Starting phenix.real_space_refine on Sun May 18 10:15:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p00_17323/05_2025/8p00_17323.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p00_17323/05_2025/8p00_17323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p00_17323/05_2025/8p00_17323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p00_17323/05_2025/8p00_17323.map" model { file = "/net/cci-nas-00/data/ceres_data/8p00_17323/05_2025/8p00_17323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p00_17323/05_2025/8p00_17323.cif" } resolution = 3.8 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= 0.004 sd= 0.058 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 96 5.16 5 C 10936 2.51 5 N 2912 2.21 5 O 3048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16992 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2124 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 13, 'TRANS': 283} Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 184 Chain: "B" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2124 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 13, 'TRANS': 283} Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 184 Chain: "C" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2124 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 13, 'TRANS': 283} Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 184 Chain: "D" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2124 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 13, 'TRANS': 283} Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 184 Chain: "E" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2124 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 13, 'TRANS': 283} Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 184 Chain: "F" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2124 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 13, 'TRANS': 283} Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 184 Chain: "G" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2124 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 13, 'TRANS': 283} Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 184 Chain: "H" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2124 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 13, 'TRANS': 283} Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 184 Time building chain proxies: 9.43, per 1000 atoms: 0.55 Number of scatterers: 16992 At special positions: 0 Unit cell: (138.46, 138.46, 88.58, 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 96 16.00 O 3048 8.00 N 2912 7.00 C 10936 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.02 Conformation dependent library (CDL) restraints added in 2.3 seconds 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4560 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 29 sheets defined 53.2% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 26 through 31 removed outlier: 3.708A pdb=" N ARG A 30 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A 31 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 46 removed outlier: 3.696A pdb=" N GLY A 46 " --> pdb=" O THR A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 59 Processing helix chain 'A' and resid 63 through 67 removed outlier: 3.713A pdb=" N ARG A 66 " --> pdb=" O PRO A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 100 Processing helix chain 'A' and resid 102 through 114 Processing helix chain 'A' and resid 124 through 136 removed outlier: 4.529A pdb=" N ASP A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 156 removed outlier: 3.645A pdb=" N PHE A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 211 through 222 removed outlier: 4.563A pdb=" N LEU A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 251 removed outlier: 3.677A pdb=" N LYS A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 262 Processing helix chain 'A' and resid 263 through 269 removed outlier: 3.614A pdb=" N CYS A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 removed outlier: 3.574A pdb=" N ASP A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 removed outlier: 4.011A pdb=" N VAL A 289 " --> pdb=" O LYS A 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 31 removed outlier: 3.720A pdb=" N ARG B 30 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR B 31 " --> pdb=" O LEU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 46 removed outlier: 3.694A pdb=" N GLY B 46 " --> pdb=" O THR B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 59 Processing helix chain 'B' and resid 63 through 67 removed outlier: 3.696A pdb=" N ARG B 66 " --> pdb=" O PRO B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 100 Processing helix chain 'B' and resid 102 through 116 removed outlier: 3.607A pdb=" N LYS B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 136 removed outlier: 4.479A pdb=" N ASP B 136 " --> pdb=" O GLN B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 155 Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'B' and resid 212 through 222 Processing helix chain 'B' and resid 241 through 251 removed outlier: 3.698A pdb=" N LYS B 247 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 262 Processing helix chain 'B' and resid 263 through 269 removed outlier: 3.617A pdb=" N CYS B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 282 removed outlier: 3.570A pdb=" N ASP B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 removed outlier: 4.013A pdb=" N VAL B 289 " --> pdb=" O LYS B 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 31 removed outlier: 3.667A pdb=" N ARG C 30 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR C 31 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 46 removed outlier: 3.702A pdb=" N GLY C 46 " --> pdb=" O THR C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 59 Processing helix chain 'C' and resid 63 through 67 removed outlier: 3.697A pdb=" N ARG C 66 " --> pdb=" O PRO C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 100 Processing helix chain 'C' and resid 102 through 116 removed outlier: 3.616A pdb=" N LYS C 116 " --> pdb=" O PHE C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 136 removed outlier: 4.510A pdb=" N ASP C 136 " --> pdb=" O GLN C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 155 Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'C' and resid 212 through 222 Processing helix chain 'C' and resid 241 through 251 removed outlier: 3.688A pdb=" N LYS C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG C 251 " --> pdb=" O LYS C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 262 Processing helix chain 'C' and resid 263 through 269 removed outlier: 3.610A pdb=" N CYS C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 282 removed outlier: 3.574A pdb=" N ASP C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 294 removed outlier: 4.023A pdb=" N VAL C 289 " --> pdb=" O LYS C 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 removed outlier: 3.723A pdb=" N ARG D 30 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR D 31 " --> pdb=" O LEU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 46 removed outlier: 3.699A pdb=" N GLY D 46 " --> pdb=" O THR D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 59 Processing helix chain 'D' and resid 63 through 67 removed outlier: 3.695A pdb=" N ARG D 66 " --> pdb=" O PRO D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 100 Processing helix chain 'D' and resid 102 through 114 Processing helix chain 'D' and resid 124 through 136 removed outlier: 4.453A pdb=" N ASP D 136 " --> pdb=" O GLN D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 155 Processing helix chain 'D' and resid 187 through 191 Processing helix chain 'D' and resid 212 through 222 Processing helix chain 'D' and resid 241 through 251 removed outlier: 3.695A pdb=" N LYS D 247 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 262 Processing helix chain 'D' and resid 263 through 269 removed outlier: 3.617A pdb=" N CYS D 269 " --> pdb=" O LEU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 282 removed outlier: 3.566A pdb=" N ASP D 275 " --> pdb=" O SER D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 294 removed outlier: 4.009A pdb=" N VAL D 289 " --> pdb=" O LYS D 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 31 removed outlier: 3.670A pdb=" N ARG E 30 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR E 31 " --> pdb=" O LEU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 46 removed outlier: 3.688A pdb=" N GLY E 46 " --> pdb=" O THR E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 59 Processing helix chain 'E' and resid 63 through 67 removed outlier: 3.699A pdb=" N ARG E 66 " --> pdb=" O PRO E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 100 Processing helix chain 'E' and resid 102 through 116 removed outlier: 3.549A pdb=" N LYS E 116 " --> pdb=" O PHE E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 136 removed outlier: 4.441A pdb=" N ASP E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 155 Processing helix chain 'E' and resid 187 through 191 Processing helix chain 'E' and resid 212 through 222 Processing helix chain 'E' and resid 241 through 251 removed outlier: 3.691A pdb=" N LYS E 247 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 262 Processing helix chain 'E' and resid 263 through 269 removed outlier: 3.602A pdb=" N CYS E 269 " --> pdb=" O LEU E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 282 removed outlier: 3.572A pdb=" N ASP E 275 " --> pdb=" O SER E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 294 removed outlier: 4.012A pdb=" N VAL E 289 " --> pdb=" O LYS E 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 31 removed outlier: 3.669A pdb=" N ARG F 30 " --> pdb=" O ALA F 27 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR F 31 " --> pdb=" O LEU F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 46 removed outlier: 3.702A pdb=" N GLY F 46 " --> pdb=" O THR F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 59 Processing helix chain 'F' and resid 63 through 67 removed outlier: 3.697A pdb=" N ARG F 66 " --> pdb=" O PRO F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 100 Processing helix chain 'F' and resid 102 through 116 removed outlier: 3.617A pdb=" N LYS F 116 " --> pdb=" O PHE F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 136 removed outlier: 4.467A pdb=" N ASP F 136 " --> pdb=" O GLN F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 155 Processing helix chain 'F' and resid 187 through 191 Processing helix chain 'F' and resid 212 through 222 Processing helix chain 'F' and resid 241 through 251 removed outlier: 3.693A pdb=" N LYS F 247 " --> pdb=" O ALA F 243 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG F 251 " --> pdb=" O LYS F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 262 Processing helix chain 'F' and resid 263 through 269 removed outlier: 3.616A pdb=" N CYS F 269 " --> pdb=" O LEU F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 282 removed outlier: 3.571A pdb=" N ASP F 275 " --> pdb=" O SER F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 294 removed outlier: 4.011A pdb=" N VAL F 289 " --> pdb=" O LYS F 285 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 31 removed outlier: 3.667A pdb=" N ARG G 30 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR G 31 " --> pdb=" O LEU G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 46 removed outlier: 3.698A pdb=" N GLY G 46 " --> pdb=" O THR G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 59 Processing helix chain 'G' and resid 63 through 67 removed outlier: 3.696A pdb=" N ARG G 66 " --> pdb=" O PRO G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 100 Processing helix chain 'G' and resid 102 through 116 removed outlier: 3.605A pdb=" N LYS G 116 " --> pdb=" O PHE G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 136 removed outlier: 4.469A pdb=" N ASP G 136 " --> pdb=" O GLN G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 155 Processing helix chain 'G' and resid 187 through 191 Processing helix chain 'G' and resid 212 through 222 Processing helix chain 'G' and resid 241 through 251 removed outlier: 3.684A pdb=" N LYS G 247 " --> pdb=" O ALA G 243 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG G 251 " --> pdb=" O LYS G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 262 Processing helix chain 'G' and resid 263 through 269 removed outlier: 3.611A pdb=" N CYS G 269 " --> pdb=" O LEU G 265 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 282 removed outlier: 3.576A pdb=" N ASP G 275 " --> pdb=" O SER G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 285 through 294 removed outlier: 4.022A pdb=" N VAL G 289 " --> pdb=" O LYS G 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 31 removed outlier: 3.722A pdb=" N ARG H 30 " --> pdb=" O ALA H 27 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR H 31 " --> pdb=" O LEU H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 46 removed outlier: 3.679A pdb=" N GLY H 46 " --> pdb=" O THR H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 59 Processing helix chain 'H' and resid 63 through 67 removed outlier: 3.696A pdb=" N ARG H 66 " --> pdb=" O PRO H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 100 Processing helix chain 'H' and resid 102 through 116 removed outlier: 3.559A pdb=" N LYS H 116 " --> pdb=" O PHE H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 136 removed outlier: 4.492A pdb=" N ASP H 136 " --> pdb=" O GLN H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 155 Processing helix chain 'H' and resid 187 through 191 Processing helix chain 'H' and resid 212 through 222 Processing helix chain 'H' and resid 241 through 251 removed outlier: 3.696A pdb=" N LYS H 247 " --> pdb=" O ALA H 243 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG H 251 " --> pdb=" O LYS H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 253 through 262 Processing helix chain 'H' and resid 263 through 269 removed outlier: 3.618A pdb=" N CYS H 269 " --> pdb=" O LEU H 265 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 282 removed outlier: 3.570A pdb=" N ASP H 275 " --> pdb=" O SER H 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 294 removed outlier: 4.012A pdb=" N VAL H 289 " --> pdb=" O LYS H 285 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 3.605A pdb=" N ALA A 122 " --> pdb=" O VAL A 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.608A pdb=" N VAL A 12 " --> pdb=" O MET A 19 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET A 19 " --> pdb=" O VAL A 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 5.990A pdb=" N VAL A 171 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLU A 182 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG A 173 " --> pdb=" O ILE A 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 225 through 226 removed outlier: 3.507A pdb=" N VAL A 237 " --> pdb=" O PHE A 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.610A pdb=" N VAL B 12 " --> pdb=" O MET B 19 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET B 19 " --> pdb=" O VAL B 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 170 through 174 removed outlier: 6.017A pdb=" N VAL B 171 " --> pdb=" O GLU B 182 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLU B 182 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG B 173 " --> pdb=" O ILE B 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 225 through 226 removed outlier: 3.505A pdb=" N VAL B 237 " --> pdb=" O PHE B 225 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.608A pdb=" N VAL C 12 " --> pdb=" O MET C 19 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET C 19 " --> pdb=" O VAL C 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 170 through 174 removed outlier: 6.015A pdb=" N VAL C 171 " --> pdb=" O GLU C 182 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLU C 182 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG C 173 " --> pdb=" O ILE C 180 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 225 through 226 removed outlier: 3.504A pdb=" N VAL C 237 " --> pdb=" O PHE C 225 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 4 through 5 removed outlier: 3.602A pdb=" N ALA D 122 " --> pdb=" O VAL D 5 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.609A pdb=" N VAL D 12 " --> pdb=" O MET D 19 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET D 19 " --> pdb=" O VAL D 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 170 through 174 removed outlier: 6.007A pdb=" N VAL D 171 " --> pdb=" O GLU D 182 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLU D 182 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG D 173 " --> pdb=" O ILE D 180 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 225 through 226 removed outlier: 3.525A pdb=" N VAL D 237 " --> pdb=" O PHE D 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.611A pdb=" N VAL E 12 " --> pdb=" O MET E 19 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET E 19 " --> pdb=" O VAL E 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 170 through 174 removed outlier: 6.014A pdb=" N VAL E 171 " --> pdb=" O GLU E 182 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLU E 182 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG E 173 " --> pdb=" O ILE E 180 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 225 through 226 removed outlier: 3.500A pdb=" N VAL E 237 " --> pdb=" O PHE E 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 4 through 5 removed outlier: 3.589A pdb=" N ALA F 122 " --> pdb=" O VAL F 5 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.584A pdb=" N VAL F 12 " --> pdb=" O MET F 19 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET F 19 " --> pdb=" O VAL F 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'F' and resid 170 through 174 removed outlier: 6.010A pdb=" N VAL F 171 " --> pdb=" O GLU F 182 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLU F 182 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG F 173 " --> pdb=" O ILE F 180 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 225 through 226 removed outlier: 3.501A pdb=" N VAL F 237 " --> pdb=" O PHE F 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 4 through 5 removed outlier: 3.595A pdb=" N ALA G 122 " --> pdb=" O VAL G 5 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.609A pdb=" N VAL G 12 " --> pdb=" O MET G 19 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET G 19 " --> pdb=" O VAL G 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'G' and resid 170 through 174 removed outlier: 6.010A pdb=" N VAL G 171 " --> pdb=" O GLU G 182 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU G 182 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG G 173 " --> pdb=" O ILE G 180 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 225 through 226 removed outlier: 3.504A pdb=" N VAL G 237 " --> pdb=" O PHE G 225 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 4 through 5 removed outlier: 3.601A pdb=" N ALA H 122 " --> pdb=" O VAL H 5 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.610A pdb=" N VAL H 12 " --> pdb=" O MET H 19 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET H 19 " --> pdb=" O VAL H 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'H' and resid 170 through 174 removed outlier: 6.017A pdb=" N VAL H 171 " --> pdb=" O GLU H 182 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU H 182 " --> pdb=" O VAL H 171 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG H 173 " --> pdb=" O ILE H 180 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 225 through 226 removed outlier: 3.506A pdb=" N VAL H 237 " --> pdb=" O PHE H 225 " (cutoff:3.500A) 742 hydrogen bonds defined for protein. 2106 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: 4.17 Time building geometry restraints manager: 4.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3679 1.33 - 1.45: 3763 1.45 - 1.57: 9782 1.57 - 1.70: 0 1.70 - 1.82: 152 Bond restraints: 17376 Sorted by residual: bond pdb=" CA LEU D 202 " pdb=" C LEU D 202 " ideal model delta sigma weight residual 1.521 1.482 0.039 1.30e-02 5.92e+03 8.80e+00 bond pdb=" CA PRO D 204 " pdb=" C PRO D 204 " ideal model delta sigma weight residual 1.522 1.492 0.030 1.18e-02 7.18e+03 6.49e+00 bond pdb=" C TYR D 203 " pdb=" O TYR D 203 " ideal model delta sigma weight residual 1.237 1.211 0.026 1.07e-02 8.73e+03 5.85e+00 bond pdb=" C LEU D 202 " pdb=" O LEU D 202 " ideal model delta sigma weight residual 1.234 1.209 0.026 1.29e-02 6.01e+03 3.91e+00 bond pdb=" CA LEU D 202 " pdb=" CB LEU D 202 " ideal model delta sigma weight residual 1.534 1.502 0.032 1.65e-02 3.67e+03 3.85e+00 ... (remaining 17371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 23428 2.40 - 4.80: 216 4.80 - 7.20: 17 7.20 - 9.60: 2 9.60 - 11.99: 9 Bond angle restraints: 23672 Sorted by residual: angle pdb=" CB MET F 149 " pdb=" CG MET F 149 " pdb=" SD MET F 149 " ideal model delta sigma weight residual 112.70 124.69 -11.99 3.00e+00 1.11e-01 1.60e+01 angle pdb=" CB MET D 149 " pdb=" CG MET D 149 " pdb=" SD MET D 149 " ideal model delta sigma weight residual 112.70 124.68 -11.98 3.00e+00 1.11e-01 1.60e+01 angle pdb=" CB MET A 149 " pdb=" CG MET A 149 " pdb=" SD MET A 149 " ideal model delta sigma weight residual 112.70 122.75 -10.05 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CB MET G 149 " pdb=" CG MET G 149 " pdb=" SD MET G 149 " ideal model delta sigma weight residual 112.70 122.30 -9.60 3.00e+00 1.11e-01 1.02e+01 angle pdb=" CB MET C 149 " pdb=" CG MET C 149 " pdb=" SD MET C 149 " ideal model delta sigma weight residual 112.70 122.21 -9.51 3.00e+00 1.11e-01 1.01e+01 ... (remaining 23667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 8821 16.61 - 33.23: 1095 33.23 - 49.84: 355 49.84 - 66.45: 71 66.45 - 83.07: 26 Dihedral angle restraints: 10368 sinusoidal: 3384 harmonic: 6984 Sorted by residual: dihedral pdb=" CA ASP D 207 " pdb=" C ASP D 207 " pdb=" N GLU D 208 " pdb=" CA GLU D 208 " ideal model delta harmonic sigma weight residual -180.00 -163.82 -16.18 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA ASP G 207 " pdb=" C ASP G 207 " pdb=" N GLU G 208 " pdb=" CA GLU G 208 " ideal model delta harmonic sigma weight residual 180.00 -164.39 -15.61 0 5.00e+00 4.00e-02 9.75e+00 dihedral pdb=" CA ASP H 207 " pdb=" C ASP H 207 " pdb=" N GLU H 208 " pdb=" CA GLU H 208 " ideal model delta harmonic sigma weight residual 180.00 -164.40 -15.60 0 5.00e+00 4.00e-02 9.73e+00 ... (remaining 10365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1767 0.027 - 0.054: 716 0.054 - 0.081: 184 0.081 - 0.108: 85 0.108 - 0.135: 40 Chirality restraints: 2792 Sorted by residual: chirality pdb=" CA ILE G 234 " pdb=" N ILE G 234 " pdb=" C ILE G 234 " pdb=" CB ILE G 234 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA ILE E 234 " pdb=" N ILE E 234 " pdb=" C ILE E 234 " pdb=" CB ILE E 234 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ILE D 234 " pdb=" N ILE D 234 " pdb=" C ILE D 234 " pdb=" CB ILE D 234 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 2789 not shown) Planarity restraints: 3016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 203 " -0.028 5.00e-02 4.00e+02 4.24e-02 2.87e+00 pdb=" N PRO A 204 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 204 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 204 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR G 203 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.87e+00 pdb=" N PRO G 204 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO G 204 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 204 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 203 " -0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO B 204 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 204 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 204 " -0.023 5.00e-02 4.00e+02 ... (remaining 3013 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 6341 2.86 - 3.37: 16281 3.37 - 3.88: 24656 3.88 - 4.39: 24662 4.39 - 4.90: 43930 Nonbonded interactions: 115870 Sorted by model distance: nonbonded pdb=" OD2 ASP E 125 " pdb=" NZ LYS E 196 " model vdw 2.353 3.120 nonbonded pdb=" NZ LYS D 13 " pdb=" OE2 GLU D 110 " model vdw 2.353 3.120 nonbonded pdb=" N ASP E 207 " pdb=" OD1 ASP E 207 " model vdw 2.356 3.120 nonbonded pdb=" OD2 ASP H 125 " pdb=" NZ LYS H 196 " model vdw 2.358 3.120 nonbonded pdb=" N ASP G 207 " pdb=" OD1 ASP G 207 " model vdw 2.359 3.120 ... (remaining 115865 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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 group one per residue 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 35.450 Find NCS groups from input model: 0.580 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: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 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 : 0.002 0.039 17376 Z= 0.120 Angle : 0.572 11.995 23672 Z= 0.290 Chirality : 0.036 0.135 2792 Planarity : 0.004 0.045 3016 Dihedral : 17.067 83.068 5808 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.06 % Allowed : 35.82 % Favored : 64.12 % 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: -0.53 (0.18), residues: 2360 helix: 1.08 (0.16), residues: 1152 sheet: -1.26 (0.48), residues: 160 loop : -1.91 (0.17), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 157 HIS 0.001 0.000 HIS A 229 PHE 0.005 0.001 PHE D 152 TYR 0.024 0.001 TYR A 189 ARG 0.011 0.001 ARG E 173 Details of bonding type rmsd hydrogen bonds : bond 0.20546 ( 742) hydrogen bonds : angle 5.67254 ( 2106) covalent geometry : bond 0.00237 (17376) covalent geometry : angle 0.57212 (23672) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 1.865 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 263 average time/residue: 0.2891 time to fit residues: 112.6590 Evaluate side-chains 255 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 254 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 205 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.3980 chunk 175 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 60 optimal weight: 0.0670 chunk 118 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 181 optimal weight: 0.0170 chunk 70 optimal weight: 0.6980 chunk 110 optimal weight: 7.9990 chunk 135 optimal weight: 9.9990 chunk 210 optimal weight: 8.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 142 HIS E 142 HIS G 142 HIS H 142 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.144719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.102380 restraints weight = 33145.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.105836 restraints weight = 19813.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.108223 restraints weight = 14401.636| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17376 Z= 0.091 Angle : 0.494 8.156 23672 Z= 0.252 Chirality : 0.035 0.133 2792 Planarity : 0.004 0.041 3016 Dihedral : 3.845 41.309 2498 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.66 % Allowed : 30.25 % Favored : 65.09 % 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: -0.40 (0.18), residues: 2360 helix: 0.99 (0.16), residues: 1208 sheet: 1.05 (1.02), residues: 48 loop : -1.83 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 157 HIS 0.002 0.000 HIS D 233 PHE 0.005 0.001 PHE H 130 TYR 0.022 0.001 TYR A 189 ARG 0.003 0.000 ARG F 173 Details of bonding type rmsd hydrogen bonds : bond 0.03131 ( 742) hydrogen bonds : angle 3.89021 ( 2106) covalent geometry : bond 0.00188 (17376) covalent geometry : angle 0.49369 (23672) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 276 time to evaluate : 2.187 Fit side-chains REVERT: A 149 MET cc_start: 0.8814 (tmm) cc_final: 0.8089 (tmm) REVERT: B 149 MET cc_start: 0.8812 (tmm) cc_final: 0.8190 (tmm) REVERT: C 149 MET cc_start: 0.8793 (tmm) cc_final: 0.8165 (tmm) REVERT: F 149 MET cc_start: 0.8381 (tmm) cc_final: 0.8095 (tmm) REVERT: G 149 MET cc_start: 0.8780 (tmm) cc_final: 0.8162 (tmm) REVERT: H 149 MET cc_start: 0.8776 (tpt) cc_final: 0.8437 (tmm) outliers start: 72 outliers final: 16 residues processed: 326 average time/residue: 0.2806 time to fit residues: 137.0509 Evaluate side-chains 269 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 253 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 181 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 209 optimal weight: 0.1980 chunk 88 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 219 optimal weight: 4.9990 chunk 205 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 224 optimal weight: 0.8980 chunk 173 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 222 optimal weight: 5.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 142 HIS E 142 HIS F 142 HIS G 142 HIS H 142 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.141583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.098322 restraints weight = 33647.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.101718 restraints weight = 20218.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.104055 restraints weight = 14798.741| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17376 Z= 0.140 Angle : 0.506 8.122 23672 Z= 0.261 Chirality : 0.036 0.132 2792 Planarity : 0.005 0.039 3016 Dihedral : 3.994 21.442 2498 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 4.21 % Allowed : 28.82 % Favored : 66.97 % 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: -0.30 (0.18), residues: 2360 helix: 1.27 (0.16), residues: 1216 sheet: -1.79 (0.44), residues: 160 loop : -1.86 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 95 HIS 0.002 0.001 HIS A 229 PHE 0.005 0.001 PHE A 190 TYR 0.022 0.002 TYR F 189 ARG 0.007 0.001 ARG D 173 Details of bonding type rmsd hydrogen bonds : bond 0.03754 ( 742) hydrogen bonds : angle 3.78001 ( 2106) covalent geometry : bond 0.00323 (17376) covalent geometry : angle 0.50579 (23672) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 288 time to evaluate : 1.947 Fit side-chains REVERT: A 149 MET cc_start: 0.8808 (tmm) cc_final: 0.7910 (tmm) REVERT: A 249 TYR cc_start: 0.7766 (OUTLIER) cc_final: 0.6814 (m-10) REVERT: B 96 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8825 (tt) REVERT: B 149 MET cc_start: 0.8809 (tmm) cc_final: 0.8601 (tmm) REVERT: B 150 ASN cc_start: 0.8695 (t0) cc_final: 0.7723 (m110) REVERT: B 249 TYR cc_start: 0.7781 (OUTLIER) cc_final: 0.6842 (m-10) REVERT: C 96 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8810 (tt) REVERT: C 149 MET cc_start: 0.8849 (tmm) cc_final: 0.8622 (tmm) REVERT: C 249 TYR cc_start: 0.7741 (OUTLIER) cc_final: 0.6829 (m-10) REVERT: D 249 TYR cc_start: 0.7771 (OUTLIER) cc_final: 0.6854 (m-10) REVERT: E 249 TYR cc_start: 0.7788 (OUTLIER) cc_final: 0.6853 (m-10) REVERT: F 249 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.6843 (m-10) REVERT: G 149 MET cc_start: 0.8836 (tmm) cc_final: 0.8606 (tmm) REVERT: G 249 TYR cc_start: 0.7763 (OUTLIER) cc_final: 0.6810 (m-10) REVERT: H 149 MET cc_start: 0.8805 (tpt) cc_final: 0.8473 (tmm) REVERT: H 249 TYR cc_start: 0.7767 (OUTLIER) cc_final: 0.6848 (m-10) outliers start: 65 outliers final: 25 residues processed: 333 average time/residue: 0.2607 time to fit residues: 131.8130 Evaluate side-chains 301 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 266 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 249 TYR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 249 TYR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 249 TYR Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 249 TYR Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 249 TYR Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 249 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 158 optimal weight: 3.9990 chunk 189 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 225 optimal weight: 0.8980 chunk 108 optimal weight: 0.0970 chunk 15 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 206 optimal weight: 10.0000 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 142 HIS E 142 HIS F 142 HIS H 142 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.143433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.099742 restraints weight = 33383.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.103297 restraints weight = 19919.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.105744 restraints weight = 14399.794| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 17376 Z= 0.097 Angle : 0.476 6.929 23672 Z= 0.245 Chirality : 0.036 0.131 2792 Planarity : 0.004 0.038 3016 Dihedral : 3.749 14.896 2496 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.73 % Allowed : 28.89 % Favored : 66.39 % 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: -0.17 (0.18), residues: 2360 helix: 1.33 (0.16), residues: 1216 sheet: -0.75 (0.80), residues: 48 loop : -1.85 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 95 HIS 0.001 0.000 HIS G 229 PHE 0.004 0.001 PHE B 190 TYR 0.007 0.001 TYR A 228 ARG 0.009 0.001 ARG D 173 Details of bonding type rmsd hydrogen bonds : bond 0.02972 ( 742) hydrogen bonds : angle 3.54209 ( 2106) covalent geometry : bond 0.00218 (17376) covalent geometry : angle 0.47594 (23672) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 286 time to evaluate : 1.871 Fit side-chains REVERT: A 96 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8812 (tt) REVERT: A 149 MET cc_start: 0.8773 (tmm) cc_final: 0.8404 (tpt) REVERT: A 249 TYR cc_start: 0.7632 (OUTLIER) cc_final: 0.6642 (m-10) REVERT: B 96 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8834 (tt) REVERT: B 132 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8625 (tt0) REVERT: B 149 MET cc_start: 0.8853 (tmm) cc_final: 0.8582 (tmm) REVERT: B 150 ASN cc_start: 0.8688 (t0) cc_final: 0.7682 (m110) REVERT: C 96 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8824 (tt) REVERT: C 149 MET cc_start: 0.8875 (tmm) cc_final: 0.8547 (tmm) REVERT: C 150 ASN cc_start: 0.7779 (m110) cc_final: 0.7357 (m110) REVERT: D 96 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8809 (tt) REVERT: D 149 MET cc_start: 0.8859 (tpt) cc_final: 0.8457 (tmm) REVERT: E 96 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8777 (tt) REVERT: E 132 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8635 (tt0) REVERT: E 149 MET cc_start: 0.8866 (tpt) cc_final: 0.8478 (tmm) REVERT: F 96 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8791 (tt) REVERT: F 149 MET cc_start: 0.8777 (tpt) cc_final: 0.8416 (tmm) REVERT: G 96 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8816 (tt) REVERT: G 149 MET cc_start: 0.8874 (tmm) cc_final: 0.8125 (tmm) REVERT: H 96 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8797 (tt) REVERT: H 149 MET cc_start: 0.8822 (tpt) cc_final: 0.8469 (tmm) outliers start: 73 outliers final: 27 residues processed: 340 average time/residue: 0.2500 time to fit residues: 130.3441 Evaluate side-chains 306 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 268 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 181 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 85 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 93 optimal weight: 0.0870 chunk 200 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 203 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 135 optimal weight: 0.0070 chunk 196 optimal weight: 9.9990 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 142 HIS E 142 HIS G 142 HIS H 142 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.142516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.099085 restraints weight = 33916.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.102476 restraints weight = 20774.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.104836 restraints weight = 15312.694| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 17376 Z= 0.114 Angle : 0.484 6.097 23672 Z= 0.249 Chirality : 0.036 0.131 2792 Planarity : 0.005 0.038 3016 Dihedral : 3.789 14.593 2496 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 5.96 % Allowed : 28.95 % Favored : 65.09 % 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: -0.09 (0.18), residues: 2360 helix: 1.45 (0.16), residues: 1216 sheet: -0.41 (0.91), residues: 48 loop : -1.90 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 95 HIS 0.002 0.001 HIS D 229 PHE 0.008 0.001 PHE E 117 TYR 0.027 0.002 TYR G 189 ARG 0.010 0.001 ARG E 173 Details of bonding type rmsd hydrogen bonds : bond 0.03185 ( 742) hydrogen bonds : angle 3.48960 ( 2106) covalent geometry : bond 0.00262 (17376) covalent geometry : angle 0.48383 (23672) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 288 time to evaluate : 2.013 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 96 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8849 (tt) REVERT: A 132 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8936 (tt0) REVERT: A 149 MET cc_start: 0.8788 (tmm) cc_final: 0.7815 (tmm) REVERT: B 96 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8861 (tt) REVERT: B 132 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8621 (tt0) REVERT: B 149 MET cc_start: 0.8886 (tmm) cc_final: 0.8570 (tmm) REVERT: B 150 ASN cc_start: 0.8727 (t0) cc_final: 0.7713 (m110) REVERT: C 96 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8852 (tt) REVERT: C 149 MET cc_start: 0.8887 (tmm) cc_final: 0.8514 (tmm) REVERT: C 150 ASN cc_start: 0.7778 (m110) cc_final: 0.7296 (m110) REVERT: D 96 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8821 (tt) REVERT: D 149 MET cc_start: 0.8820 (tpt) cc_final: 0.8441 (tmm) REVERT: E 96 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8814 (tt) REVERT: E 132 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8666 (tt0) REVERT: E 149 MET cc_start: 0.8836 (tpt) cc_final: 0.8451 (tmm) REVERT: F 96 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8832 (tt) REVERT: F 149 MET cc_start: 0.8800 (tpt) cc_final: 0.8453 (tmm) REVERT: G 96 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8850 (tt) REVERT: G 149 MET cc_start: 0.8893 (tmm) cc_final: 0.8523 (tmm) REVERT: G 150 ASN cc_start: 0.7782 (m110) cc_final: 0.7307 (m110) REVERT: H 96 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8813 (tt) REVERT: H 149 MET cc_start: 0.8817 (tpt) cc_final: 0.8465 (tmm) outliers start: 92 outliers final: 51 residues processed: 343 average time/residue: 0.2727 time to fit residues: 141.7794 Evaluate side-chains 342 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 280 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 249 TYR Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 249 TYR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 249 TYR Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 249 TYR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 249 TYR Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 249 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 0.0000 chunk 10 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 chunk 85 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 223 optimal weight: 10.0000 overall best weight: 2.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 142 HIS D 268 GLN E 142 HIS E 268 GLN G 142 HIS H 142 HIS H 268 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.140919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.097239 restraints weight = 34448.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.100664 restraints weight = 21231.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.102941 restraints weight = 15644.543| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 17376 Z= 0.152 Angle : 0.516 8.868 23672 Z= 0.267 Chirality : 0.036 0.135 2792 Planarity : 0.005 0.038 3016 Dihedral : 4.012 15.208 2496 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 6.35 % Allowed : 29.47 % Favored : 64.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.18), residues: 2360 helix: 1.44 (0.16), residues: 1216 sheet: -2.23 (0.44), residues: 160 loop : -1.95 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 95 HIS 0.003 0.001 HIS C 229 PHE 0.008 0.001 PHE H 117 TYR 0.006 0.001 TYR A 228 ARG 0.009 0.001 ARG C 173 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 742) hydrogen bonds : angle 3.58108 ( 2106) covalent geometry : bond 0.00352 (17376) covalent geometry : angle 0.51552 (23672) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 291 time to evaluate : 1.853 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 149 MET cc_start: 0.8794 (tmm) cc_final: 0.7776 (tmm) REVERT: B 96 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8892 (tt) REVERT: B 132 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8670 (tt0) REVERT: B 149 MET cc_start: 0.8869 (tmm) cc_final: 0.8516 (tmm) REVERT: B 150 ASN cc_start: 0.8788 (t0) cc_final: 0.7747 (m110) REVERT: C 96 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8891 (tt) REVERT: C 149 MET cc_start: 0.8920 (tmm) cc_final: 0.8489 (tmm) REVERT: C 150 ASN cc_start: 0.7837 (m110) cc_final: 0.7312 (m110) REVERT: D 96 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8900 (tt) REVERT: D 149 MET cc_start: 0.8800 (tpt) cc_final: 0.8442 (tmm) REVERT: E 132 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8720 (tt0) REVERT: E 149 MET cc_start: 0.8801 (tpt) cc_final: 0.8435 (tmm) REVERT: F 149 MET cc_start: 0.8807 (tpt) cc_final: 0.8409 (tmm) REVERT: F 150 ASN cc_start: 0.7936 (m110) cc_final: 0.6990 (m110) REVERT: G 149 MET cc_start: 0.8906 (tmm) cc_final: 0.8488 (tmm) REVERT: G 150 ASN cc_start: 0.7833 (m110) cc_final: 0.7314 (m110) REVERT: H 96 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8902 (tt) REVERT: H 149 MET cc_start: 0.8791 (tpt) cc_final: 0.8460 (tmm) outliers start: 98 outliers final: 71 residues processed: 358 average time/residue: 0.2802 time to fit residues: 149.9513 Evaluate side-chains 360 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 283 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 249 TYR Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 249 TYR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 249 TYR Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 249 TYR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 249 TYR Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 249 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 85 optimal weight: 10.0000 chunk 106 optimal weight: 0.0970 chunk 227 optimal weight: 10.0000 chunk 228 optimal weight: 5.9990 chunk 218 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 123 optimal weight: 0.0060 chunk 150 optimal weight: 0.7980 chunk 161 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN B 268 GLN C 268 GLN D 142 HIS F 268 GLN G 268 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.143529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.100032 restraints weight = 34180.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.103577 restraints weight = 20585.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.105922 restraints weight = 15042.985| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17376 Z= 0.094 Angle : 0.489 8.674 23672 Z= 0.249 Chirality : 0.035 0.131 2792 Planarity : 0.005 0.044 3016 Dihedral : 3.740 14.562 2496 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 5.05 % Allowed : 30.63 % Favored : 64.31 % 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: -0.11 (0.18), residues: 2360 helix: 1.47 (0.16), residues: 1216 sheet: -0.47 (0.93), residues: 48 loop : -1.95 (0.17), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 95 HIS 0.001 0.000 HIS E 229 PHE 0.004 0.001 PHE H 117 TYR 0.007 0.001 TYR E 228 ARG 0.011 0.001 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.02773 ( 742) hydrogen bonds : angle 3.38723 ( 2106) covalent geometry : bond 0.00217 (17376) covalent geometry : angle 0.48915 (23672) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 282 time to evaluate : 2.135 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 132 GLN cc_start: 0.9040 (tp40) cc_final: 0.8779 (tt0) REVERT: A 149 MET cc_start: 0.8807 (tmm) cc_final: 0.7837 (tmm) REVERT: B 36 GLN cc_start: 0.9039 (mt0) cc_final: 0.8694 (tt0) REVERT: B 96 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8853 (tt) REVERT: B 132 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8641 (tt0) REVERT: B 149 MET cc_start: 0.8845 (tmm) cc_final: 0.8505 (tmm) REVERT: B 150 ASN cc_start: 0.8734 (t0) cc_final: 0.7684 (m110) REVERT: C 36 GLN cc_start: 0.9048 (mt0) cc_final: 0.8701 (tt0) REVERT: C 96 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8871 (tt) REVERT: C 149 MET cc_start: 0.8890 (tmm) cc_final: 0.8468 (tmm) REVERT: C 150 ASN cc_start: 0.7839 (m110) cc_final: 0.7299 (m110) REVERT: D 36 GLN cc_start: 0.9012 (mt0) cc_final: 0.8676 (tt0) REVERT: D 96 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8838 (tt) REVERT: D 149 MET cc_start: 0.8752 (tpt) cc_final: 0.8403 (tmm) REVERT: D 268 GLN cc_start: 0.8776 (tp40) cc_final: 0.8541 (tp-100) REVERT: E 36 GLN cc_start: 0.9046 (mt0) cc_final: 0.8744 (tt0) REVERT: E 132 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8668 (tt0) REVERT: E 149 MET cc_start: 0.8764 (tpt) cc_final: 0.8423 (tmm) REVERT: E 268 GLN cc_start: 0.8766 (tp40) cc_final: 0.8548 (tp-100) REVERT: F 149 MET cc_start: 0.8756 (tpt) cc_final: 0.8421 (tmm) REVERT: F 150 ASN cc_start: 0.7938 (m110) cc_final: 0.7009 (m110) REVERT: G 36 GLN cc_start: 0.9033 (mt0) cc_final: 0.8720 (tt0) REVERT: G 149 MET cc_start: 0.8879 (tmm) cc_final: 0.8470 (tmm) REVERT: G 150 ASN cc_start: 0.7844 (m110) cc_final: 0.7316 (m110) REVERT: H 96 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8853 (tt) REVERT: H 268 GLN cc_start: 0.8778 (tp40) cc_final: 0.8545 (tp-100) outliers start: 78 outliers final: 65 residues processed: 332 average time/residue: 0.2765 time to fit residues: 138.6754 Evaluate side-chains 341 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 270 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 249 TYR Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 249 TYR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 249 TYR Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 249 TYR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 249 TYR Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 249 TYR Chi-restraints excluded: chain H residue 286 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 218 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 209 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 191 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 48 optimal weight: 0.0020 overall best weight: 3.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 142 HIS E 142 HIS G 142 HIS H 142 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.139222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.095624 restraints weight = 34209.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.098847 restraints weight = 21249.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.100942 restraints weight = 15845.994| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 17376 Z= 0.214 Angle : 0.571 7.647 23672 Z= 0.296 Chirality : 0.038 0.138 2792 Planarity : 0.005 0.051 3016 Dihedral : 4.323 16.091 2496 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 6.28 % Allowed : 29.47 % Favored : 64.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.43 (0.18), residues: 2360 helix: 1.44 (0.16), residues: 1184 sheet: -2.84 (0.39), residues: 160 loop : -2.02 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 95 HIS 0.003 0.001 HIS G 229 PHE 0.008 0.001 PHE A 190 TYR 0.026 0.002 TYR G 189 ARG 0.014 0.001 ARG E 173 Details of bonding type rmsd hydrogen bonds : bond 0.04161 ( 742) hydrogen bonds : angle 3.73667 ( 2106) covalent geometry : bond 0.00494 (17376) covalent geometry : angle 0.57135 (23672) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 292 time to evaluate : 1.987 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 149 MET cc_start: 0.8854 (tmm) cc_final: 0.7770 (tmm) REVERT: B 96 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8895 (tt) REVERT: B 132 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.8805 (tt0) REVERT: B 149 MET cc_start: 0.8908 (tmm) cc_final: 0.8501 (tmm) REVERT: B 150 ASN cc_start: 0.8846 (t0) cc_final: 0.7774 (m110) REVERT: B 268 GLN cc_start: 0.8781 (tp40) cc_final: 0.8551 (tp-100) REVERT: C 96 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8910 (tt) REVERT: C 149 MET cc_start: 0.8938 (tmm) cc_final: 0.8453 (tmm) REVERT: C 150 ASN cc_start: 0.7918 (m110) cc_final: 0.7331 (m110) REVERT: C 268 GLN cc_start: 0.8785 (tp40) cc_final: 0.8553 (tp-100) REVERT: D 96 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8942 (tt) REVERT: D 149 MET cc_start: 0.8818 (tpt) cc_final: 0.8432 (tmm) REVERT: E 132 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8860 (tt0) REVERT: E 149 MET cc_start: 0.8812 (tpt) cc_final: 0.8446 (tmm) REVERT: F 149 MET cc_start: 0.8815 (tpt) cc_final: 0.8388 (tmm) REVERT: F 150 ASN cc_start: 0.7954 (m110) cc_final: 0.6997 (m110) REVERT: F 268 GLN cc_start: 0.8794 (tp40) cc_final: 0.8556 (tp-100) REVERT: G 149 MET cc_start: 0.8931 (tmm) cc_final: 0.8465 (tmm) REVERT: G 150 ASN cc_start: 0.7920 (m110) cc_final: 0.7329 (m110) REVERT: H 96 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8944 (tt) REVERT: H 149 MET cc_start: 0.8861 (tmm) cc_final: 0.8226 (tmm) outliers start: 97 outliers final: 64 residues processed: 360 average time/residue: 0.2730 time to fit residues: 147.9262 Evaluate side-chains 358 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 288 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 249 TYR Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 249 TYR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 249 TYR Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 249 TYR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 249 TYR Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 249 TYR Chi-restraints excluded: chain H residue 286 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 197 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 205 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 188 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN D 142 HIS D 268 GLN E 142 HIS E 268 GLN G 142 HIS G 268 GLN H 142 HIS H 268 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.137893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.094566 restraints weight = 34888.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.097700 restraints weight = 21694.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.099863 restraints weight = 16188.129| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 17376 Z= 0.277 Angle : 0.636 7.120 23672 Z= 0.331 Chirality : 0.040 0.158 2792 Planarity : 0.005 0.053 3016 Dihedral : 4.803 17.062 2496 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 4.86 % Allowed : 31.09 % Favored : 64.05 % 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: -0.98 (0.17), residues: 2360 helix: 1.20 (0.16), residues: 1176 sheet: -3.76 (0.34), residues: 160 loop : -2.43 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP D 95 HIS 0.004 0.001 HIS E 229 PHE 0.009 0.002 PHE B 190 TYR 0.012 0.002 TYR E 18 ARG 0.013 0.001 ARG E 173 Details of bonding type rmsd hydrogen bonds : bond 0.04726 ( 742) hydrogen bonds : angle 4.04640 ( 2106) covalent geometry : bond 0.00634 (17376) covalent geometry : angle 0.63579 (23672) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 314 time to evaluate : 1.966 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 149 MET cc_start: 0.8917 (tmm) cc_final: 0.8311 (tmm) REVERT: B 96 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8950 (tt) REVERT: B 132 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8890 (tt0) REVERT: B 149 MET cc_start: 0.8970 (tmm) cc_final: 0.8524 (tmm) REVERT: B 150 ASN cc_start: 0.8891 (t0) cc_final: 0.7800 (m110) REVERT: C 96 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8919 (tt) REVERT: C 149 MET cc_start: 0.8934 (tmm) cc_final: 0.8419 (tmm) REVERT: C 150 ASN cc_start: 0.7982 (m110) cc_final: 0.7371 (m110) REVERT: D 96 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8948 (tt) REVERT: D 149 MET cc_start: 0.8796 (tpt) cc_final: 0.8449 (tmm) REVERT: D 150 ASN cc_start: 0.7995 (m110) cc_final: 0.7479 (m110) REVERT: E 132 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.8861 (tt0) REVERT: E 149 MET cc_start: 0.8814 (tpt) cc_final: 0.8446 (tmm) REVERT: F 149 MET cc_start: 0.8810 (tpt) cc_final: 0.8403 (tmm) REVERT: F 150 ASN cc_start: 0.8068 (m110) cc_final: 0.7518 (m110) REVERT: G 149 MET cc_start: 0.8936 (tmm) cc_final: 0.8433 (tmm) REVERT: G 150 ASN cc_start: 0.7982 (m110) cc_final: 0.7378 (m110) REVERT: H 96 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8952 (tt) outliers start: 75 outliers final: 64 residues processed: 369 average time/residue: 0.2688 time to fit residues: 150.0369 Evaluate side-chains 371 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 301 time to evaluate : 2.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 249 TYR Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 249 TYR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 249 TYR Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 249 TYR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 249 TYR Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 249 TYR Chi-restraints excluded: chain H residue 286 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 16 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 172 optimal weight: 2.9990 chunk 178 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN B 268 GLN C 268 GLN D 268 GLN E 268 GLN F 268 GLN G 268 GLN H 268 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.140382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.097053 restraints weight = 34245.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.100515 restraints weight = 20298.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.102893 restraints weight = 14774.727| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17376 Z= 0.138 Angle : 0.554 7.695 23672 Z= 0.282 Chirality : 0.037 0.139 2792 Planarity : 0.005 0.053 3016 Dihedral : 4.321 15.697 2496 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 4.60 % Allowed : 31.41 % Favored : 63.99 % 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: -0.83 (0.18), residues: 2360 helix: 1.27 (0.16), residues: 1184 sheet: -3.75 (0.34), residues: 160 loop : -2.30 (0.17), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 95 HIS 0.003 0.001 HIS B 229 PHE 0.010 0.001 PHE F 117 TYR 0.025 0.002 TYR D 189 ARG 0.014 0.001 ARG E 173 Details of bonding type rmsd hydrogen bonds : bond 0.03508 ( 742) hydrogen bonds : angle 3.67285 ( 2106) covalent geometry : bond 0.00323 (17376) covalent geometry : angle 0.55448 (23672) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 302 time to evaluate : 1.876 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 132 GLN cc_start: 0.9147 (tp40) cc_final: 0.8806 (tt0) REVERT: A 149 MET cc_start: 0.8836 (tmm) cc_final: 0.7739 (tmm) REVERT: B 96 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8845 (tt) REVERT: B 132 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8692 (tt0) REVERT: B 149 MET cc_start: 0.8949 (tmm) cc_final: 0.8527 (tmm) REVERT: B 150 ASN cc_start: 0.8828 (t0) cc_final: 0.7732 (m110) REVERT: C 96 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8838 (tt) REVERT: C 149 MET cc_start: 0.8919 (tmm) cc_final: 0.8415 (tmm) REVERT: C 150 ASN cc_start: 0.7918 (m110) cc_final: 0.7325 (m110) REVERT: D 149 MET cc_start: 0.8796 (tpt) cc_final: 0.8390 (tmm) REVERT: E 36 GLN cc_start: 0.9091 (mt0) cc_final: 0.8600 (tt0) REVERT: E 132 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8695 (tt0) REVERT: E 149 MET cc_start: 0.8822 (tpt) cc_final: 0.8378 (tmm) REVERT: F 149 MET cc_start: 0.8827 (tpt) cc_final: 0.8380 (tmm) REVERT: F 150 ASN cc_start: 0.7976 (m110) cc_final: 0.6995 (m110) REVERT: G 149 MET cc_start: 0.8905 (tmm) cc_final: 0.8412 (tmm) REVERT: G 150 ASN cc_start: 0.7941 (m110) cc_final: 0.7340 (m110) outliers start: 71 outliers final: 63 residues processed: 351 average time/residue: 0.2674 time to fit residues: 142.5794 Evaluate side-chains 351 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 284 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 249 TYR Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 249 TYR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 249 TYR Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 249 TYR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 249 TYR Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 249 TYR Chi-restraints excluded: chain H residue 286 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 67 optimal weight: 3.9990 chunk 36 optimal weight: 0.0170 chunk 143 optimal weight: 4.9990 chunk 156 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 168 optimal weight: 0.0370 chunk 214 optimal weight: 0.9980 chunk 172 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 204 optimal weight: 2.9990 overall best weight: 1.2100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS A 268 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.142884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.099286 restraints weight = 33784.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.102825 restraints weight = 19949.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.105249 restraints weight = 14437.267| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17376 Z= 0.098 Angle : 0.522 8.289 23672 Z= 0.260 Chirality : 0.036 0.140 2792 Planarity : 0.004 0.035 3016 Dihedral : 3.889 14.886 2496 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.37 % Allowed : 32.58 % Favored : 64.05 % 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: -0.57 (0.18), residues: 2360 helix: 1.25 (0.16), residues: 1216 sheet: -3.71 (0.46), residues: 48 loop : -2.22 (0.17), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 95 HIS 0.006 0.001 HIS A 231 PHE 0.006 0.001 PHE F 117 TYR 0.009 0.001 TYR B 228 ARG 0.001 0.000 ARG E 129 Details of bonding type rmsd hydrogen bonds : bond 0.02831 ( 742) hydrogen bonds : angle 3.46594 ( 2106) covalent geometry : bond 0.00225 (17376) covalent geometry : angle 0.52156 (23672) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5266.04 seconds wall clock time: 92 minutes 45.73 seconds (5565.73 seconds total)