (mp10) cc_final: 0.7105 (mp10) REVERT: B 423 LEU cc_start: 0.9238 (tp) cc_final: 0.8996 (tt) REVERT: B 439 GLU cc_start: 0.6799 (tm-30) cc_final: 0.6463 (tm-30) REVERT: C 39 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7582 (p0) REVERT: C 422 PHE cc_start: 0.8953 (t80) cc_final: 0.8711 (t80) REVERT: C 426 ASN cc_start: 0.8394 (m110) cc_final: 0.7320 (m110) REVERT: D 138 ASP cc_start: 0.6914 (p0) cc_final: 0.6494 (p0) REVERT: D 140 LYS cc_start: 0.8928 (mtpp) cc_final: 0.8571 (mtmm) REVERT: D 311 MET cc_start: 0.8792 (mmm) cc_final: 0.8176 (mmm) REVERT: E 426 ASN cc_start: 0.8565 (m-40) cc_final: 0.8065 (m110) outliers start: 41 outliers final: 27 residues processed: 415 average time/residue: 0.2230 time to fit residues: 141.0941 Evaluate side-chains 392 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 363 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 269 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 159 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 151 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN B 290 GLN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15000 Z= 0.213 Angle : 0.649 10.589 20325 Z= 0.336 Chirality : 0.045 0.167 2290 Planarity : 0.003 0.044 2545 Dihedral : 4.649 27.806 2060 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.55 % Allowed : 16.88 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.19), residues: 1775 helix: 2.16 (0.19), residues: 670 sheet: 0.71 (0.26), residues: 380 loop : -1.97 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.003 TRP E 267 HIS 0.003 0.001 HIS C 335 PHE 0.026 0.002 PHE D 72 TYR 0.018 0.002 TYR D 246 ARG 0.003 0.000 ARG D 400 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 377 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7612 (p0) cc_final: 0.7376 (p0) REVERT: A 115 ASP cc_start: 0.7693 (p0) cc_final: 0.7224 (p0) REVERT: A 140 LYS cc_start: 0.8658 (mtmm) cc_final: 0.8164 (mtmm) REVERT: A 174 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7839 (mm110) REVERT: A 201 GLN cc_start: 0.7373 (mp10) cc_final: 0.6901 (mp10) REVERT: B 105 ASP cc_start: 0.8088 (p0) cc_final: 0.7779 (p0) REVERT: B 138 ASP cc_start: 0.5962 (p0) cc_final: 0.5605 (p0) REVERT: B 201 GLN cc_start: 0.7425 (mp10) cc_final: 0.7093 (mp10) REVERT: B 423 LEU cc_start: 0.9234 (tp) cc_final: 0.8969 (tt) REVERT: B 426 ASN cc_start: 0.8607 (m-40) cc_final: 0.8373 (m-40) REVERT: B 439 GLU cc_start: 0.6909 (tm-30) cc_final: 0.6697 (tm-30) REVERT: C 422 PHE cc_start: 0.8911 (t80) cc_final: 0.8646 (t80) REVERT: C 426 ASN cc_start: 0.8383 (m110) cc_final: 0.7235 (m110) REVERT: D 138 ASP cc_start: 0.6989 (p0) cc_final: 0.6594 (p0) REVERT: D 140 LYS cc_start: 0.8892 (mtpp) cc_final: 0.8535 (mtmm) REVERT: D 308 ASP cc_start: 0.8134 (m-30) cc_final: 0.7801 (m-30) REVERT: E 201 GLN cc_start: 0.7500 (mp10) cc_final: 0.7104 (mp10) outliers start: 57 outliers final: 41 residues processed: 413 average time/residue: 0.2279 time to fit residues: 142.6531 Evaluate side-chains 402 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 360 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 235 GLU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 269 ASN 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 140 optimal weight: 0.0980 chunk 96 optimal weight: 1.9990 chunk 2 optimal weight: 0.0060 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN C 179 GLN ** C 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN E 426 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15000 Z= 0.205 Angle : 0.658 11.184 20325 Z= 0.336 Chirality : 0.045 0.163 2290 Planarity : 0.003 0.036 2545 Dihedral : 4.562 30.629 2060 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.12 % Allowed : 18.26 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.19), residues: 1775 helix: 2.10 (0.19), residues: 665 sheet: 0.71 (0.26), residues: 380 loop : -2.00 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.003 TRP E 267 HIS 0.003 0.001 HIS D 239 PHE 0.024 0.002 PHE A 266 TYR 0.015 0.002 TYR D 429 ARG 0.006 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 374 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7585 (p0) cc_final: 0.7350 (p0) REVERT: A 115 ASP cc_start: 0.7698 (p0) cc_final: 0.7260 (p0) REVERT: A 174 GLN cc_start: 0.8129 (mp10) cc_final: 0.7887 (mm110) REVERT: A 201 GLN cc_start: 0.7346 (mp10) cc_final: 0.6919 (mp10) REVERT: B 105 ASP cc_start: 0.8090 (p0) cc_final: 0.7787 (p0) REVERT: B 201 GLN cc_start: 0.7408 (mp10) cc_final: 0.7080 (mp10) REVERT: B 423 LEU cc_start: 0.9204 (tp) cc_final: 0.8917 (tt) REVERT: B 439 GLU cc_start: 0.6913 (tm-30) cc_final: 0.6681 (tm-30) REVERT: C 426 ASN cc_start: 0.8435 (m110) cc_final: 0.7197 (m110) REVERT: D 134 GLU cc_start: 0.6844 (pm20) cc_final: 0.6609 (pm20) REVERT: D 138 ASP cc_start: 0.7058 (p0) cc_final: 0.6662 (p0) REVERT: D 140 LYS cc_start: 0.8913 (mtpp) cc_final: 0.8559 (mtmm) REVERT: E 90 GLN cc_start: 0.8133 (pt0) cc_final: 0.7847 (mt0) REVERT: E 201 GLN cc_start: 0.7500 (mp10) cc_final: 0.7080 (mp10) REVERT: E 251 MET cc_start: 0.8710 (mpp) cc_final: 0.8473 (mpp) REVERT: E 308 ASP cc_start: 0.8190 (m-30) cc_final: 0.7971 (m-30) outliers start: 50 outliers final: 41 residues processed: 404 average time/residue: 0.2261 time to fit residues: 139.1186 Evaluate side-chains 395 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 354 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 267 TRP Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 269 ASN 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 32 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 235 GLU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 269 ASN 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 56 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 14 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 ASN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN E 426 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15000 Z= 0.242 Angle : 0.665 11.733 20325 Z= 0.336 Chirality : 0.044 0.146 2290 Planarity : 0.003 0.036 2545 Dihedral : 4.537 31.869 2060 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.49 % Allowed : 18.07 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.19), residues: 1775 helix: 2.17 (0.19), residues: 670 sheet: 0.81 (0.26), residues: 375 loop : -2.07 (0.19), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP A 267 HIS 0.003 0.001 HIS C 239 PHE 0.027 0.002 PHE C 422 TYR 0.024 0.002 TYR B 246 ARG 0.005 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 363 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7546 (p0) cc_final: 0.7334 (p0) REVERT: A 115 ASP cc_start: 0.7717 (p0) cc_final: 0.7294 (p0) REVERT: A 174 GLN cc_start: 0.8137 (mp10) cc_final: 0.7883 (mm110) REVERT: A 201 GLN cc_start: 0.7500 (mp10) cc_final: 0.7085 (mp10) REVERT: A 263 TRP cc_start: 0.6440 (m-10) cc_final: 0.6097 (m-10) REVERT: B 105 ASP cc_start: 0.8098 (p0) cc_final: 0.7755 (p0) REVERT: B 138 ASP cc_start: 0.5600 (p0) cc_final: 0.5397 (p0) REVERT: B 152 TYR cc_start: 0.7960 (t80) cc_final: 0.7710 (t80) REVERT: B 201 GLN cc_start: 0.7445 (mp10) cc_final: 0.7107 (mp10) REVERT: B 423 LEU cc_start: 0.9232 (tp) cc_final: 0.8947 (tt) REVERT: B 439 GLU cc_start: 0.7007 (tm-30) cc_final: 0.6779 (tm-30) REVERT: C 426 ASN cc_start: 0.8477 (m-40) cc_final: 0.8165 (m110) REVERT: D 134 GLU cc_start: 0.6966 (pm20) cc_final: 0.6720 (pm20) REVERT: D 251 MET cc_start: 0.8447 (mpp) cc_final: 0.8025 (mpp) REVERT: D 308 ASP cc_start: 0.8126 (m-30) cc_final: 0.7713 (m-30) REVERT: E 90 GLN cc_start: 0.8164 (pt0) cc_final: 0.7881 (mt0) REVERT: E 201 GLN cc_start: 0.7608 (mp10) cc_final: 0.7166 (mp10) REVERT: E 251 MET cc_start: 0.8637 (mpp) cc_final: 0.8430 (mpp) REVERT: E 308 ASP cc_start: 0.8215 (m-30) cc_final: 0.7991 (m-30) REVERT: E 422 PHE cc_start: 0.8902 (t80) cc_final: 0.8633 (t80) outliers start: 56 outliers final: 45 residues processed: 397 average time/residue: 0.2249 time to fit residues: 136.0836 Evaluate side-chains 391 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 346 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 267 TRP Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 235 GLU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 269 ASN 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 19 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 142 optimal weight: 0.0040 chunk 94 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN B 426 ASN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN C 210 GLN ** C 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 ASN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN E 426 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15000 Z= 0.200 Angle : 0.678 12.846 20325 Z= 0.337 Chirality : 0.045 0.157 2290 Planarity : 0.003 0.035 2545 Dihedral : 4.468 31.177 2060 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.24 % Allowed : 19.25 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.19), residues: 1775 helix: 2.20 (0.19), residues: 665 sheet: 0.83 (0.27), residues: 375 loop : -2.08 (0.19), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.003 TRP B 267 HIS 0.003 0.001 HIS D 239 PHE 0.022 0.001 PHE D 72 TYR 0.037 0.002 TYR D 152 ARG 0.005 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 369 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7650 (p0) cc_final: 0.7444 (p0) REVERT: A 115 ASP cc_start: 0.7781 (p0) cc_final: 0.7332 (p0) REVERT: A 138 ASP cc_start: 0.6387 (p0) cc_final: 0.6107 (p0) REVERT: A 140 LYS cc_start: 0.8428 (mtmm) cc_final: 0.8183 (ptpp) REVERT: A 174 GLN cc_start: 0.8106 (mp10) cc_final: 0.7860 (mm110) REVERT: A 201 GLN cc_start: 0.7462 (mp10) cc_final: 0.7044 (mp10) REVERT: B 105 ASP cc_start: 0.7968 (p0) cc_final: 0.7645 (p0) REVERT: B 201 GLN cc_start: 0.7378 (mp10) cc_final: 0.7028 (mp10) REVERT: B 423 LEU cc_start: 0.9227 (tp) cc_final: 0.8949 (tt) REVERT: B 439 GLU cc_start: 0.7051 (tm-30) cc_final: 0.6799 (tm-30) REVERT: D 134 GLU cc_start: 0.7041 (pm20) cc_final: 0.6797 (pm20) REVERT: D 152 TYR cc_start: 0.7673 (t80) cc_final: 0.7406 (t80) REVERT: D 201 GLN cc_start: 0.7333 (mp10) cc_final: 0.6865 (mp10) REVERT: D 251 MET cc_start: 0.8453 (mpp) cc_final: 0.8038 (mpp) REVERT: E 90 GLN cc_start: 0.8071 (pt0) cc_final: 0.7837 (mt0) REVERT: E 201 GLN cc_start: 0.7472 (mp10) cc_final: 0.7028 (mp10) REVERT: E 235 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6823 (tt0) REVERT: E 237 ARG cc_start: 0.8436 (mtp85) cc_final: 0.7884 (mtt90) REVERT: E 308 ASP cc_start: 0.8201 (m-30) cc_final: 0.7986 (m-30) outliers start: 52 outliers final: 41 residues processed: 400 average time/residue: 0.2467 time to fit residues: 151.5539 Evaluate side-chains 395 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 353 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 267 TRP Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 235 GLU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 269 ASN 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 67 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 114 optimal weight: 0.0270 chunk 83 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 132 optimal weight: 0.4980 chunk 153 optimal weight: 1.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN B 210 GLN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 GLN ** C 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 ASN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15000 Z= 0.191 Angle : 0.685 13.812 20325 Z= 0.339 Chirality : 0.045 0.155 2290 Planarity : 0.003 0.034 2545 Dihedral : 4.435 31.019 2060 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.99 % Allowed : 20.62 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.19), residues: 1775 helix: 1.89 (0.19), residues: 700 sheet: 0.84 (0.27), residues: 375 loop : -2.08 (0.20), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.003 TRP D 267 HIS 0.002 0.001 HIS A 335 PHE 0.023 0.001 PHE D 72 TYR 0.033 0.001 TYR D 152 ARG 0.007 0.000 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 365 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7638 (p0) cc_final: 0.7436 (p0) REVERT: A 115 ASP cc_start: 0.7795 (p0) cc_final: 0.7348 (p0) REVERT: A 140 LYS cc_start: 0.8554 (mtmm) cc_final: 0.8326 (ptpp) REVERT: A 174 GLN cc_start: 0.8064 (mp10) cc_final: 0.7817 (mm110) REVERT: A 201 GLN cc_start: 0.7488 (mp10) cc_final: 0.7068 (mp10) REVERT: A 263 TRP cc_start: 0.6059 (m-10) cc_final: 0.5833 (m-10) REVERT: B 105 ASP cc_start: 0.7957 (p0) cc_final: 0.7658 (p0) REVERT: B 201 GLN cc_start: 0.7362 (mp10) cc_final: 0.7011 (mp10) REVERT: B 423 LEU cc_start: 0.9230 (tp) cc_final: 0.8951 (tt) REVERT: B 439 GLU cc_start: 0.7048 (tm-30) cc_final: 0.6800 (tm-30) REVERT: D 201 GLN cc_start: 0.7321 (mp10) cc_final: 0.6889 (mp10) REVERT: D 235 GLU cc_start: 0.7360 (tm-30) cc_final: 0.6996 (tm-30) REVERT: D 251 MET cc_start: 0.8498 (mpp) cc_final: 0.8030 (mpp) REVERT: D 263 TRP cc_start: 0.5974 (m-10) cc_final: 0.5741 (m-10) REVERT: E 201 GLN cc_start: 0.7457 (mp10) cc_final: 0.7178 (mp10) REVERT: E 308 ASP cc_start: 0.8183 (m-30) cc_final: 0.7966 (m-30) outliers start: 48 outliers final: 39 residues processed: 394 average time/residue: 0.2332 time to fit residues: 141.0450 Evaluate side-chains 384 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 345 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 267 TRP Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 269 ASN 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 161 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 123 optimal weight: 0.0050 chunk 48 optimal weight: 0.0970 chunk 142 optimal weight: 0.0030 chunk 148 optimal weight: 0.0770 chunk 156 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 overall best weight: 0.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN B 210 GLN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 GLN C 290 GLN ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15000 Z= 0.179 Angle : 0.707 14.997 20325 Z= 0.344 Chirality : 0.045 0.166 2290 Planarity : 0.003 0.035 2545 Dihedral : 4.362 31.061 2060 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.74 % Allowed : 21.06 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.20), residues: 1775 helix: 1.94 (0.19), residues: 700 sheet: 0.96 (0.27), residues: 370 loop : -2.05 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.003 TRP D 267 HIS 0.002 0.001 HIS C 335 PHE 0.033 0.001 PHE C 72 TYR 0.040 0.001 TYR D 152 ARG 0.006 0.000 ARG B 437 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 379 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ASP cc_start: 0.7694 (p0) cc_final: 0.7259 (p0) REVERT: A 138 ASP cc_start: 0.6274 (p0) cc_final: 0.5983 (p0) REVERT: A 174 GLN cc_start: 0.8000 (mp10) cc_final: 0.7744 (mm110) REVERT: A 201 GLN cc_start: 0.7477 (mp10) cc_final: 0.7045 (mp10) REVERT: A 263 TRP cc_start: 0.5942 (m-10) cc_final: 0.5563 (m-10) REVERT: B 105 ASP cc_start: 0.7984 (p0) cc_final: 0.7690 (p0) REVERT: B 201 GLN cc_start: 0.7276 (mp10) cc_final: 0.6925 (mp10) REVERT: B 439 GLU cc_start: 0.6987 (tm-30) cc_final: 0.6733 (tm-30) REVERT: C 422 PHE cc_start: 0.8887 (t80) cc_final: 0.8671 (t80) REVERT: D 134 GLU cc_start: 0.7114 (pm20) cc_final: 0.6847 (pm20) REVERT: D 138 ASP cc_start: 0.7055 (p0) cc_final: 0.6760 (p0) REVERT: D 176 CYS cc_start: 0.6128 (m) cc_final: 0.5595 (m) REVERT: D 201 GLN cc_start: 0.7258 (mp10) cc_final: 0.6755 (mp10) REVERT: D 235 GLU cc_start: 0.7322 (tm-30) cc_final: 0.6976 (tm-30) outliers start: 44 outliers final: 35 residues processed: 405 average time/residue: 0.2299 time to fit residues: 140.7504 Evaluate side-chains 389 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 354 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 267 TRP Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 269 ASN Chi-restraints excluded: chain E residue 399 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 0.9990 chunk 101 optimal weight: 0.0270 chunk 78 optimal weight: 0.5980 chunk 115 optimal weight: 0.0670 chunk 174 optimal weight: 0.6980 chunk 160 optimal weight: 5.9990 chunk 138 optimal weight: 0.4980 chunk 14 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 0.0670 chunk 110 optimal weight: 0.8980 overall best weight: 0.2514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN B 210 GLN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 GLN ** C 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15000 Z= 0.183 Angle : 0.727 14.912 20325 Z= 0.348 Chirality : 0.045 0.158 2290 Planarity : 0.003 0.043 2545 Dihedral : 4.319 30.780 2060 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.24 % Allowed : 22.43 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.19), residues: 1775 helix: 2.19 (0.19), residues: 670 sheet: 0.95 (0.27), residues: 370 loop : -1.99 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP D 267 HIS 0.002 0.001 HIS B 239 PHE 0.034 0.001 PHE B 72 TYR 0.013 0.001 TYR D 429 ARG 0.012 0.000 ARG A 437 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 372 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8619 (tp) cc_final: 0.8370 (tp) REVERT: A 115 ASP cc_start: 0.7770 (p0) cc_final: 0.7352 (p0) REVERT: A 174 GLN cc_start: 0.7993 (mp10) cc_final: 0.7749 (mm110) REVERT: A 201 GLN cc_start: 0.7534 (mp10) cc_final: 0.7099 (mp10) REVERT: A 263 TRP cc_start: 0.5917 (m-10) cc_final: 0.5563 (m-10) REVERT: B 105 ASP cc_start: 0.7956 (p0) cc_final: 0.7681 (p0) REVERT: B 201 GLN cc_start: 0.7303 (mp10) cc_final: 0.6948 (mp10) REVERT: B 439 GLU cc_start: 0.7008 (tm-30) cc_final: 0.6749 (tm-30) REVERT: D 140 LYS cc_start: 0.8860 (mtmm) cc_final: 0.8647 (mttm) REVERT: D 176 CYS cc_start: 0.6212 (m) cc_final: 0.5693 (m) REVERT: D 201 GLN cc_start: 0.7286 (mp10) cc_final: 0.6880 (mp10) REVERT: D 263 TRP cc_start: 0.5761 (m-10) cc_final: 0.5465 (m-10) REVERT: E 201 GLN cc_start: 0.7390 (mp10) cc_final: 0.7128 (mp10) outliers start: 36 outliers final: 33 residues processed: 395 average time/residue: 0.2295 time to fit residues: 137.8343 Evaluate side-chains 388 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 355 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 267 TRP Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 269 ASN Chi-restraints excluded: chain E residue 399 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.4454 > 50: distance: 45 - 49: 16.513 distance: 49 - 50: 28.219 distance: 50 - 51: 32.558 distance: 50 - 53: 43.137 distance: 51 - 52: 31.539 distance: 51 - 58: 24.682 distance: 53 - 54: 40.740 distance: 54 - 55: 17.642 distance: 55 - 56: 20.769 distance: 55 - 57: 19.187 distance: 59 - 60: 24.435 distance: 59 - 62: 17.105 distance: 60 - 61: 14.592 distance: 60 - 70: 20.776 distance: 62 - 63: 5.547 distance: 63 - 64: 26.932 distance: 63 - 65: 30.974 distance: 64 - 66: 15.677 distance: 66 - 68: 30.245 distance: 67 - 68: 32.927 distance: 68 - 69: 10.595 distance: 70 - 76: 18.183 distance: 71 - 72: 19.550 distance: 71 - 74: 15.700 distance: 72 - 73: 21.663 distance: 72 - 77: 15.717 distance: 74 - 75: 19.818 distance: 75 - 76: 15.313 distance: 77 - 78: 12.891 distance: 78 - 79: 11.430 distance: 78 - 81: 10.747 distance: 79 - 80: 6.999 distance: 79 - 85: 4.286 distance: 81 - 82: 7.108 distance: 82 - 83: 4.830 distance: 82 - 84: 12.636 distance: 85 - 86: 21.031 distance: 86 - 87: 15.878 distance: 86 - 89: 13.834 distance: 87 - 88: 5.133 distance: 87 - 93: 10.171 distance: 89 - 90: 14.240 distance: 90 - 91: 17.512 distance: 90 - 92: 26.871 distance: 93 - 94: 6.104 distance: 94 - 95: 13.487 distance: 94 - 97: 15.858 distance: 95 - 96: 8.016 distance: 95 - 99: 9.684 distance: 97 - 98: 9.942 distance: 99 - 100: 4.692 distance: 99 - 172: 17.001 distance: 100 - 101: 15.495 distance: 100 - 103: 9.789 distance: 101 - 102: 8.889 distance: 101 - 107: 9.333 distance: 102 - 169: 16.303 distance: 103 - 104: 3.526 distance: 104 - 105: 7.985 distance: 104 - 106: 14.819 distance: 107 - 108: 18.073 distance: 108 - 109: 9.316 distance: 108 - 111: 23.854 distance: 109 - 110: 8.991 distance: 109 - 115: 8.890 distance: 111 - 112: 12.816 distance: 112 - 113: 10.625 distance: 112 - 114: 5.642 distance: 115 - 116: 17.533 distance: 116 - 117: 22.885 distance: 116 - 119: 11.922 distance: 117 - 118: 17.823 distance: 117 - 123: 20.255 distance: 119 - 120: 17.990 distance: 120 - 121: 13.727 distance: 120 - 122: 25.367 distance: 123 - 124: 8.420 distance: 124 - 125: 19.286 distance: 124 - 127: 4.960 distance: 125 - 126: 15.226 distance: 125 - 131: 20.706 distance: 127 - 128: 5.780 distance: 128 - 130: 10.509