Starting phenix.real_space_refine on Tue Apr 9 17:44:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p00_17323/04_2024/8p00_17323.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p00_17323/04_2024/8p00_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p00_17323/04_2024/8p00_17323.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p00_17323/04_2024/8p00_17323.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p00_17323/04_2024/8p00_17323.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p00_17323/04_2024/8p00_17323.pdb" } 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 Residue "G GLU 110": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 9.28, 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.44 Conformation dependent library (CDL) restraints added in 3.4 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: 1.68 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: 4.72 Time building geometry restraints manager: 7.00 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: 99.94 - 106.76: 506 106.76 - 113.58: 9641 113.58 - 120.39: 6131 120.39 - 127.21: 7223 127.21 - 134.03: 171 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 2.520 nonbonded pdb=" NZ LYS D 13 " pdb=" OE2 GLU D 110 " model vdw 2.353 2.520 nonbonded pdb=" N ASP E 207 " pdb=" OD1 ASP E 207 " model vdw 2.356 2.520 nonbonded pdb=" OD2 ASP H 125 " pdb=" NZ LYS H 196 " model vdw 2.358 2.520 nonbonded pdb=" N ASP G 207 " pdb=" OD1 ASP G 207 " model vdw 2.359 2.520 ... (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 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.620 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 44.580 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.970 ------------------------------------------------------------------------------- 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= 0.161 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 262 time to evaluate : 2.083 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 263 average time/residue: 0.3029 time to fit residues: 118.2401 Evaluate side-chains 255 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 254 time to evaluate : 2.121 ------------------------------------------------------------------------------- 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: 5.9990 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 118 optimal weight: 0.0970 chunk 93 optimal weight: 1.9990 chunk 181 optimal weight: 0.4980 chunk 70 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 135 optimal weight: 0.0870 chunk 210 optimal weight: 9.9990 overall best weight: 1.3360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 HIS D 142 HIS E 142 HIS F 142 HIS G 142 HIS H 142 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17376 Z= 0.152 Angle : 0.486 7.769 23672 Z= 0.248 Chirality : 0.035 0.130 2792 Planarity : 0.004 0.041 3016 Dihedral : 3.972 40.830 2498 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 5.25 % Allowed : 30.89 % Favored : 63.86 % 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: -0.37 (0.18), residues: 2360 helix: 1.11 (0.16), residues: 1216 sheet: 0.94 (1.00), residues: 48 loop : -1.96 (0.17), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 95 HIS 0.002 0.000 HIS F 229 PHE 0.005 0.001 PHE A 152 TYR 0.020 0.001 TYR A 189 ARG 0.004 0.001 ARG F 173 *********************** 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 353 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 272 time to evaluate : 1.944 Fit side-chains REVERT: A 96 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8866 (tt) REVERT: B 96 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8849 (tt) REVERT: C 96 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8883 (tt) REVERT: D 96 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8853 (tt) REVERT: E 96 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8876 (tt) REVERT: F 96 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8865 (tt) REVERT: F 149 MET cc_start: 0.8459 (tmm) cc_final: 0.8107 (tmm) REVERT: G 96 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8881 (tt) REVERT: H 96 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8853 (tt) REVERT: H 149 MET cc_start: 0.8794 (tpt) cc_final: 0.8447 (tmm) outliers start: 81 outliers final: 37 residues processed: 334 average time/residue: 0.2861 time to fit residues: 143.5989 Evaluate side-chains 299 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 254 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 186 VAL 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 186 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 186 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 175 optimal weight: 0.4980 chunk 143 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 211 optimal weight: 0.5980 chunk 228 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 209 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 169 optimal weight: 9.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 HIS D 142 HIS E 142 HIS F 142 HIS G 142 HIS H 142 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 17376 Z= 0.150 Angle : 0.474 8.414 23672 Z= 0.242 Chirality : 0.035 0.131 2792 Planarity : 0.005 0.039 3016 Dihedral : 3.821 21.624 2498 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 5.57 % Allowed : 29.47 % Favored : 64.96 % 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: -0.21 (0.18), residues: 2360 helix: 1.31 (0.16), residues: 1216 sheet: -0.31 (0.88), residues: 48 loop : -1.91 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 95 HIS 0.001 0.000 HIS G 229 PHE 0.004 0.001 PHE D 199 TYR 0.023 0.001 TYR F 189 ARG 0.008 0.001 ARG C 173 *********************** 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 363 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 277 time to evaluate : 2.100 Fit side-chains REVERT: B 149 MET cc_start: 0.8912 (tmm) cc_final: 0.8183 (tmm) REVERT: C 149 MET cc_start: 0.8930 (tmm) cc_final: 0.8197 (tmm) REVERT: G 149 MET cc_start: 0.8917 (tmm) cc_final: 0.8193 (tmm) REVERT: H 96 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8869 (tt) REVERT: H 149 MET cc_start: 0.8782 (tpt) cc_final: 0.8443 (tmm) outliers start: 86 outliers final: 36 residues processed: 343 average time/residue: 0.2931 time to fit residues: 155.3996 Evaluate side-chains 296 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 259 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 6 SER 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 H residue 6 SER Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 181 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 109 optimal weight: 20.0000 chunk 23 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 224 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 200 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 HIS D 142 HIS E 142 HIS F 142 HIS G 142 HIS H 142 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 17376 Z= 0.354 Angle : 0.575 6.532 23672 Z= 0.298 Chirality : 0.038 0.139 2792 Planarity : 0.005 0.040 3016 Dihedral : 4.434 16.734 2496 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 9.65 % Allowed : 25.52 % Favored : 64.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.18), residues: 2360 helix: 1.46 (0.16), residues: 1184 sheet: -2.41 (0.42), residues: 160 loop : -2.18 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 95 HIS 0.004 0.001 HIS D 229 PHE 0.010 0.001 PHE A 190 TYR 0.009 0.002 TYR G 18 ARG 0.010 0.001 ARG F 173 *********************** 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 425 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 276 time to evaluate : 2.030 Fit side-chains REVERT: A 96 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8935 (tt) REVERT: A 149 MET cc_start: 0.8726 (tpt) cc_final: 0.8243 (tmm) REVERT: A 249 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.6892 (m-10) REVERT: B 96 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8922 (tt) REVERT: B 132 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8783 (tt0) REVERT: B 150 ASN cc_start: 0.8768 (t0) cc_final: 0.7800 (m110) REVERT: B 249 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.6888 (m-10) REVERT: C 96 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8921 (tt) REVERT: C 132 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.8869 (tt0) REVERT: C 249 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.6895 (m-10) REVERT: D 96 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8922 (tt) REVERT: D 132 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8949 (tt0) REVERT: D 149 MET cc_start: 0.8795 (tpt) cc_final: 0.8431 (tmm) REVERT: D 249 TYR cc_start: 0.7766 (OUTLIER) cc_final: 0.6881 (m-10) REVERT: E 96 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8897 (tt) REVERT: E 132 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.8858 (tt0) REVERT: E 149 MET cc_start: 0.8780 (tpt) cc_final: 0.8392 (tmm) REVERT: E 249 TYR cc_start: 0.7774 (OUTLIER) cc_final: 0.6898 (m-10) REVERT: F 96 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8931 (tt) REVERT: F 132 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.8846 (tt0) REVERT: F 149 MET cc_start: 0.8768 (tpt) cc_final: 0.8436 (tmm) REVERT: F 249 TYR cc_start: 0.7766 (OUTLIER) cc_final: 0.6892 (m-10) REVERT: G 96 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8918 (tt) REVERT: G 132 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8822 (tt0) REVERT: G 249 TYR cc_start: 0.7768 (OUTLIER) cc_final: 0.6887 (m-10) REVERT: H 132 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8823 (tt0) REVERT: H 149 MET cc_start: 0.8783 (tpt) cc_final: 0.8500 (tmm) REVERT: H 249 TYR cc_start: 0.7756 (OUTLIER) cc_final: 0.6872 (m-10) outliers start: 149 outliers final: 55 residues processed: 389 average time/residue: 0.2758 time to fit residues: 161.6350 Evaluate side-chains 342 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 265 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 68 THR 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 6 SER Chi-restraints excluded: chain C residue 68 THR 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 132 GLN 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 6 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 175 THR 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 205 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 6 SER Chi-restraints excluded: chain E residue 68 THR 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 6 SER Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 68 THR 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 132 GLN 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 6 SER Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 132 GLN 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 6 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 132 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 166 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 201 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 HIS D 142 HIS E 142 HIS E 268 GLN F 142 HIS G 142 HIS H 142 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 17376 Z= 0.224 Angle : 0.521 8.514 23672 Z= 0.267 Chirality : 0.037 0.135 2792 Planarity : 0.005 0.038 3016 Dihedral : 4.176 15.869 2496 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 6.99 % Allowed : 28.76 % 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: -0.52 (0.18), residues: 2360 helix: 1.41 (0.16), residues: 1216 sheet: -2.56 (0.41), residues: 160 loop : -2.30 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 95 HIS 0.002 0.001 HIS F 229 PHE 0.006 0.001 PHE B 190 TYR 0.006 0.001 TYR D 228 ARG 0.009 0.001 ARG D 173 *********************** 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 386 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 278 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8896 (tt) REVERT: B 96 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8891 (tt) REVERT: B 132 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8732 (tt0) REVERT: B 149 MET cc_start: 0.8826 (tmm) cc_final: 0.8162 (tmm) REVERT: B 249 TYR cc_start: 0.7673 (OUTLIER) cc_final: 0.6917 (m-10) REVERT: C 96 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8882 (tt) REVERT: C 132 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8744 (tt0) REVERT: C 149 MET cc_start: 0.8900 (tmm) cc_final: 0.8200 (tmm) REVERT: C 150 ASN cc_start: 0.7825 (m110) cc_final: 0.7124 (m110) REVERT: C 249 TYR cc_start: 0.7660 (OUTLIER) cc_final: 0.6903 (m-10) REVERT: D 96 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8888 (tt) REVERT: D 132 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.8830 (tt0) REVERT: D 149 MET cc_start: 0.8803 (tpt) cc_final: 0.8448 (tmm) REVERT: D 249 TYR cc_start: 0.7662 (OUTLIER) cc_final: 0.6912 (m-10) REVERT: E 96 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8899 (tt) REVERT: E 132 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.8795 (tt0) REVERT: E 149 MET cc_start: 0.8814 (tpt) cc_final: 0.8468 (tmm) REVERT: E 249 TYR cc_start: 0.7663 (OUTLIER) cc_final: 0.6918 (m-10) REVERT: F 96 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8909 (tt) REVERT: F 132 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8819 (tt0) REVERT: F 149 MET cc_start: 0.8749 (tpt) cc_final: 0.8400 (tmm) REVERT: F 249 TYR cc_start: 0.7656 (OUTLIER) cc_final: 0.6910 (m-10) REVERT: G 96 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8866 (tt) REVERT: G 132 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8812 (tt0) REVERT: G 149 MET cc_start: 0.8901 (tmm) cc_final: 0.8186 (tmm) REVERT: H 132 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.8802 (tt0) REVERT: H 150 ASN cc_start: 0.8821 (t0) cc_final: 0.7776 (m110) REVERT: H 249 TYR cc_start: 0.7662 (OUTLIER) cc_final: 0.6914 (m-10) outliers start: 108 outliers final: 70 residues processed: 349 average time/residue: 0.2611 time to fit residues: 141.3615 Evaluate side-chains 356 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 266 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 205 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 6 SER Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 172 VAL 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 6 SER Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 172 VAL 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 6 SER Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 175 THR 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 D residue 249 TYR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 172 VAL 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 6 SER Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 68 THR 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 132 GLN Chi-restraints excluded: chain F residue 172 VAL 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 6 SER Chi-restraints excluded: chain G residue 11 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 132 GLN Chi-restraints excluded: chain G residue 172 VAL 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 6 SER Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 132 GLN Chi-restraints excluded: chain H residue 172 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 4.9990 chunk 201 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 chunk 224 optimal weight: 3.9990 chunk 186 optimal weight: 0.0970 chunk 103 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 overall best weight: 2.6184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 17376 Z= 0.225 Angle : 0.519 8.829 23672 Z= 0.264 Chirality : 0.036 0.135 2792 Planarity : 0.005 0.040 3016 Dihedral : 4.131 15.524 2496 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 7.97 % Allowed : 28.63 % Favored : 63.41 % 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: -0.50 (0.18), residues: 2360 helix: 1.47 (0.16), residues: 1216 sheet: -2.68 (0.40), residues: 160 loop : -2.35 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 95 HIS 0.002 0.001 HIS E 229 PHE 0.009 0.001 PHE H 117 TYR 0.007 0.001 TYR C 228 ARG 0.011 0.001 ARG D 173 *********************** 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 408 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 285 time to evaluate : 1.919 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 91 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9012 (tp) REVERT: A 96 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8875 (tt) REVERT: B 96 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8885 (tt) REVERT: B 132 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8814 (tt0) REVERT: B 150 ASN cc_start: 0.8770 (t0) cc_final: 0.7832 (m110) REVERT: C 91 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.9013 (tp) REVERT: C 96 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8899 (tt) REVERT: C 132 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.8821 (tt0) REVERT: C 149 MET cc_start: 0.8913 (tmm) cc_final: 0.8122 (tmm) REVERT: C 150 ASN cc_start: 0.7880 (m110) cc_final: 0.7105 (m110) REVERT: D 96 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8895 (tt) REVERT: D 132 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.8916 (tt0) REVERT: D 149 MET cc_start: 0.8794 (tpt) cc_final: 0.8436 (tmm) REVERT: E 91 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9022 (tp) REVERT: E 96 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8891 (tt) REVERT: E 132 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8775 (tt0) REVERT: E 149 MET cc_start: 0.8787 (tpt) cc_final: 0.8415 (tmm) REVERT: E 268 GLN cc_start: 0.8757 (tp40) cc_final: 0.8555 (tp-100) REVERT: F 91 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9027 (tp) REVERT: F 96 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8911 (tt) REVERT: F 132 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8769 (tt0) REVERT: F 149 MET cc_start: 0.8743 (tpt) cc_final: 0.8384 (tmm) REVERT: F 150 ASN cc_start: 0.7936 (m110) cc_final: 0.6982 (m110) REVERT: G 91 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.9024 (tp) REVERT: G 96 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8881 (tt) REVERT: G 132 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8823 (tt0) REVERT: G 149 MET cc_start: 0.8919 (tmm) cc_final: 0.8129 (tmm) REVERT: G 150 ASN cc_start: 0.7875 (m110) cc_final: 0.7107 (m110) REVERT: H 132 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8842 (tt0) REVERT: H 149 MET cc_start: 0.8848 (tmm) cc_final: 0.8189 (tmm) outliers start: 123 outliers final: 87 residues processed: 377 average time/residue: 0.2628 time to fit residues: 152.4857 Evaluate side-chains 378 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 272 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 96 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 205 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 6 SER Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 68 THR 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 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 6 SER Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 91 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 132 GLN 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 6 SER Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 175 THR 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 6 SER Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 100 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 249 TYR Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 91 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 132 GLN 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 6 SER Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 132 GLN 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 6 SER Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 132 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 163 optimal weight: 0.0010 chunk 188 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 223 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 136 optimal weight: 0.0050 chunk 103 optimal weight: 10.0000 chunk 138 optimal weight: 6.9990 overall best weight: 1.7604 ------------------------------------------------------------------------------- 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 D 268 GLN E 142 HIS F 268 GLN G 142 HIS G 268 GLN ** H 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 HIS H 268 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17376 Z= 0.173 Angle : 0.519 9.236 23672 Z= 0.259 Chirality : 0.036 0.141 2792 Planarity : 0.005 0.045 3016 Dihedral : 3.944 15.250 2496 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 7.19 % Allowed : 30.38 % Favored : 62.44 % 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: -0.37 (0.18), residues: 2360 helix: 1.51 (0.16), residues: 1216 sheet: -2.56 (0.41), residues: 160 loop : -2.19 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 95 HIS 0.005 0.001 HIS A 231 PHE 0.009 0.001 PHE E 117 TYR 0.007 0.001 TYR D 228 ARG 0.011 0.001 ARG A 173 *********************** 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 387 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 276 time to evaluate : 2.044 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: 0.9139 (OUTLIER) cc_final: 0.8894 (tt) REVERT: A 149 MET cc_start: 0.8750 (tpt) cc_final: 0.8288 (tmm) REVERT: B 91 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.9019 (tp) REVERT: B 96 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8866 (tt) REVERT: B 132 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8714 (tt0) REVERT: B 149 MET cc_start: 0.8810 (tmm) cc_final: 0.8171 (tmm) REVERT: C 96 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8870 (tt) REVERT: C 132 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8727 (tt0) REVERT: C 149 MET cc_start: 0.8936 (tmm) cc_final: 0.8097 (tmm) REVERT: C 150 ASN cc_start: 0.7872 (m110) cc_final: 0.7058 (m110) REVERT: D 91 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9016 (tp) REVERT: D 96 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8868 (tt) REVERT: D 132 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8810 (tt0) REVERT: D 149 MET cc_start: 0.8766 (tpt) cc_final: 0.8412 (tmm) REVERT: E 96 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8886 (tt) REVERT: E 132 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8744 (tt0) REVERT: E 149 MET cc_start: 0.8759 (tpt) cc_final: 0.8415 (tmm) REVERT: F 96 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8889 (tt) REVERT: F 132 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8809 (tt0) REVERT: F 149 MET cc_start: 0.8724 (tpt) cc_final: 0.8375 (tmm) REVERT: F 150 ASN cc_start: 0.7925 (m110) cc_final: 0.6965 (m110) REVERT: G 96 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8885 (tt) REVERT: G 132 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8783 (tt0) REVERT: G 149 MET cc_start: 0.8930 (tmm) cc_final: 0.8079 (tmm) REVERT: G 150 ASN cc_start: 0.7877 (m110) cc_final: 0.7063 (m110) REVERT: H 91 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9036 (tp) REVERT: H 132 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8707 (tt0) REVERT: H 149 MET cc_start: 0.8826 (tmm) cc_final: 0.8138 (tmm) outliers start: 111 outliers final: 86 residues processed: 359 average time/residue: 0.2798 time to fit residues: 155.1161 Evaluate side-chains 377 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 274 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 11 ILE 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 127 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 175 THR 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 6 SER Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 93 THR 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 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 6 SER Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 68 THR 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 132 GLN 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 6 SER Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 175 THR 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 6 SER Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 100 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 249 TYR Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain F residue 6 SER 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 132 GLN 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 6 SER Chi-restraints excluded: chain G residue 11 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 132 GLN Chi-restraints excluded: chain G residue 172 VAL 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 6 SER Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 132 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 142 optimal weight: 7.9990 chunk 152 optimal weight: 0.0030 chunk 110 optimal weight: 0.0270 chunk 20 optimal weight: 0.8980 chunk 175 optimal weight: 0.8980 chunk 203 optimal weight: 10.0000 chunk 214 optimal weight: 5.9990 overall best weight: 0.7650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 HIS E 268 GLN ** H 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17376 Z= 0.134 Angle : 0.522 9.904 23672 Z= 0.254 Chirality : 0.036 0.139 2792 Planarity : 0.005 0.050 3016 Dihedral : 3.634 14.580 2496 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 4.86 % Allowed : 32.90 % Favored : 62.24 % 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: 1.55 (0.16), residues: 1216 sheet: -1.36 (0.80), residues: 48 loop : -2.01 (0.17), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 157 HIS 0.006 0.001 HIS C 231 PHE 0.006 0.001 PHE B 117 TYR 0.008 0.001 TYR D 228 ARG 0.013 0.001 ARG D 173 *********************** 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 371 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 296 time to evaluate : 2.394 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: 0.9101 (OUTLIER) cc_final: 0.8886 (tt) REVERT: A 132 GLN cc_start: 0.9145 (tp40) cc_final: 0.8670 (tt0) REVERT: A 149 MET cc_start: 0.8764 (tpt) cc_final: 0.8338 (tmm) REVERT: B 96 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8869 (tt) REVERT: B 132 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8699 (tt0) REVERT: B 149 MET cc_start: 0.8815 (tmm) cc_final: 0.8169 (tmm) REVERT: C 96 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8871 (tt) REVERT: C 132 GLN cc_start: 0.9098 (OUTLIER) cc_final: 0.8765 (tt0) REVERT: C 149 MET cc_start: 0.8936 (tmm) cc_final: 0.8084 (tmm) REVERT: C 150 ASN cc_start: 0.7848 (m110) cc_final: 0.7038 (m110) REVERT: D 96 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8869 (tt) REVERT: D 132 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8861 (tt0) REVERT: D 149 MET cc_start: 0.8730 (tpt) cc_final: 0.8392 (tmm) REVERT: E 96 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8881 (tt) REVERT: E 132 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8769 (tt0) REVERT: E 149 MET cc_start: 0.8739 (tpt) cc_final: 0.8434 (tmm) REVERT: F 132 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8795 (tt0) REVERT: F 149 MET cc_start: 0.8741 (tpt) cc_final: 0.8395 (tmm) REVERT: F 150 ASN cc_start: 0.7902 (m110) cc_final: 0.6897 (m110) REVERT: G 96 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8893 (tt) REVERT: G 132 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8767 (tt0) REVERT: G 149 MET cc_start: 0.8920 (tmm) cc_final: 0.8059 (tmm) REVERT: G 150 ASN cc_start: 0.7855 (m110) cc_final: 0.7046 (m110) REVERT: H 132 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8786 (tt0) REVERT: H 149 MET cc_start: 0.8838 (tmm) cc_final: 0.8188 (tmm) outliers start: 75 outliers final: 58 residues processed: 336 average time/residue: 0.2800 time to fit residues: 142.5394 Evaluate side-chains 343 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 272 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 LEU 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 B residue 6 SER 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 249 TYR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 93 THR 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 132 GLN 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 6 SER Chi-restraints excluded: chain D residue 50 ARG 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 132 GLN 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 D residue 249 TYR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain E residue 6 SER 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 181 LEU Chi-restraints excluded: chain E residue 249 TYR Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 50 ARG 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 132 GLN 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 6 SER Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 132 GLN 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 6 SER Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 132 GLN Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 249 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 9.9990 chunk 208 optimal weight: 5.9990 chunk 214 optimal weight: 7.9990 chunk 125 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 163 optimal weight: 0.0270 chunk 63 optimal weight: 1.9990 chunk 188 optimal weight: 8.9990 chunk 197 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 overall best weight: 2.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 HIS A 268 GLN B 268 GLN C 268 GLN D 142 HIS D 268 GLN ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 HIS F 268 GLN G 142 HIS G 268 GLN H 142 HIS H 268 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17376 Z= 0.226 Angle : 0.541 9.599 23672 Z= 0.268 Chirality : 0.037 0.136 2792 Planarity : 0.004 0.037 3016 Dihedral : 3.907 14.913 2496 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 6.87 % Allowed : 32.12 % Favored : 61.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.21 (0.18), residues: 2360 helix: 1.56 (0.16), residues: 1224 sheet: -2.54 (0.41), residues: 160 loop : -2.02 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 95 HIS 0.002 0.001 HIS E 229 PHE 0.010 0.001 PHE B 117 TYR 0.027 0.002 TYR D 189 ARG 0.002 0.000 ARG D 173 *********************** 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 382 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 276 time to evaluate : 2.144 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: 0.9159 (OUTLIER) cc_final: 0.8896 (tt) REVERT: A 149 MET cc_start: 0.8771 (tpt) cc_final: 0.8312 (tmm) REVERT: B 91 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.9010 (tp) REVERT: B 96 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8898 (tt) REVERT: B 132 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8724 (tt0) REVERT: B 149 MET cc_start: 0.8803 (tmm) cc_final: 0.8119 (tmm) REVERT: C 91 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9014 (tp) REVERT: C 96 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8890 (tt) REVERT: C 132 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8760 (tt0) REVERT: C 149 MET cc_start: 0.8965 (tmm) cc_final: 0.8664 (tmm) REVERT: C 150 ASN cc_start: 0.7898 (m110) cc_final: 0.7408 (m110) REVERT: D 91 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.9008 (tp) REVERT: D 96 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8890 (tt) REVERT: D 132 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8844 (tt0) REVERT: D 149 MET cc_start: 0.8745 (tpt) cc_final: 0.8417 (tmm) REVERT: E 96 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8876 (tt) REVERT: E 132 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8781 (tt0) REVERT: E 149 MET cc_start: 0.8757 (tpt) cc_final: 0.8405 (tmm) REVERT: F 91 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9012 (tp) REVERT: F 132 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.8816 (tt0) REVERT: F 149 MET cc_start: 0.8759 (tpt) cc_final: 0.8378 (tmm) REVERT: F 150 ASN cc_start: 0.7974 (m110) cc_final: 0.6984 (m110) REVERT: G 91 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.9023 (tp) REVERT: G 96 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8904 (tt) REVERT: G 132 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8790 (tt0) REVERT: G 149 MET cc_start: 0.8970 (tmm) cc_final: 0.8665 (tmm) REVERT: G 150 ASN cc_start: 0.7904 (m110) cc_final: 0.7411 (m110) REVERT: H 91 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9014 (tp) REVERT: H 132 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8756 (tt0) REVERT: H 149 MET cc_start: 0.8915 (tmm) cc_final: 0.8121 (tmm) outliers start: 106 outliers final: 74 residues processed: 347 average time/residue: 0.2410 time to fit residues: 133.5952 Evaluate side-chains 369 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 276 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 175 THR 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 B residue 6 SER Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 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 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 6 SER Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 91 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 132 GLN 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 6 SER Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 172 VAL 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 6 SER Chi-restraints excluded: chain E residue 11 ILE 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 172 VAL 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 6 SER Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 132 GLN Chi-restraints excluded: chain F residue 172 VAL 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 6 SER Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 132 GLN Chi-restraints excluded: chain G residue 172 VAL 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 6 SER Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 132 GLN 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 220 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 231 optimal weight: 20.0000 chunk 212 optimal weight: 4.9990 chunk 184 optimal weight: 0.7980 chunk 19 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 HIS D 142 HIS ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 HIS E 268 GLN G 142 HIS H 142 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 17376 Z= 0.167 Angle : 0.530 9.682 23672 Z= 0.259 Chirality : 0.036 0.141 2792 Planarity : 0.004 0.037 3016 Dihedral : 3.805 14.614 2496 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 5.96 % Allowed : 32.84 % Favored : 61.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.22 (0.18), residues: 2360 helix: 1.52 (0.16), residues: 1216 sheet: -2.48 (0.42), residues: 160 loop : -1.95 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 95 HIS 0.006 0.001 HIS E 231 PHE 0.010 0.001 PHE C 117 TYR 0.006 0.001 TYR D 228 ARG 0.003 0.000 ARG G 173 ********************** 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 366 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 274 time to evaluate : 2.004 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 91 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8997 (tp) REVERT: A 96 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8882 (tt) REVERT: A 132 GLN cc_start: 0.9173 (tp40) cc_final: 0.8691 (tt0) REVERT: A 149 MET cc_start: 0.8769 (tpt) cc_final: 0.8334 (tmm) REVERT: B 91 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.9011 (tp) REVERT: B 96 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8882 (tt) REVERT: B 132 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8687 (tt0) REVERT: B 149 MET cc_start: 0.8802 (tmm) cc_final: 0.8108 (tmm) REVERT: C 96 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8865 (tt) REVERT: C 132 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8700 (tt0) REVERT: C 149 MET cc_start: 0.8954 (tmm) cc_final: 0.8056 (tmm) REVERT: C 150 ASN cc_start: 0.7892 (m110) cc_final: 0.7047 (m110) REVERT: D 91 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8999 (tp) REVERT: D 96 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8877 (tt) REVERT: D 132 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8803 (tt0) REVERT: D 149 MET cc_start: 0.8723 (tpt) cc_final: 0.8404 (tmm) REVERT: D 150 ASN cc_start: 0.8781 (t0) cc_final: 0.8076 (t0) REVERT: E 91 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.9007 (tp) REVERT: E 96 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8883 (tt) REVERT: E 132 GLN cc_start: 0.9098 (OUTLIER) cc_final: 0.8736 (tt0) REVERT: E 149 MET cc_start: 0.8753 (tpt) cc_final: 0.8416 (tmm) REVERT: F 132 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8752 (tt0) REVERT: F 149 MET cc_start: 0.8733 (tpt) cc_final: 0.8407 (tmm) REVERT: F 150 ASN cc_start: 0.7949 (m110) cc_final: 0.6988 (m110) REVERT: G 96 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8897 (tt) REVERT: G 132 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8769 (tt0) REVERT: G 149 MET cc_start: 0.8953 (tmm) cc_final: 0.8050 (tmm) REVERT: G 150 ASN cc_start: 0.7899 (m110) cc_final: 0.7050 (m110) REVERT: H 132 GLN cc_start: 0.9125 (OUTLIER) cc_final: 0.8720 (tt0) REVERT: H 149 MET cc_start: 0.8927 (tmm) cc_final: 0.8160 (tmm) outliers start: 92 outliers final: 74 residues processed: 330 average time/residue: 0.2507 time to fit residues: 130.0215 Evaluate side-chains 366 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 275 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 175 THR 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 6 SER Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 91 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 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 6 SER Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 93 THR 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 132 GLN 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 6 SER Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 172 VAL 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 6 SER Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 172 VAL 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 6 SER Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 132 GLN 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 6 SER Chi-restraints excluded: chain G residue 11 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 132 GLN 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 6 SER Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 132 GLN 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 196 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 189 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 161 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.138001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.094637 restraints weight = 34963.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.097891 restraints weight = 21173.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.100021 restraints weight = 15610.321| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 17376 Z= 0.418 Angle : 0.660 8.627 23672 Z= 0.332 Chirality : 0.040 0.150 2792 Planarity : 0.005 0.041 3016 Dihedral : 4.598 16.464 2496 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 8.03 % Allowed : 30.31 % Favored : 61.66 % 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: -0.66 (0.18), residues: 2360 helix: 1.44 (0.16), residues: 1184 sheet: -3.43 (0.35), residues: 160 loop : -2.30 (0.17), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP H 95 HIS 0.005 0.001 HIS C 231 PHE 0.011 0.002 PHE A 190 TYR 0.020 0.002 TYR H 189 ARG 0.003 0.000 ARG E 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3418.44 seconds wall clock time: 63 minutes 33.94 seconds (3813.94 seconds total)