Starting phenix.real_space_refine on Sun Aug 24 04:06:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p00_17323/08_2025/8p00_17323.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p00_17323/08_2025/8p00_17323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p00_17323/08_2025/8p00_17323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p00_17323/08_2025/8p00_17323.map" model { file = "/net/cci-nas-00/data/ceres_data/8p00_17323/08_2025/8p00_17323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p00_17323/08_2025/8p00_17323.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 10936 2.51 5 N 2912 2.21 5 O 3048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASP:plan': 12, 'ARG:plan': 8, 'GLU:plan': 15, 'GLN:plan1': 5, 'ASN:plan1': 4, 'PHE:plan': 2, 'TYR:plan': 1} 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: {'ASP:plan': 12, 'ARG:plan': 8, 'GLU:plan': 15, 'GLN:plan1': 5, 'ASN:plan1': 4, 'PHE:plan': 2, 'TYR:plan': 1} 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: {'ASP:plan': 12, 'ARG:plan': 8, 'GLU:plan': 15, 'GLN:plan1': 5, 'ASN:plan1': 4, 'PHE:plan': 2, 'TYR:plan': 1} 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: {'ASP:plan': 12, 'ARG:plan': 8, 'GLU:plan': 15, 'GLN:plan1': 5, 'ASN:plan1': 4, 'PHE:plan': 2, 'TYR:plan': 1} 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: {'ASP:plan': 12, 'ARG:plan': 8, 'GLU:plan': 15, 'GLN:plan1': 5, 'ASN:plan1': 4, 'PHE:plan': 2, 'TYR:plan': 1} 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: {'ASP:plan': 12, 'ARG:plan': 8, 'GLU:plan': 15, 'GLN:plan1': 5, 'ASN:plan1': 4, 'PHE:plan': 2, 'TYR:plan': 1} 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: {'ASP:plan': 12, 'ARG:plan': 8, 'GLU:plan': 15, 'GLN:plan1': 5, 'ASN:plan1': 4, 'PHE:plan': 2, 'TYR:plan': 1} 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: {'ASP:plan': 12, 'ARG:plan': 8, 'GLU:plan': 15, 'GLN:plan1': 5, 'ASN:plan1': 4, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 184 Time building chain proxies: 4.20, per 1000 atoms: 0.25 Number of scatterers: 16992 At special positions: 0 Unit cell: (138.46, 138.46, 88.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 3048 8.00 N 2912 7.00 C 10936 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 775.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.46 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: 2.68 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3679 1.33 - 1.45: 3763 1.45 - 1.57: 9782 1.57 - 1.70: 0 1.70 - 1.82: 152 Bond restraints: 17376 Sorted by residual: bond pdb=" CA LEU D 202 " pdb=" C LEU D 202 " ideal model delta sigma weight residual 1.521 1.482 0.039 1.30e-02 5.92e+03 8.80e+00 bond pdb=" CA PRO D 204 " pdb=" C PRO D 204 " ideal model delta sigma weight residual 1.522 1.492 0.030 1.18e-02 7.18e+03 6.49e+00 bond pdb=" C TYR D 203 " pdb=" O TYR D 203 " ideal model delta sigma weight residual 1.237 1.211 0.026 1.07e-02 8.73e+03 5.85e+00 bond pdb=" C LEU D 202 " pdb=" O LEU D 202 " ideal model delta sigma weight residual 1.234 1.209 0.026 1.29e-02 6.01e+03 3.91e+00 bond pdb=" CA LEU D 202 " pdb=" CB LEU D 202 " ideal model delta sigma weight residual 1.534 1.502 0.032 1.65e-02 3.67e+03 3.85e+00 ... (remaining 17371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 23428 2.40 - 4.80: 216 4.80 - 7.20: 17 7.20 - 9.60: 2 9.60 - 11.99: 9 Bond angle restraints: 23672 Sorted by residual: angle pdb=" CB MET F 149 " pdb=" CG MET F 149 " pdb=" SD MET F 149 " ideal model delta sigma weight residual 112.70 124.69 -11.99 3.00e+00 1.11e-01 1.60e+01 angle pdb=" CB MET D 149 " pdb=" CG MET D 149 " pdb=" SD MET D 149 " ideal model delta sigma weight residual 112.70 124.68 -11.98 3.00e+00 1.11e-01 1.60e+01 angle pdb=" CB MET A 149 " pdb=" CG MET A 149 " pdb=" SD MET A 149 " ideal model delta sigma weight residual 112.70 122.75 -10.05 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CB MET G 149 " pdb=" CG MET G 149 " pdb=" SD MET G 149 " ideal model delta sigma weight residual 112.70 122.30 -9.60 3.00e+00 1.11e-01 1.02e+01 angle pdb=" CB MET C 149 " pdb=" CG MET C 149 " pdb=" SD MET C 149 " ideal model delta sigma weight residual 112.70 122.21 -9.51 3.00e+00 1.11e-01 1.01e+01 ... (remaining 23667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 8821 16.61 - 33.23: 1095 33.23 - 49.84: 355 49.84 - 66.45: 71 66.45 - 83.07: 26 Dihedral angle restraints: 10368 sinusoidal: 3384 harmonic: 6984 Sorted by residual: dihedral pdb=" CA ASP D 207 " pdb=" C ASP D 207 " pdb=" N GLU D 208 " pdb=" CA GLU D 208 " ideal model delta harmonic sigma weight residual -180.00 -163.82 -16.18 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA ASP G 207 " pdb=" C ASP G 207 " pdb=" N GLU G 208 " pdb=" CA GLU G 208 " ideal model delta harmonic sigma weight residual 180.00 -164.39 -15.61 0 5.00e+00 4.00e-02 9.75e+00 dihedral pdb=" CA ASP H 207 " pdb=" C ASP H 207 " pdb=" N GLU H 208 " pdb=" CA GLU H 208 " ideal model delta harmonic sigma weight residual 180.00 -164.40 -15.60 0 5.00e+00 4.00e-02 9.73e+00 ... (remaining 10365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1767 0.027 - 0.054: 716 0.054 - 0.081: 184 0.081 - 0.108: 85 0.108 - 0.135: 40 Chirality restraints: 2792 Sorted by residual: chirality pdb=" CA ILE G 234 " pdb=" N ILE G 234 " pdb=" C ILE G 234 " pdb=" CB ILE G 234 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA ILE E 234 " pdb=" N ILE E 234 " pdb=" C ILE E 234 " pdb=" CB ILE E 234 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ILE D 234 " pdb=" N ILE D 234 " pdb=" C ILE D 234 " pdb=" CB ILE D 234 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 2789 not shown) Planarity restraints: 3016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 203 " -0.028 5.00e-02 4.00e+02 4.24e-02 2.87e+00 pdb=" N PRO A 204 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 204 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 204 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR G 203 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.87e+00 pdb=" N PRO G 204 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO G 204 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 204 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 203 " -0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO B 204 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 204 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 204 " -0.023 5.00e-02 4.00e+02 ... (remaining 3013 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 6341 2.86 - 3.37: 16281 3.37 - 3.88: 24656 3.88 - 4.39: 24662 4.39 - 4.90: 43930 Nonbonded interactions: 115870 Sorted by model distance: nonbonded pdb=" OD2 ASP E 125 " pdb=" NZ LYS E 196 " model vdw 2.353 3.120 nonbonded pdb=" NZ LYS D 13 " pdb=" OE2 GLU D 110 " model vdw 2.353 3.120 nonbonded pdb=" N ASP E 207 " pdb=" OD1 ASP E 207 " model vdw 2.356 3.120 nonbonded pdb=" OD2 ASP H 125 " pdb=" NZ LYS H 196 " model vdw 2.358 3.120 nonbonded pdb=" N ASP G 207 " pdb=" OD1 ASP G 207 " model vdw 2.359 3.120 ... (remaining 115865 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.320 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17376 Z= 0.120 Angle : 0.572 11.995 23672 Z= 0.290 Chirality : 0.036 0.135 2792 Planarity : 0.004 0.045 3016 Dihedral : 17.067 83.068 5808 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.06 % Allowed : 35.82 % Favored : 64.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.011 0.001 ARG E 173 TYR 0.024 0.001 TYR A 189 PHE 0.005 0.001 PHE D 152 TRP 0.007 0.001 TRP C 157 HIS 0.001 0.000 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00237 (17376) covalent geometry : angle 0.57212 (23672) hydrogen bonds : bond 0.20546 ( 742) hydrogen bonds : angle 5.67254 ( 2106) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 0.604 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 263 average time/residue: 0.1387 time to fit residues: 54.0167 Evaluate side-chains 255 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 254 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.0060 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.0970 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 20.0000 overall best weight: 2.4200 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.141150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.098238 restraints weight = 33964.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.101493 restraints weight = 20820.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.103739 restraints weight = 15386.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.105256 restraints weight = 12704.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.106274 restraints weight = 11181.948| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17376 Z= 0.140 Angle : 0.520 7.802 23672 Z= 0.268 Chirality : 0.036 0.130 2792 Planarity : 0.004 0.041 3016 Dihedral : 4.196 43.371 2498 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 5.70 % Allowed : 30.63 % Favored : 63.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.18), residues: 2360 helix: 1.17 (0.16), residues: 1184 sheet: 0.74 (0.97), residues: 48 loop : -1.95 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 173 TYR 0.019 0.001 TYR A 189 PHE 0.006 0.001 PHE A 152 TRP 0.007 0.001 TRP F 95 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00324 (17376) covalent geometry : angle 0.52008 (23672) hydrogen bonds : bond 0.04005 ( 742) hydrogen bonds : angle 4.06888 ( 2106) *********************** 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 367 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 279 time to evaluate : 0.679 Fit side-chains REVERT: A 96 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8849 (tt) REVERT: A 149 MET cc_start: 0.8798 (tmm) cc_final: 0.7983 (tmm) REVERT: B 96 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8844 (tt) REVERT: C 96 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8859 (tt) REVERT: D 96 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8846 (tt) REVERT: F 96 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8832 (tt) REVERT: G 96 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8863 (tt) REVERT: H 96 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8839 (tt) REVERT: H 149 MET cc_start: 0.8745 (tpt) cc_final: 0.8358 (tmm) outliers start: 88 outliers final: 20 residues processed: 348 average time/residue: 0.1311 time to fit residues: 68.5423 Evaluate side-chains 284 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 257 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER 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 B residue 96 LEU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 181 LEU 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 D residue 96 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 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 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 96 LEU Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 181 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 43 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 115 optimal weight: 30.0000 chunk 8 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 177 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 161 optimal weight: 0.0670 chunk 141 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 126 optimal weight: 1.9990 overall best weight: 3.8126 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.139174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.096171 restraints weight = 34290.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.099351 restraints weight = 21273.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.101434 restraints weight = 15829.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.102959 restraints weight = 13097.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.103877 restraints weight = 11541.742| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 17376 Z= 0.202 Angle : 0.547 6.479 23672 Z= 0.287 Chirality : 0.037 0.136 2792 Planarity : 0.005 0.040 3016 Dihedral : 4.437 25.431 2498 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 7.71 % Allowed : 26.94 % Favored : 65.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.18), residues: 2360 helix: 1.25 (0.16), residues: 1184 sheet: -2.26 (0.43), residues: 160 loop : -2.10 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 173 TYR 0.022 0.002 TYR F 189 PHE 0.008 0.001 PHE A 190 TRP 0.011 0.002 TRP B 95 HIS 0.003 0.001 HIS D 229 Details of bonding type rmsd covalent geometry : bond 0.00464 (17376) covalent geometry : angle 0.54655 (23672) hydrogen bonds : bond 0.04421 ( 742) hydrogen bonds : angle 4.01441 ( 2106) *********************** 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 404 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 285 time to evaluate : 0.696 Fit side-chains REVERT: A 96 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8856 (tt) REVERT: A 149 MET cc_start: 0.8817 (tmm) cc_final: 0.8384 (tmm) REVERT: A 249 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.6799 (m-10) REVERT: B 96 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8899 (tt) REVERT: B 249 TYR cc_start: 0.7785 (OUTLIER) cc_final: 0.6817 (m-10) REVERT: C 149 MET cc_start: 0.8892 (tmm) cc_final: 0.8110 (tmm) REVERT: C 249 TYR cc_start: 0.7771 (OUTLIER) cc_final: 0.6801 (m-10) REVERT: D 96 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8894 (tt) REVERT: D 149 MET cc_start: 0.8745 (tpt) cc_final: 0.8387 (tmm) REVERT: D 249 TYR cc_start: 0.7793 (OUTLIER) cc_final: 0.6820 (m-10) REVERT: E 149 MET cc_start: 0.8773 (tpt) cc_final: 0.8388 (tmm) REVERT: E 249 TYR cc_start: 0.7775 (OUTLIER) cc_final: 0.6810 (m-10) REVERT: F 96 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8849 (tt) REVERT: F 149 MET cc_start: 0.8750 (tpt) cc_final: 0.8392 (tmm) REVERT: F 249 TYR cc_start: 0.7773 (OUTLIER) cc_final: 0.6807 (m-10) REVERT: G 249 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.6804 (m-10) REVERT: H 96 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8888 (tt) REVERT: H 149 MET cc_start: 0.8784 (tpt) cc_final: 0.8412 (tmm) REVERT: H 249 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.6815 (m-10) outliers start: 119 outliers final: 57 residues processed: 378 average time/residue: 0.1251 time to fit residues: 71.4987 Evaluate side-chains 332 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 262 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 127 LEU 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 59 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 127 LEU 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 59 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 249 TYR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 93 THR 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 93 THR Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 249 TYR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 127 LEU 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 59 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 249 TYR Chi-restraints excluded: chain H residue 286 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 24 optimal weight: 0.0670 chunk 117 optimal weight: 0.7980 chunk 197 optimal weight: 20.0000 chunk 100 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 220 optimal weight: 1.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 142 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.143126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.099632 restraints weight = 34167.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.103171 restraints weight = 20594.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.105600 restraints weight = 15017.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.107202 restraints weight = 12267.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.108238 restraints weight = 10756.415| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1397 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= 0.090 Angle : 0.482 5.688 23672 Z= 0.250 Chirality : 0.036 0.128 2792 Planarity : 0.004 0.038 3016 Dihedral : 3.894 15.003 2496 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 6.15 % Allowed : 28.76 % Favored : 65.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.18), residues: 2360 helix: 1.26 (0.16), residues: 1216 sheet: -0.58 (0.86), residues: 48 loop : -2.08 (0.17), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 173 TYR 0.025 0.001 TYR D 189 PHE 0.004 0.001 PHE A 130 TRP 0.008 0.001 TRP B 95 HIS 0.001 0.000 HIS D 233 Details of bonding type rmsd covalent geometry : bond 0.00197 (17376) covalent geometry : angle 0.48151 (23672) hydrogen bonds : bond 0.02972 ( 742) hydrogen bonds : angle 3.62435 ( 2106) *********************** 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 385 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 290 time to evaluate : 0.633 Fit side-chains REVERT: A 149 MET cc_start: 0.8756 (tmm) cc_final: 0.7774 (tmm) REVERT: A 249 TYR cc_start: 0.7667 (OUTLIER) cc_final: 0.6773 (m-10) REVERT: B 96 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8834 (tt) REVERT: B 149 MET cc_start: 0.8867 (tmm) cc_final: 0.8157 (tmm) REVERT: B 249 TYR cc_start: 0.7696 (OUTLIER) cc_final: 0.6792 (m-10) REVERT: C 132 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8833 (tt0) REVERT: C 149 MET cc_start: 0.8900 (tmm) cc_final: 0.8051 (tmm) REVERT: C 150 ASN cc_start: 0.7803 (m110) cc_final: 0.7073 (m110) REVERT: C 249 TYR cc_start: 0.7689 (OUTLIER) cc_final: 0.6768 (m-10) REVERT: D 149 MET cc_start: 0.8748 (tpt) cc_final: 0.8409 (tmm) REVERT: D 249 TYR cc_start: 0.7698 (OUTLIER) cc_final: 0.6779 (m-10) REVERT: E 96 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8831 (tt) REVERT: E 149 MET cc_start: 0.8741 (tpt) cc_final: 0.8418 (tmm) REVERT: E 249 TYR cc_start: 0.7698 (OUTLIER) cc_final: 0.6776 (m-10) REVERT: F 132 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8839 (tt0) REVERT: F 149 MET cc_start: 0.8712 (tpt) cc_final: 0.8388 (tmm) REVERT: F 249 TYR cc_start: 0.7725 (OUTLIER) cc_final: 0.6794 (m-10) REVERT: G 132 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8830 (tt0) REVERT: G 149 MET cc_start: 0.8879 (tmm) cc_final: 0.8150 (tmm) REVERT: G 249 TYR cc_start: 0.7686 (OUTLIER) cc_final: 0.6767 (m-10) REVERT: H 132 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8881 (tt0) REVERT: H 149 MET cc_start: 0.8734 (tpt) cc_final: 0.8395 (tmm) REVERT: H 249 TYR cc_start: 0.7696 (OUTLIER) cc_final: 0.6797 (m-10) outliers start: 95 outliers final: 53 residues processed: 348 average time/residue: 0.1185 time to fit residues: 64.1481 Evaluate side-chains 342 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 275 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 59 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 217 LEU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 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 11 ILE Chi-restraints excluded: chain C residue 59 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 181 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 249 TYR Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 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 11 ILE Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 96 LEU 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 11 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 132 GLN Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 249 TYR Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 132 GLN Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 249 TYR Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 59 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 214 optimal weight: 0.0980 chunk 141 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 216 optimal weight: 1.9990 chunk 205 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 225 optimal weight: 20.0000 chunk 48 optimal weight: 8.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 142 HIS G 142 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.141784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.098415 restraints weight = 34459.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.101858 restraints weight = 20967.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.104205 restraints weight = 15412.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.105814 restraints weight = 12657.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.106667 restraints weight = 11127.582| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17376 Z= 0.122 Angle : 0.489 5.056 23672 Z= 0.256 Chirality : 0.036 0.133 2792 Planarity : 0.005 0.038 3016 Dihedral : 3.952 15.305 2496 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 6.28 % Allowed : 29.73 % Favored : 63.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.18), residues: 2360 helix: 1.39 (0.16), residues: 1216 sheet: -2.15 (0.44), residues: 160 loop : -1.98 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 173 TYR 0.007 0.001 TYR G 228 PHE 0.005 0.001 PHE B 190 TRP 0.009 0.001 TRP B 95 HIS 0.002 0.001 HIS D 229 Details of bonding type rmsd covalent geometry : bond 0.00284 (17376) covalent geometry : angle 0.48897 (23672) hydrogen bonds : bond 0.03356 ( 742) hydrogen bonds : angle 3.57188 ( 2106) *********************** 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 to be fit. rotamer outliers: 97 poor density : 289 time to evaluate : 0.651 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: 0.9116 (OUTLIER) cc_final: 0.8859 (tt) REVERT: A 149 MET cc_start: 0.8758 (tmm) cc_final: 0.7755 (tmm) REVERT: B 96 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8856 (tt) REVERT: B 150 ASN cc_start: 0.8717 (t0) cc_final: 0.7778 (m110) REVERT: C 149 MET cc_start: 0.8919 (tmm) cc_final: 0.8066 (tmm) REVERT: C 150 ASN cc_start: 0.7797 (m110) cc_final: 0.6965 (m110) REVERT: D 96 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8841 (tt) REVERT: D 149 MET cc_start: 0.8737 (tpt) cc_final: 0.8399 (tmm) REVERT: E 96 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8808 (tt) REVERT: E 149 MET cc_start: 0.8740 (tpt) cc_final: 0.8414 (tmm) REVERT: F 96 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8836 (tt) REVERT: F 149 MET cc_start: 0.8739 (tpt) cc_final: 0.8387 (tmm) REVERT: G 149 MET cc_start: 0.8901 (tmm) cc_final: 0.8077 (tmm) REVERT: G 150 ASN cc_start: 0.7777 (m110) cc_final: 0.7016 (m110) REVERT: H 96 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8838 (tt) REVERT: H 149 MET cc_start: 0.8707 (tpt) cc_final: 0.8415 (tmm) outliers start: 97 outliers final: 67 residues processed: 349 average time/residue: 0.1228 time to fit residues: 66.2293 Evaluate side-chains 355 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 282 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 172 VAL Chi-restraints excluded: chain A residue 179 MET 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 11 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 249 TYR Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 249 TYR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 249 TYR Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 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 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 59 LEU Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 249 TYR Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 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 230 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 184 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 183 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 0.4980 chunk 29 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 142 HIS E 268 GLN G 142 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.141428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.098016 restraints weight = 34144.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.101563 restraints weight = 20423.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.103987 restraints weight = 14832.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.105587 restraints weight = 12070.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.106613 restraints weight = 10579.456| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1556 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= 0.132 Angle : 0.501 9.146 23672 Z= 0.261 Chirality : 0.036 0.136 2792 Planarity : 0.005 0.042 3016 Dihedral : 4.003 15.107 2496 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 6.22 % Allowed : 30.89 % Favored : 62.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.18), residues: 2360 helix: 1.44 (0.16), residues: 1216 sheet: -2.52 (0.41), residues: 160 loop : -2.01 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 173 TYR 0.007 0.001 TYR E 228 PHE 0.007 0.001 PHE H 117 TRP 0.009 0.001 TRP B 95 HIS 0.002 0.001 HIS E 229 Details of bonding type rmsd covalent geometry : bond 0.00306 (17376) covalent geometry : angle 0.50143 (23672) hydrogen bonds : bond 0.03397 ( 742) hydrogen bonds : angle 3.51827 ( 2106) *********************** 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 400 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 304 time to evaluate : 0.797 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: 0.9023 (tp) REVERT: A 96 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8829 (tt) REVERT: A 149 MET cc_start: 0.8772 (tmm) cc_final: 0.7727 (tmm) REVERT: B 91 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8991 (tp) REVERT: B 96 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8831 (tt) REVERT: B 149 MET cc_start: 0.8797 (tmm) cc_final: 0.8169 (tmm) REVERT: C 91 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.9011 (tp) REVERT: C 96 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8822 (tt) REVERT: C 149 MET cc_start: 0.8980 (tmm) cc_final: 0.8584 (tmm) REVERT: C 150 ASN cc_start: 0.7829 (m110) cc_final: 0.7316 (m110) REVERT: D 91 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8987 (tp) REVERT: D 96 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8808 (tt) REVERT: D 149 MET cc_start: 0.8779 (tpt) cc_final: 0.8395 (tmm) REVERT: E 91 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.9007 (tp) REVERT: E 96 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8833 (tt) REVERT: E 149 MET cc_start: 0.8754 (tpt) cc_final: 0.8370 (tmm) REVERT: F 91 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9020 (tp) REVERT: F 96 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8829 (tt) REVERT: F 149 MET cc_start: 0.8775 (tpt) cc_final: 0.8366 (tmm) REVERT: F 150 ASN cc_start: 0.7945 (m110) cc_final: 0.7025 (m110) REVERT: G 91 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.9020 (tp) REVERT: G 96 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8826 (tt) REVERT: G 149 MET cc_start: 0.8927 (tmm) cc_final: 0.8049 (tmm) REVERT: G 150 ASN cc_start: 0.7815 (m110) cc_final: 0.6996 (m110) REVERT: H 91 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9012 (tp) REVERT: H 96 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8805 (tt) REVERT: H 150 ASN cc_start: 0.8778 (t0) cc_final: 0.7751 (m110) outliers start: 96 outliers final: 73 residues processed: 368 average time/residue: 0.1203 time to fit residues: 68.5460 Evaluate side-chains 370 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 281 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 59 LEU 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 179 MET 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 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 127 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain C residue 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 172 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 249 TYR Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 249 TYR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 59 LEU 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 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 11 ILE Chi-restraints excluded: chain F residue 59 LEU 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 172 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 249 TYR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 249 TYR Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 217 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 214 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 182 optimal weight: 0.9990 chunk 192 optimal weight: 0.0040 chunk 109 optimal weight: 9.9990 chunk 86 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN B 268 GLN C 268 GLN D 268 GLN E 268 GLN F 268 GLN G 268 GLN H 268 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.142609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.099132 restraints weight = 34054.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.102610 restraints weight = 20674.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.105042 restraints weight = 15164.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.106669 restraints weight = 12400.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.107668 restraints weight = 10873.020| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1664 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= 0.106 Angle : 0.505 9.519 23672 Z= 0.255 Chirality : 0.035 0.133 2792 Planarity : 0.005 0.045 3016 Dihedral : 3.835 15.171 2496 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 6.54 % Allowed : 29.92 % Favored : 63.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.18), residues: 2360 helix: 1.47 (0.16), residues: 1216 sheet: -1.48 (0.82), residues: 48 loop : -2.03 (0.17), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 173 TYR 0.027 0.001 TYR E 189 PHE 0.006 0.001 PHE H 117 TRP 0.008 0.001 TRP B 95 HIS 0.002 0.000 HIS H 229 Details of bonding type rmsd covalent geometry : bond 0.00245 (17376) covalent geometry : angle 0.50514 (23672) hydrogen bonds : bond 0.02998 ( 742) hydrogen bonds : angle 3.38926 ( 2106) *********************** 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 385 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 284 time to evaluate : 0.669 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: 0.9243 (OUTLIER) cc_final: 0.9018 (tp) REVERT: A 96 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8853 (tt) REVERT: A 149 MET cc_start: 0.8747 (tmm) cc_final: 0.7751 (tmm) REVERT: B 96 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8845 (tt) REVERT: B 149 MET cc_start: 0.8811 (tmm) cc_final: 0.8138 (tmm) REVERT: C 91 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.9007 (tp) REVERT: C 96 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8855 (tt) REVERT: C 149 MET cc_start: 0.8972 (tmm) cc_final: 0.8566 (tmm) REVERT: C 150 ASN cc_start: 0.7837 (m110) cc_final: 0.7327 (m110) REVERT: D 96 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8862 (tt) REVERT: D 149 MET cc_start: 0.8700 (tpt) cc_final: 0.8368 (tmm) REVERT: E 91 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9021 (tp) REVERT: E 96 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8851 (tt) REVERT: E 149 MET cc_start: 0.8717 (tpt) cc_final: 0.8395 (tmm) REVERT: F 91 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9023 (tp) REVERT: F 96 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8842 (tt) REVERT: F 149 MET cc_start: 0.8760 (tpt) cc_final: 0.8409 (tmm) REVERT: F 150 ASN cc_start: 0.7928 (m110) cc_final: 0.7008 (m110) REVERT: G 91 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.9008 (tp) REVERT: G 96 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8878 (tt) REVERT: G 149 MET cc_start: 0.8945 (tmm) cc_final: 0.8074 (tmm) REVERT: G 150 ASN cc_start: 0.7825 (m110) cc_final: 0.6974 (m110) REVERT: H 36 GLN cc_start: 0.9050 (mt0) cc_final: 0.8560 (tt0) REVERT: H 96 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8857 (tt) REVERT: H 149 MET cc_start: 0.8807 (tmm) cc_final: 0.8222 (tmm) outliers start: 101 outliers final: 79 residues processed: 353 average time/residue: 0.1216 time to fit residues: 66.2751 Evaluate side-chains 368 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 276 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 59 LEU 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 179 MET Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 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 172 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 249 TYR Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 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 11 ILE 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 172 VAL Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 249 TYR Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 59 LEU 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 172 VAL Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 249 TYR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 91 LEU 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 172 VAL Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 249 TYR Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 217 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 88 optimal weight: 0.0060 chunk 199 optimal weight: 6.9990 chunk 202 optimal weight: 30.0000 chunk 89 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 209 optimal weight: 0.9990 chunk 198 optimal weight: 10.0000 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.142443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.098771 restraints weight = 34347.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.102248 restraints weight = 20978.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.104672 restraints weight = 15436.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.106289 restraints weight = 12666.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.107325 restraints weight = 11139.488| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17376 Z= 0.115 Angle : 0.525 8.952 23672 Z= 0.263 Chirality : 0.037 0.155 2792 Planarity : 0.005 0.050 3016 Dihedral : 3.865 14.872 2496 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 6.74 % Allowed : 30.25 % Favored : 63.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.18), residues: 2360 helix: 1.45 (0.16), residues: 1216 sheet: -2.48 (0.43), residues: 160 loop : -1.93 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 173 TYR 0.007 0.001 TYR A 228 PHE 0.008 0.001 PHE E 117 TRP 0.009 0.001 TRP B 95 HIS 0.002 0.001 HIS H 229 Details of bonding type rmsd covalent geometry : bond 0.00269 (17376) covalent geometry : angle 0.52486 (23672) hydrogen bonds : bond 0.03103 ( 742) hydrogen bonds : angle 3.41154 ( 2106) *********************** 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 391 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 287 time to evaluate : 0.644 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: 0.9240 (OUTLIER) cc_final: 0.9005 (tp) REVERT: A 96 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8869 (tt) REVERT: A 132 GLN cc_start: 0.9173 (tp40) cc_final: 0.8684 (tt0) REVERT: A 149 MET cc_start: 0.8741 (tmm) cc_final: 0.7752 (tmm) REVERT: A 268 GLN cc_start: 0.8834 (tp40) cc_final: 0.8631 (tp-100) REVERT: B 91 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8999 (tp) REVERT: B 96 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8865 (tt) REVERT: B 132 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.8795 (tt0) REVERT: B 150 ASN cc_start: 0.8745 (t0) cc_final: 0.7856 (m110) REVERT: B 268 GLN cc_start: 0.8819 (tp40) cc_final: 0.8610 (tp-100) REVERT: C 91 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.9000 (tp) REVERT: C 96 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8852 (tt) REVERT: C 149 MET cc_start: 0.8971 (tmm) cc_final: 0.8544 (tmm) REVERT: C 150 ASN cc_start: 0.7854 (m110) cc_final: 0.7335 (m110) REVERT: D 91 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.9006 (tp) REVERT: D 96 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8860 (tt) REVERT: D 149 MET cc_start: 0.8678 (tpt) cc_final: 0.8352 (tmm) REVERT: D 268 GLN cc_start: 0.8816 (tp40) cc_final: 0.8598 (tp-100) REVERT: E 91 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9009 (tp) REVERT: E 96 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8865 (tt) REVERT: E 149 MET cc_start: 0.8703 (tpt) cc_final: 0.8380 (tmm) REVERT: F 91 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9009 (tp) REVERT: F 96 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8872 (tt) REVERT: F 149 MET cc_start: 0.8764 (tpt) cc_final: 0.8399 (tmm) REVERT: F 150 ASN cc_start: 0.7950 (m110) cc_final: 0.7013 (m110) REVERT: G 91 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9024 (tp) REVERT: G 96 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8870 (tt) REVERT: G 149 MET cc_start: 0.8930 (tmm) cc_final: 0.8582 (tmm) REVERT: G 150 ASN cc_start: 0.7849 (m110) cc_final: 0.7375 (m110) REVERT: G 268 GLN cc_start: 0.8824 (tp40) cc_final: 0.8614 (tp-100) REVERT: H 96 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8852 (tt) REVERT: H 149 MET cc_start: 0.8803 (tmm) cc_final: 0.8138 (tmm) REVERT: H 268 GLN cc_start: 0.8809 (tp40) cc_final: 0.8600 (tp-100) outliers start: 104 outliers final: 85 residues processed: 359 average time/residue: 0.1295 time to fit residues: 71.1746 Evaluate side-chains 375 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 274 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 59 LEU 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 179 MET Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 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 127 LEU Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 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 172 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 249 TYR Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 249 TYR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain E residue 11 ILE 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 100 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 249 TYR Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 59 LEU 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 172 VAL Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 249 TYR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 91 LEU 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 172 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 249 TYR Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 249 TYR Chi-restraints excluded: chain H residue 286 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 172 optimal weight: 10.0000 chunk 191 optimal weight: 4.9990 chunk 52 optimal weight: 0.0770 chunk 201 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 180 optimal weight: 0.4980 chunk 163 optimal weight: 0.5980 chunk 87 optimal weight: 6.9990 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 268 GLN E 268 GLN F 268 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.143887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.100226 restraints weight = 34043.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.103835 restraints weight = 20525.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.106310 restraints weight = 14976.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.107936 restraints weight = 12226.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.108978 restraints weight = 10749.824| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1847 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= 0.090 Angle : 0.515 9.139 23672 Z= 0.254 Chirality : 0.036 0.139 2792 Planarity : 0.004 0.036 3016 Dihedral : 3.674 14.852 2496 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 5.18 % Allowed : 32.64 % Favored : 62.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.18), residues: 2360 helix: 1.44 (0.16), residues: 1216 sheet: -1.37 (0.86), residues: 48 loop : -1.92 (0.17), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 173 TYR 0.007 0.001 TYR E 228 PHE 0.008 0.001 PHE G 117 TRP 0.008 0.001 TRP B 95 HIS 0.001 0.000 HIS E 229 Details of bonding type rmsd covalent geometry : bond 0.00203 (17376) covalent geometry : angle 0.51515 (23672) hydrogen bonds : bond 0.02689 ( 742) hydrogen bonds : angle 3.35228 ( 2106) *********************** 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 360 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 280 time to evaluate : 0.704 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: 0.9078 (OUTLIER) cc_final: 0.8832 (tt) REVERT: A 132 GLN cc_start: 0.9161 (tp40) cc_final: 0.8678 (tt0) REVERT: A 149 MET cc_start: 0.8763 (tmm) cc_final: 0.8393 (tpt) REVERT: A 268 GLN cc_start: 0.8814 (tp40) cc_final: 0.8597 (tp-100) REVERT: B 132 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8777 (tt0) REVERT: B 149 MET cc_start: 0.8779 (tmm) cc_final: 0.8153 (tmm) REVERT: B 150 ASN cc_start: 0.8702 (t0) cc_final: 0.7588 (m110) REVERT: B 268 GLN cc_start: 0.8803 (tp40) cc_final: 0.8591 (tp-100) REVERT: C 149 MET cc_start: 0.8949 (tmm) cc_final: 0.8531 (tmm) REVERT: C 150 ASN cc_start: 0.7843 (m110) cc_final: 0.7311 (m110) REVERT: D 96 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8838 (tt) REVERT: D 149 MET cc_start: 0.8688 (tpt) cc_final: 0.8362 (tmm) REVERT: D 268 GLN cc_start: 0.8795 (tp40) cc_final: 0.8577 (tp-100) REVERT: E 96 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8843 (tt) REVERT: E 149 MET cc_start: 0.8715 (tpt) cc_final: 0.8401 (tmm) REVERT: F 96 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8858 (tt) REVERT: F 149 MET cc_start: 0.8719 (tpt) cc_final: 0.8369 (tmm) REVERT: F 150 ASN cc_start: 0.7904 (m110) cc_final: 0.6941 (m110) REVERT: G 149 MET cc_start: 0.8945 (tmm) cc_final: 0.8056 (tmm) REVERT: G 150 ASN cc_start: 0.7846 (m110) cc_final: 0.6958 (m110) REVERT: G 268 GLN cc_start: 0.8803 (tp40) cc_final: 0.8582 (tp-100) REVERT: H 96 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8834 (tt) REVERT: H 149 MET cc_start: 0.8802 (tmm) cc_final: 0.8172 (tmm) REVERT: H 268 GLN cc_start: 0.8795 (tp40) cc_final: 0.8579 (tp-100) outliers start: 80 outliers final: 69 residues processed: 325 average time/residue: 0.1140 time to fit residues: 58.9404 Evaluate side-chains 347 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 272 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 179 MET Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 249 TYR Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 249 TYR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 249 TYR Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 59 LEU 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 180 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 249 TYR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 249 TYR Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 217 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 18 optimal weight: 0.1980 chunk 92 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 chunk 151 optimal weight: 0.9990 chunk 144 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 219 optimal weight: 5.9990 chunk 143 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 202 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 142 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.140000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.096006 restraints weight = 34102.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.099386 restraints weight = 20918.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.101594 restraints weight = 15463.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.103215 restraints weight = 12785.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.104107 restraints weight = 11256.556| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 17376 Z= 0.187 Angle : 0.574 8.354 23672 Z= 0.290 Chirality : 0.038 0.141 2792 Planarity : 0.004 0.038 3016 Dihedral : 4.147 15.974 2496 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 5.96 % Allowed : 31.74 % Favored : 62.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.18), residues: 2360 helix: 1.44 (0.16), residues: 1192 sheet: -3.01 (0.38), residues: 160 loop : -1.91 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 129 TYR 0.028 0.002 TYR D 189 PHE 0.014 0.001 PHE F 117 TRP 0.013 0.002 TRP B 95 HIS 0.003 0.001 HIS H 229 Details of bonding type rmsd covalent geometry : bond 0.00431 (17376) covalent geometry : angle 0.57422 (23672) hydrogen bonds : bond 0.03836 ( 742) hydrogen bonds : angle 3.60075 ( 2106) ********************** 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 372 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 280 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8880 (tt) REVERT: A 132 GLN cc_start: 0.9211 (tp40) cc_final: 0.8739 (tt0) REVERT: A 149 MET cc_start: 0.8814 (tmm) cc_final: 0.7713 (tmm) REVERT: A 268 GLN cc_start: 0.8760 (tp40) cc_final: 0.8510 (tp-100) REVERT: B 91 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8998 (tp) REVERT: B 132 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.8852 (tt0) REVERT: B 149 MET cc_start: 0.8804 (tmm) cc_final: 0.8153 (tmm) REVERT: B 268 GLN cc_start: 0.8805 (tp40) cc_final: 0.8580 (tp-100) REVERT: C 149 MET cc_start: 0.8982 (tmm) cc_final: 0.8534 (tmm) REVERT: C 150 ASN cc_start: 0.7907 (m110) cc_final: 0.7329 (m110) REVERT: D 91 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8996 (tp) REVERT: D 96 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8883 (tt) REVERT: D 149 MET cc_start: 0.8768 (tpt) cc_final: 0.8414 (tmm) REVERT: D 268 GLN cc_start: 0.8809 (tp40) cc_final: 0.8581 (tp-100) REVERT: E 96 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8905 (tt) REVERT: E 132 GLN cc_start: 0.9232 (OUTLIER) cc_final: 0.8871 (tt0) REVERT: E 149 MET cc_start: 0.8753 (tpt) cc_final: 0.8397 (tmm) REVERT: F 91 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9003 (tp) REVERT: F 96 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8867 (tt) REVERT: F 132 GLN cc_start: 0.9185 (tp40) cc_final: 0.8728 (tt0) REVERT: F 149 MET cc_start: 0.8780 (tpt) cc_final: 0.8393 (tmm) REVERT: F 150 ASN cc_start: 0.7931 (m110) cc_final: 0.6974 (m110) REVERT: G 91 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.9006 (tp) REVERT: G 132 GLN cc_start: 0.9197 (tp40) cc_final: 0.8730 (tt0) REVERT: G 149 MET cc_start: 0.8965 (tmm) cc_final: 0.8577 (tmm) REVERT: G 150 ASN cc_start: 0.7903 (m110) cc_final: 0.7363 (m110) REVERT: G 268 GLN cc_start: 0.8793 (tp40) cc_final: 0.8563 (tp-100) REVERT: H 91 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.9001 (tp) REVERT: H 96 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8871 (tt) REVERT: H 268 GLN cc_start: 0.8799 (tp40) cc_final: 0.8573 (tp-100) outliers start: 92 outliers final: 63 residues processed: 337 average time/residue: 0.1094 time to fit residues: 59.0050 Evaluate side-chains 352 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 277 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 180 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 249 TYR Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 LEU 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 11 ILE Chi-restraints excluded: chain E residue 59 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 180 ILE Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 249 TYR Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 249 TYR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 249 TYR Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 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 89 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 172 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 195 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 36 GLN C 268 GLN D 36 GLN E 142 HIS F 268 GLN G 36 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.140324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.096898 restraints weight = 34163.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.100307 restraints weight = 20462.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.102563 restraints weight = 14976.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.104127 restraints weight = 12292.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.105168 restraints weight = 10814.904| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17376 Z= 0.172 Angle : 0.573 8.323 23672 Z= 0.287 Chirality : 0.038 0.144 2792 Planarity : 0.004 0.038 3016 Dihedral : 4.192 15.577 2496 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 5.18 % Allowed : 32.45 % Favored : 62.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.18), residues: 2360 helix: 1.33 (0.16), residues: 1192 sheet: -3.23 (0.36), residues: 160 loop : -2.02 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 173 TYR 0.011 0.001 TYR B 228 PHE 0.008 0.001 PHE F 117 TRP 0.011 0.002 TRP B 95 HIS 0.006 0.001 HIS F 231 Details of bonding type rmsd covalent geometry : bond 0.00401 (17376) covalent geometry : angle 0.57285 (23672) hydrogen bonds : bond 0.03681 ( 742) hydrogen bonds : angle 3.61222 ( 2106) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2961.76 seconds wall clock time: 51 minutes 53.32 seconds (3113.32 seconds total)