Starting phenix.real_space_refine on Mon Nov 18 16:02:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p00_17323/11_2024/8p00_17323.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p00_17323/11_2024/8p00_17323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p00_17323/11_2024/8p00_17323.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p00_17323/11_2024/8p00_17323.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p00_17323/11_2024/8p00_17323.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p00_17323/11_2024/8p00_17323.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 10936 2.51 5 N 2912 2.21 5 O 3048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 16992 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2124 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 13, 'TRANS': 283} Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 184 Chain: "B" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2124 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 13, 'TRANS': 283} Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 184 Chain: "C" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2124 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 13, 'TRANS': 283} Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 184 Chain: "D" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2124 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 13, 'TRANS': 283} Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 184 Chain: "E" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2124 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 13, 'TRANS': 283} Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 184 Chain: "F" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2124 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 13, 'TRANS': 283} Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 184 Chain: "G" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2124 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 13, 'TRANS': 283} Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 184 Chain: "H" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2124 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 13, 'TRANS': 283} Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 184 Time building chain proxies: 10.12, per 1000 atoms: 0.60 Number of scatterers: 16992 At special positions: 0 Unit cell: (138.46, 138.46, 88.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 3048 8.00 N 2912 7.00 C 10936 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.34 Conformation dependent library (CDL) restraints added in 2.5 seconds 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4560 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 29 sheets defined 53.2% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 26 through 31 removed outlier: 3.708A pdb=" N ARG A 30 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A 31 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 46 removed outlier: 3.696A pdb=" N GLY A 46 " --> pdb=" O THR A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 59 Processing helix chain 'A' and resid 63 through 67 removed outlier: 3.713A pdb=" N ARG A 66 " --> pdb=" O PRO A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 100 Processing helix chain 'A' and resid 102 through 114 Processing helix chain 'A' and resid 124 through 136 removed outlier: 4.529A pdb=" N ASP A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 156 removed outlier: 3.645A pdb=" N PHE A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 211 through 222 removed outlier: 4.563A pdb=" N LEU A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 251 removed outlier: 3.677A pdb=" N LYS A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 262 Processing helix chain 'A' and resid 263 through 269 removed outlier: 3.614A pdb=" N CYS A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 removed outlier: 3.574A pdb=" N ASP A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 removed outlier: 4.011A pdb=" N VAL A 289 " --> pdb=" O LYS A 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 31 removed outlier: 3.720A pdb=" N ARG B 30 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR B 31 " --> pdb=" O LEU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 46 removed outlier: 3.694A pdb=" N GLY B 46 " --> pdb=" O THR B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 59 Processing helix chain 'B' and resid 63 through 67 removed outlier: 3.696A pdb=" N ARG B 66 " --> pdb=" O PRO B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 100 Processing helix chain 'B' and resid 102 through 116 removed outlier: 3.607A pdb=" N LYS B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 136 removed outlier: 4.479A pdb=" N ASP B 136 " --> pdb=" O GLN B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 155 Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'B' and resid 212 through 222 Processing helix chain 'B' and resid 241 through 251 removed outlier: 3.698A pdb=" N LYS B 247 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 262 Processing helix chain 'B' and resid 263 through 269 removed outlier: 3.617A pdb=" N CYS B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 282 removed outlier: 3.570A pdb=" N ASP B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 removed outlier: 4.013A pdb=" N VAL B 289 " --> pdb=" O LYS B 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 31 removed outlier: 3.667A pdb=" N ARG C 30 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR C 31 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 46 removed outlier: 3.702A pdb=" N GLY C 46 " --> pdb=" O THR C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 59 Processing helix chain 'C' and resid 63 through 67 removed outlier: 3.697A pdb=" N ARG C 66 " --> pdb=" O PRO C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 100 Processing helix chain 'C' and resid 102 through 116 removed outlier: 3.616A pdb=" N LYS C 116 " --> pdb=" O PHE C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 136 removed outlier: 4.510A pdb=" N ASP C 136 " --> pdb=" O GLN C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 155 Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'C' and resid 212 through 222 Processing helix chain 'C' and resid 241 through 251 removed outlier: 3.688A pdb=" N LYS C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG C 251 " --> pdb=" O LYS C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 262 Processing helix chain 'C' and resid 263 through 269 removed outlier: 3.610A pdb=" N CYS C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 282 removed outlier: 3.574A pdb=" N ASP C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 294 removed outlier: 4.023A pdb=" N VAL C 289 " --> pdb=" O LYS C 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 removed outlier: 3.723A pdb=" N ARG D 30 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR D 31 " --> pdb=" O LEU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 46 removed outlier: 3.699A pdb=" N GLY D 46 " --> pdb=" O THR D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 59 Processing helix chain 'D' and resid 63 through 67 removed outlier: 3.695A pdb=" N ARG D 66 " --> pdb=" O PRO D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 100 Processing helix chain 'D' and resid 102 through 114 Processing helix chain 'D' and resid 124 through 136 removed outlier: 4.453A pdb=" N ASP D 136 " --> pdb=" O GLN D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 155 Processing helix chain 'D' and resid 187 through 191 Processing helix chain 'D' and resid 212 through 222 Processing helix chain 'D' and resid 241 through 251 removed outlier: 3.695A pdb=" N LYS D 247 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 262 Processing helix chain 'D' and resid 263 through 269 removed outlier: 3.617A pdb=" N CYS D 269 " --> pdb=" O LEU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 282 removed outlier: 3.566A pdb=" N ASP D 275 " --> pdb=" O SER D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 294 removed outlier: 4.009A pdb=" N VAL D 289 " --> pdb=" O LYS D 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 31 removed outlier: 3.670A pdb=" N ARG E 30 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR E 31 " --> pdb=" O LEU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 46 removed outlier: 3.688A pdb=" N GLY E 46 " --> pdb=" O THR E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 59 Processing helix chain 'E' and resid 63 through 67 removed outlier: 3.699A pdb=" N ARG E 66 " --> pdb=" O PRO E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 100 Processing helix chain 'E' and resid 102 through 116 removed outlier: 3.549A pdb=" N LYS E 116 " --> pdb=" O PHE E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 136 removed outlier: 4.441A pdb=" N ASP E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 155 Processing helix chain 'E' and resid 187 through 191 Processing helix chain 'E' and resid 212 through 222 Processing helix chain 'E' and resid 241 through 251 removed outlier: 3.691A pdb=" N LYS E 247 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 262 Processing helix chain 'E' and resid 263 through 269 removed outlier: 3.602A pdb=" N CYS E 269 " --> pdb=" O LEU E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 282 removed outlier: 3.572A pdb=" N ASP E 275 " --> pdb=" O SER E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 294 removed outlier: 4.012A pdb=" N VAL E 289 " --> pdb=" O LYS E 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 31 removed outlier: 3.669A pdb=" N ARG F 30 " --> pdb=" O ALA F 27 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR F 31 " --> pdb=" O LEU F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 46 removed outlier: 3.702A pdb=" N GLY F 46 " --> pdb=" O THR F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 59 Processing helix chain 'F' and resid 63 through 67 removed outlier: 3.697A pdb=" N ARG F 66 " --> pdb=" O PRO F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 100 Processing helix chain 'F' and resid 102 through 116 removed outlier: 3.617A pdb=" N LYS F 116 " --> pdb=" O PHE F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 136 removed outlier: 4.467A pdb=" N ASP F 136 " --> pdb=" O GLN F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 155 Processing helix chain 'F' and resid 187 through 191 Processing helix chain 'F' and resid 212 through 222 Processing helix chain 'F' and resid 241 through 251 removed outlier: 3.693A pdb=" N LYS F 247 " --> pdb=" O ALA F 243 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG F 251 " --> pdb=" O LYS F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 262 Processing helix chain 'F' and resid 263 through 269 removed outlier: 3.616A pdb=" N CYS F 269 " --> pdb=" O LEU F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 282 removed outlier: 3.571A pdb=" N ASP F 275 " --> pdb=" O SER F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 294 removed outlier: 4.011A pdb=" N VAL F 289 " --> pdb=" O LYS F 285 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 31 removed outlier: 3.667A pdb=" N ARG G 30 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR G 31 " --> pdb=" O LEU G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 46 removed outlier: 3.698A pdb=" N GLY G 46 " --> pdb=" O THR G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 59 Processing helix chain 'G' and resid 63 through 67 removed outlier: 3.696A pdb=" N ARG G 66 " --> pdb=" O PRO G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 100 Processing helix chain 'G' and resid 102 through 116 removed outlier: 3.605A pdb=" N LYS G 116 " --> pdb=" O PHE G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 136 removed outlier: 4.469A pdb=" N ASP G 136 " --> pdb=" O GLN G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 155 Processing helix chain 'G' and resid 187 through 191 Processing helix chain 'G' and resid 212 through 222 Processing helix chain 'G' and resid 241 through 251 removed outlier: 3.684A pdb=" N LYS G 247 " --> pdb=" O ALA G 243 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG G 251 " --> pdb=" O LYS G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 262 Processing helix chain 'G' and resid 263 through 269 removed outlier: 3.611A pdb=" N CYS G 269 " --> pdb=" O LEU G 265 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 282 removed outlier: 3.576A pdb=" N ASP G 275 " --> pdb=" O SER G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 285 through 294 removed outlier: 4.022A pdb=" N VAL G 289 " --> pdb=" O LYS G 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 31 removed outlier: 3.722A pdb=" N ARG H 30 " --> pdb=" O ALA H 27 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR H 31 " --> pdb=" O LEU H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 46 removed outlier: 3.679A pdb=" N GLY H 46 " --> pdb=" O THR H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 59 Processing helix chain 'H' and resid 63 through 67 removed outlier: 3.696A pdb=" N ARG H 66 " --> pdb=" O PRO H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 100 Processing helix chain 'H' and resid 102 through 116 removed outlier: 3.559A pdb=" N LYS H 116 " --> pdb=" O PHE H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 136 removed outlier: 4.492A pdb=" N ASP H 136 " --> pdb=" O GLN H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 155 Processing helix chain 'H' and resid 187 through 191 Processing helix chain 'H' and resid 212 through 222 Processing helix chain 'H' and resid 241 through 251 removed outlier: 3.696A pdb=" N LYS H 247 " --> pdb=" O ALA H 243 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG H 251 " --> pdb=" O LYS H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 253 through 262 Processing helix chain 'H' and resid 263 through 269 removed outlier: 3.618A pdb=" N CYS H 269 " --> pdb=" O LEU H 265 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 282 removed outlier: 3.570A pdb=" N ASP H 275 " --> pdb=" O SER H 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 294 removed outlier: 4.012A pdb=" N VAL H 289 " --> pdb=" O LYS H 285 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 3.605A pdb=" N ALA A 122 " --> pdb=" O VAL A 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.608A pdb=" N VAL A 12 " --> pdb=" O MET A 19 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET A 19 " --> pdb=" O VAL A 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 5.990A pdb=" N VAL A 171 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLU A 182 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG A 173 " --> pdb=" O ILE A 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 225 through 226 removed outlier: 3.507A pdb=" N VAL A 237 " --> pdb=" O PHE A 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.610A pdb=" N VAL B 12 " --> pdb=" O MET B 19 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET B 19 " --> pdb=" O VAL B 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 170 through 174 removed outlier: 6.017A pdb=" N VAL B 171 " --> pdb=" O GLU B 182 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLU B 182 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG B 173 " --> pdb=" O ILE B 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 225 through 226 removed outlier: 3.505A pdb=" N VAL B 237 " --> pdb=" O PHE B 225 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.608A pdb=" N VAL C 12 " --> pdb=" O MET C 19 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET C 19 " --> pdb=" O VAL C 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 170 through 174 removed outlier: 6.015A pdb=" N VAL C 171 " --> pdb=" O GLU C 182 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLU C 182 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG C 173 " --> pdb=" O ILE C 180 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 225 through 226 removed outlier: 3.504A pdb=" N VAL C 237 " --> pdb=" O PHE C 225 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 4 through 5 removed outlier: 3.602A pdb=" N ALA D 122 " --> pdb=" O VAL D 5 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.609A pdb=" N VAL D 12 " --> pdb=" O MET D 19 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET D 19 " --> pdb=" O VAL D 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 170 through 174 removed outlier: 6.007A pdb=" N VAL D 171 " --> pdb=" O GLU D 182 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLU D 182 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG D 173 " --> pdb=" O ILE D 180 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 225 through 226 removed outlier: 3.525A pdb=" N VAL D 237 " --> pdb=" O PHE D 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.611A pdb=" N VAL E 12 " --> pdb=" O MET E 19 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET E 19 " --> pdb=" O VAL E 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 170 through 174 removed outlier: 6.014A pdb=" N VAL E 171 " --> pdb=" O GLU E 182 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLU E 182 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG E 173 " --> pdb=" O ILE E 180 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 225 through 226 removed outlier: 3.500A pdb=" N VAL E 237 " --> pdb=" O PHE E 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 4 through 5 removed outlier: 3.589A pdb=" N ALA F 122 " --> pdb=" O VAL F 5 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.584A pdb=" N VAL F 12 " --> pdb=" O MET F 19 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET F 19 " --> pdb=" O VAL F 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'F' and resid 170 through 174 removed outlier: 6.010A pdb=" N VAL F 171 " --> pdb=" O GLU F 182 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLU F 182 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG F 173 " --> pdb=" O ILE F 180 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 225 through 226 removed outlier: 3.501A pdb=" N VAL F 237 " --> pdb=" O PHE F 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 4 through 5 removed outlier: 3.595A pdb=" N ALA G 122 " --> pdb=" O VAL G 5 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.609A pdb=" N VAL G 12 " --> pdb=" O MET G 19 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET G 19 " --> pdb=" O VAL G 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'G' and resid 170 through 174 removed outlier: 6.010A pdb=" N VAL G 171 " --> pdb=" O GLU G 182 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU G 182 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG G 173 " --> pdb=" O ILE G 180 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 225 through 226 removed outlier: 3.504A pdb=" N VAL G 237 " --> pdb=" O PHE G 225 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 4 through 5 removed outlier: 3.601A pdb=" N ALA H 122 " --> pdb=" O VAL H 5 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.610A pdb=" N VAL H 12 " --> pdb=" O MET H 19 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET H 19 " --> pdb=" O VAL H 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'H' and resid 170 through 174 removed outlier: 6.017A pdb=" N VAL H 171 " --> pdb=" O GLU H 182 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU H 182 " --> pdb=" O VAL H 171 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG H 173 " --> pdb=" O ILE H 180 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 225 through 226 removed outlier: 3.506A pdb=" N VAL H 237 " --> pdb=" O PHE H 225 " (cutoff:3.500A) 742 hydrogen bonds defined for protein. 2106 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.83 Time building geometry restraints manager: 4.95 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: 0.00 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.180 Process input model: 37.280 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17376 Z= 0.161 Angle : 0.572 11.995 23672 Z= 0.290 Chirality : 0.036 0.135 2792 Planarity : 0.004 0.045 3016 Dihedral : 17.067 83.068 5808 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.06 % Allowed : 35.82 % Favored : 64.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.18), residues: 2360 helix: 1.08 (0.16), residues: 1152 sheet: -1.26 (0.48), residues: 160 loop : -1.91 (0.17), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 157 HIS 0.001 0.000 HIS A 229 PHE 0.005 0.001 PHE D 152 TYR 0.024 0.001 TYR A 189 ARG 0.011 0.001 ARG E 173 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 2.056 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 263 average time/residue: 0.3005 time to fit residues: 118.1896 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 : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 205 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.3980 chunk 175 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 60 optimal weight: 0.0670 chunk 118 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 181 optimal weight: 0.0170 chunk 70 optimal weight: 0.6980 chunk 110 optimal weight: 7.9990 chunk 135 optimal weight: 9.9990 chunk 210 optimal weight: 8.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 142 HIS E 142 HIS G 142 HIS H 142 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17376 Z= 0.127 Angle : 0.494 8.156 23672 Z= 0.252 Chirality : 0.035 0.133 2792 Planarity : 0.004 0.041 3016 Dihedral : 3.845 41.309 2498 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.66 % Allowed : 30.25 % Favored : 65.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.18), residues: 2360 helix: 0.99 (0.16), residues: 1208 sheet: 1.05 (1.02), residues: 48 loop : -1.83 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 157 HIS 0.002 0.000 HIS D 233 PHE 0.005 0.001 PHE H 130 TYR 0.022 0.001 TYR A 189 ARG 0.003 0.000 ARG F 173 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 276 time to evaluate : 1.813 Fit side-chains REVERT: A 149 MET cc_start: 0.8814 (tmm) cc_final: 0.8089 (tmm) REVERT: B 149 MET cc_start: 0.8807 (tmm) cc_final: 0.8187 (tmm) REVERT: C 149 MET cc_start: 0.8791 (tmm) cc_final: 0.8166 (tmm) REVERT: F 149 MET cc_start: 0.8388 (tmm) cc_final: 0.8103 (tmm) REVERT: G 149 MET cc_start: 0.8784 (tmm) cc_final: 0.8164 (tmm) REVERT: H 149 MET cc_start: 0.8773 (tpt) cc_final: 0.8444 (tmm) outliers start: 72 outliers final: 16 residues processed: 326 average time/residue: 0.2941 time to fit residues: 143.6056 Evaluate side-chains 269 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 253 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 181 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 211 optimal weight: 0.4980 chunk 228 optimal weight: 8.9990 chunk 187 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 169 optimal weight: 8.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 142 HIS E 142 HIS G 142 HIS H 142 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17376 Z= 0.194 Angle : 0.495 8.024 23672 Z= 0.255 Chirality : 0.036 0.131 2792 Planarity : 0.005 0.039 3016 Dihedral : 3.915 21.740 2498 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.08 % Allowed : 28.43 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.18), residues: 2360 helix: 1.28 (0.16), residues: 1216 sheet: -1.75 (0.45), residues: 160 loop : -1.81 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 95 HIS 0.002 0.001 HIS A 229 PHE 0.005 0.001 PHE E 190 TYR 0.022 0.002 TYR F 189 ARG 0.008 0.001 ARG F 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 293 time to evaluate : 1.980 Fit side-chains REVERT: A 149 MET cc_start: 0.8794 (tmm) cc_final: 0.7890 (tmm) REVERT: A 249 TYR cc_start: 0.7804 (OUTLIER) cc_final: 0.6827 (m-10) REVERT: B 96 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8853 (tt) REVERT: B 150 ASN cc_start: 0.8687 (t0) cc_final: 0.7797 (m110) REVERT: B 249 TYR cc_start: 0.7838 (OUTLIER) cc_final: 0.6885 (m-10) REVERT: C 96 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8831 (tt) REVERT: C 149 MET cc_start: 0.8847 (tmm) cc_final: 0.8624 (tmm) REVERT: C 249 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.6834 (m-10) REVERT: D 249 TYR cc_start: 0.7821 (OUTLIER) cc_final: 0.6866 (m-10) REVERT: E 249 TYR cc_start: 0.7831 (OUTLIER) cc_final: 0.6868 (m-10) REVERT: F 249 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.6872 (m-10) REVERT: G 149 MET cc_start: 0.8848 (tmm) cc_final: 0.8618 (tmm) REVERT: G 249 TYR cc_start: 0.7752 (OUTLIER) cc_final: 0.6800 (m-10) REVERT: H 149 MET cc_start: 0.8753 (tpt) cc_final: 0.8452 (tmm) REVERT: H 249 TYR cc_start: 0.7819 (OUTLIER) cc_final: 0.6887 (m-10) outliers start: 63 outliers final: 27 residues processed: 336 average time/residue: 0.2791 time to fit residues: 142.1876 Evaluate side-chains 304 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 267 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 249 TYR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 249 TYR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 249 TYR Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 249 TYR Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 249 TYR Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 249 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 0.4980 chunk 158 optimal weight: 4.9990 chunk 109 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 211 optimal weight: 0.9980 chunk 224 optimal weight: 6.9990 chunk 110 optimal weight: 20.0000 chunk 200 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 142 HIS E 142 HIS G 142 HIS H 142 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1370 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= 0.219 Angle : 0.504 6.725 23672 Z= 0.261 Chirality : 0.037 0.135 2792 Planarity : 0.004 0.039 3016 Dihedral : 4.012 15.209 2496 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 6.74 % Allowed : 26.88 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.18), residues: 2360 helix: 1.32 (0.16), residues: 1216 sheet: -2.14 (0.42), residues: 160 loop : -1.91 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 95 HIS 0.002 0.001 HIS E 229 PHE 0.005 0.001 PHE E 190 TYR 0.007 0.001 TYR E 228 ARG 0.009 0.001 ARG E 173 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 285 time to evaluate : 1.834 Fit side-chains REVERT: A 96 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8884 (tt) REVERT: A 149 MET cc_start: 0.8775 (tmm) cc_final: 0.7776 (tmm) REVERT: A 249 TYR cc_start: 0.7725 (OUTLIER) cc_final: 0.6790 (m-10) REVERT: B 96 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8882 (tt) REVERT: B 132 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8661 (tt0) REVERT: B 149 MET cc_start: 0.8852 (tmm) cc_final: 0.8215 (tmm) REVERT: B 249 TYR cc_start: 0.7744 (OUTLIER) cc_final: 0.6810 (m-10) REVERT: C 96 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8879 (tt) REVERT: C 149 MET cc_start: 0.8853 (tmm) cc_final: 0.8550 (tmm) REVERT: C 249 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.6792 (m-10) REVERT: D 96 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8855 (tt) REVERT: D 132 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8769 (tt0) REVERT: D 149 MET cc_start: 0.8829 (tpt) cc_final: 0.8461 (tmm) REVERT: D 249 TYR cc_start: 0.7731 (OUTLIER) cc_final: 0.6795 (m-10) REVERT: E 132 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8688 (tt0) REVERT: E 149 MET cc_start: 0.8835 (tpt) cc_final: 0.8459 (tmm) REVERT: E 249 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.6725 (m-10) REVERT: F 96 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8882 (tt) REVERT: F 149 MET cc_start: 0.8749 (tpt) cc_final: 0.8398 (tmm) REVERT: F 249 TYR cc_start: 0.7719 (OUTLIER) cc_final: 0.6793 (m-10) REVERT: G 96 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8853 (tt) REVERT: G 149 MET cc_start: 0.8856 (tmm) cc_final: 0.8557 (tmm) REVERT: G 249 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.6793 (m-10) REVERT: H 96 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8853 (tt) REVERT: H 149 MET cc_start: 0.8757 (tpt) cc_final: 0.8496 (tmm) REVERT: H 249 TYR cc_start: 0.7737 (OUTLIER) cc_final: 0.6802 (m-10) outliers start: 104 outliers final: 40 residues processed: 362 average time/residue: 0.2589 time to fit residues: 145.0404 Evaluate side-chains 338 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 280 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 249 TYR Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 249 TYR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 249 TYR Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 249 TYR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 249 TYR Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 186 VAL 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 186 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 166 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 191 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 201 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 142 HIS G 142 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 17376 Z= 0.312 Angle : 0.551 5.841 23672 Z= 0.290 Chirality : 0.038 0.136 2792 Planarity : 0.005 0.038 3016 Dihedral : 4.382 16.267 2496 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 6.99 % Allowed : 27.33 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.18), residues: 2360 helix: 1.41 (0.16), residues: 1184 sheet: -2.65 (0.41), residues: 160 loop : -2.08 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 95 HIS 0.003 0.001 HIS A 229 PHE 0.009 0.001 PHE A 190 TYR 0.025 0.002 TYR D 189 ARG 0.011 0.001 ARG D 173 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 293 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.8845 (tmm) cc_final: 0.7799 (tmm) REVERT: B 96 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8890 (tt) REVERT: B 132 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.8727 (tt0) REVERT: B 150 ASN cc_start: 0.8801 (t0) cc_final: 0.7828 (m110) REVERT: C 96 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8873 (tt) REVERT: C 149 MET cc_start: 0.8895 (tmm) cc_final: 0.8503 (tmm) REVERT: D 132 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8831 (tt0) REVERT: D 149 MET cc_start: 0.8797 (tpt) cc_final: 0.8491 (tmm) REVERT: E 132 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8758 (tt0) REVERT: E 149 MET cc_start: 0.8800 (tpt) cc_final: 0.8454 (tmm) REVERT: F 149 MET cc_start: 0.8799 (tpt) cc_final: 0.8458 (tmm) REVERT: G 149 MET cc_start: 0.8894 (tmm) cc_final: 0.8511 (tmm) REVERT: H 149 MET cc_start: 0.8770 (tpt) cc_final: 0.8495 (tmm) outliers start: 108 outliers final: 56 residues processed: 366 average time/residue: 0.2889 time to fit residues: 158.3072 Evaluate side-chains 346 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 285 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 249 TYR Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 249 TYR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 249 TYR Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 249 TYR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 249 TYR Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 249 TYR Chi-restraints excluded: chain H residue 286 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 5.9990 chunk 201 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 131 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 224 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1600 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= 0.197 Angle : 0.502 6.017 23672 Z= 0.263 Chirality : 0.036 0.136 2792 Planarity : 0.005 0.040 3016 Dihedral : 4.103 15.315 2496 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 5.70 % Allowed : 30.12 % Favored : 64.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.18), residues: 2360 helix: 1.48 (0.16), residues: 1184 sheet: -2.63 (0.41), residues: 160 loop : -1.95 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 95 HIS 0.002 0.001 HIS D 229 PHE 0.005 0.001 PHE F 163 TYR 0.007 0.001 TYR H 228 ARG 0.010 0.001 ARG E 173 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 295 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.8784 (tmm) cc_final: 0.7761 (tmm) REVERT: B 96 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8900 (tt) REVERT: B 132 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8647 (tt0) REVERT: B 149 MET cc_start: 0.8809 (tmm) cc_final: 0.8189 (tmm) REVERT: C 96 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8880 (tt) REVERT: C 149 MET cc_start: 0.8910 (tmm) cc_final: 0.8474 (tmm) REVERT: C 150 ASN cc_start: 0.7872 (m110) cc_final: 0.7331 (m110) REVERT: D 132 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.8740 (tt0) REVERT: D 149 MET cc_start: 0.8789 (tpt) cc_final: 0.8440 (tmm) REVERT: E 132 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8656 (tt0) REVERT: E 149 MET cc_start: 0.8791 (tpt) cc_final: 0.8424 (tmm) REVERT: F 149 MET cc_start: 0.8766 (tpt) cc_final: 0.8387 (tmm) REVERT: F 150 ASN cc_start: 0.7917 (m110) cc_final: 0.6965 (m110) REVERT: G 149 MET cc_start: 0.8898 (tmm) cc_final: 0.8477 (tmm) REVERT: G 150 ASN cc_start: 0.7885 (m110) cc_final: 0.7343 (m110) REVERT: H 150 ASN cc_start: 0.8842 (t0) cc_final: 0.7765 (m110) outliers start: 88 outliers final: 70 residues processed: 354 average time/residue: 0.2693 time to fit residues: 145.9038 Evaluate side-chains 362 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 287 time to evaluate : 1.894 ------------------------------------------------------------------------------- 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 127 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 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 132 GLN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 249 TYR Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 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 100 LEU Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 249 TYR Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 249 TYR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain G residue 59 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 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 172 VAL Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 249 TYR Chi-restraints excluded: chain H residue 286 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 chunk 188 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 223 optimal weight: 9.9990 chunk 139 optimal weight: 0.0050 chunk 136 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 overall best weight: 3.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 17376 Z= 0.268 Angle : 0.541 8.903 23672 Z= 0.279 Chirality : 0.037 0.144 2792 Planarity : 0.005 0.045 3016 Dihedral : 4.265 15.819 2496 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 5.76 % Allowed : 30.96 % Favored : 63.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.18), residues: 2360 helix: 1.45 (0.16), residues: 1184 sheet: -3.05 (0.38), residues: 160 loop : -2.12 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 95 HIS 0.003 0.001 HIS G 229 PHE 0.006 0.001 PHE A 190 TYR 0.022 0.002 TYR E 189 ARG 0.011 0.001 ARG D 173 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 300 time to evaluate : 2.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.8822 (tmm) cc_final: 0.7700 (tmm) REVERT: B 96 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8871 (tt) REVERT: B 132 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8669 (tt0) REVERT: C 96 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8876 (tt) REVERT: C 149 MET cc_start: 0.8919 (tmm) cc_final: 0.8456 (tmm) REVERT: C 150 ASN cc_start: 0.7919 (m110) cc_final: 0.7350 (m110) REVERT: D 132 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.8794 (tt0) REVERT: D 149 MET cc_start: 0.8793 (tpt) cc_final: 0.8438 (tmm) REVERT: E 132 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8734 (tt0) REVERT: E 149 MET cc_start: 0.8800 (tpt) cc_final: 0.8443 (tmm) REVERT: E 268 GLN cc_start: 0.8805 (tp40) cc_final: 0.8581 (tp-100) REVERT: F 149 MET cc_start: 0.8782 (tpt) cc_final: 0.8373 (tmm) REVERT: F 150 ASN cc_start: 0.7942 (m110) cc_final: 0.6977 (m110) REVERT: F 268 GLN cc_start: 0.8812 (tp40) cc_final: 0.8578 (tp-100) REVERT: G 149 MET cc_start: 0.8909 (tmm) cc_final: 0.8447 (tmm) REVERT: G 150 ASN cc_start: 0.7924 (m110) cc_final: 0.7355 (m110) REVERT: H 149 MET cc_start: 0.8842 (tmm) cc_final: 0.8172 (tmm) outliers start: 89 outliers final: 77 residues processed: 365 average time/residue: 0.2730 time to fit residues: 152.1359 Evaluate side-chains 369 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 287 time to evaluate : 2.011 ------------------------------------------------------------------------------- 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 127 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 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 132 GLN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 249 TYR Chi-restraints excluded: chain 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 132 GLN Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 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 100 LEU Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 249 TYR Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 249 TYR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 59 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 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 172 VAL Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 249 TYR Chi-restraints excluded: chain H residue 286 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 214 optimal weight: 5.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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 G 268 GLN H 268 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 17376 Z= 0.248 Angle : 0.551 9.172 23672 Z= 0.281 Chirality : 0.037 0.139 2792 Planarity : 0.005 0.050 3016 Dihedral : 4.242 15.402 2496 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 5.89 % Allowed : 31.61 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.18), residues: 2360 helix: 1.40 (0.16), residues: 1184 sheet: -3.28 (0.36), residues: 160 loop : -2.13 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 95 HIS 0.002 0.001 HIS B 229 PHE 0.006 0.001 PHE F 163 TYR 0.007 0.001 TYR D 228 ARG 0.013 0.001 ARG D 173 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 298 time to evaluate : 2.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.8810 (tmm) cc_final: 0.7741 (tmm) REVERT: B 96 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8894 (tt) REVERT: B 132 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8667 (tt0) REVERT: B 149 MET cc_start: 0.8812 (tmm) cc_final: 0.8188 (tmm) REVERT: C 91 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.9022 (tp) REVERT: C 96 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8885 (tt) REVERT: C 149 MET cc_start: 0.8905 (tmm) cc_final: 0.8422 (tmm) REVERT: C 150 ASN cc_start: 0.7928 (m110) cc_final: 0.7350 (m110) REVERT: D 132 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8793 (tt0) REVERT: D 149 MET cc_start: 0.8782 (tpt) cc_final: 0.8412 (tmm) REVERT: E 132 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8664 (tt0) REVERT: E 149 MET cc_start: 0.8791 (tpt) cc_final: 0.8411 (tmm) REVERT: E 268 GLN cc_start: 0.8815 (tp40) cc_final: 0.8575 (tp-100) REVERT: F 91 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9026 (tp) REVERT: F 149 MET cc_start: 0.8774 (tpt) cc_final: 0.8368 (tmm) REVERT: F 150 ASN cc_start: 0.7944 (m110) cc_final: 0.6976 (m110) REVERT: G 91 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9033 (tp) REVERT: G 149 MET cc_start: 0.8903 (tmm) cc_final: 0.8429 (tmm) REVERT: G 150 ASN cc_start: 0.7937 (m110) cc_final: 0.7359 (m110) REVERT: H 149 MET cc_start: 0.8840 (tmm) cc_final: 0.8184 (tmm) outliers start: 91 outliers final: 81 residues processed: 362 average time/residue: 0.2699 time to fit residues: 149.3762 Evaluate side-chains 381 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 292 time to evaluate : 2.043 ------------------------------------------------------------------------------- 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 127 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 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 132 GLN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 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 186 VAL 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 132 GLN Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 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 100 LEU Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 186 VAL 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 100 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 249 TYR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain G residue 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 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 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 172 VAL Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 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 195 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 214 optimal weight: 7.9990 chunk 125 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 163 optimal weight: 0.7980 chunk 63 optimal weight: 0.4980 chunk 188 optimal weight: 9.9990 chunk 197 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN C 268 GLN F 268 GLN G 268 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1755 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= 0.172 Angle : 0.530 9.282 23672 Z= 0.266 Chirality : 0.036 0.156 2792 Planarity : 0.005 0.051 3016 Dihedral : 3.973 14.803 2496 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 5.44 % Allowed : 32.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.18), residues: 2360 helix: 1.42 (0.16), residues: 1184 sheet: -3.05 (0.38), residues: 160 loop : -1.97 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 95 HIS 0.002 0.000 HIS F 229 PHE 0.005 0.001 PHE B 163 TYR 0.031 0.002 TYR D 189 ARG 0.012 0.001 ARG D 173 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 295 time to evaluate : 1.969 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: 0.9248 (OUTLIER) cc_final: 0.9021 (tp) REVERT: A 132 GLN cc_start: 0.9174 (tp40) cc_final: 0.8679 (tt0) REVERT: A 149 MET cc_start: 0.8810 (tmm) cc_final: 0.7780 (tmm) REVERT: B 96 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8885 (tt) REVERT: B 132 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8670 (tt0) REVERT: B 149 MET cc_start: 0.8796 (tmm) cc_final: 0.8155 (tmm) REVERT: C 96 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8881 (tt) REVERT: C 149 MET cc_start: 0.8879 (tmm) cc_final: 0.8414 (tmm) REVERT: C 150 ASN cc_start: 0.7906 (m110) cc_final: 0.7335 (m110) REVERT: D 149 MET cc_start: 0.8757 (tpt) cc_final: 0.8363 (tmm) REVERT: D 268 GLN cc_start: 0.8794 (tp40) cc_final: 0.8589 (tp-100) REVERT: E 132 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8678 (tt0) REVERT: E 149 MET cc_start: 0.8767 (tpt) cc_final: 0.8391 (tmm) REVERT: E 268 GLN cc_start: 0.8809 (tp40) cc_final: 0.8583 (tp-100) REVERT: F 149 MET cc_start: 0.8734 (tpt) cc_final: 0.8386 (tmm) REVERT: F 150 ASN cc_start: 0.7948 (m110) cc_final: 0.6987 (m110) REVERT: G 149 MET cc_start: 0.8872 (tmm) cc_final: 0.8416 (tmm) REVERT: G 150 ASN cc_start: 0.7914 (m110) cc_final: 0.7345 (m110) REVERT: H 149 MET cc_start: 0.8827 (tmm) cc_final: 0.8146 (tmm) outliers start: 84 outliers final: 78 residues processed: 355 average time/residue: 0.2718 time to fit residues: 148.5076 Evaluate side-chains 361 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 278 time to evaluate : 2.039 ------------------------------------------------------------------------------- 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 100 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 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 59 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 186 VAL 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 93 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 249 TYR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 186 VAL 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 100 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 249 TYR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 249 TYR Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 186 VAL 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 220 optimal weight: 0.8980 chunk 134 optimal weight: 0.0870 chunk 104 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 231 optimal weight: 0.0370 chunk 212 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 overall best weight: 0.9838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 GLN H 268 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17376 Z= 0.140 Angle : 0.528 10.091 23672 Z= 0.258 Chirality : 0.036 0.145 2792 Planarity : 0.004 0.037 3016 Dihedral : 3.746 14.622 2496 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.95 % Allowed : 33.29 % Favored : 62.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.18), residues: 2360 helix: 1.35 (0.16), residues: 1216 sheet: -2.23 (0.69), residues: 48 loop : -2.06 (0.17), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 95 HIS 0.001 0.000 HIS D 229 PHE 0.009 0.001 PHE E 117 TYR 0.007 0.001 TYR F 228 ARG 0.001 0.000 ARG G 173 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 286 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.9143 (tp40) cc_final: 0.8660 (tt0) REVERT: A 149 MET cc_start: 0.8783 (tmm) cc_final: 0.7782 (tmm) REVERT: B 96 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8888 (tt) REVERT: B 132 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8682 (tt0) REVERT: B 149 MET cc_start: 0.8824 (tmm) cc_final: 0.8160 (tmm) REVERT: C 96 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8879 (tt) REVERT: C 149 MET cc_start: 0.8851 (tmm) cc_final: 0.8394 (tmm) REVERT: C 150 ASN cc_start: 0.7879 (m110) cc_final: 0.7329 (m110) REVERT: D 132 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8734 (tt0) REVERT: D 149 MET cc_start: 0.8706 (tpt) cc_final: 0.8405 (tmm) REVERT: D 268 GLN cc_start: 0.8753 (tp40) cc_final: 0.8534 (tp-100) REVERT: E 132 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8695 (tt0) REVERT: E 149 MET cc_start: 0.8745 (tpt) cc_final: 0.8407 (tmm) REVERT: E 268 GLN cc_start: 0.8779 (tp40) cc_final: 0.8545 (tp-100) REVERT: F 149 MET cc_start: 0.8732 (tpt) cc_final: 0.8368 (tmm) REVERT: F 150 ASN cc_start: 0.7908 (m110) cc_final: 0.6898 (m110) REVERT: G 149 MET cc_start: 0.8865 (tmm) cc_final: 0.8399 (tmm) REVERT: G 150 ASN cc_start: 0.7889 (m110) cc_final: 0.7340 (m110) REVERT: H 149 MET cc_start: 0.8844 (tmm) cc_final: 0.8141 (tmm) outliers start: 61 outliers final: 54 residues processed: 321 average time/residue: 0.2463 time to fit residues: 125.4929 Evaluate side-chains 336 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 277 time to evaluate : 1.894 ------------------------------------------------------------------------------- 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 127 LEU 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 132 GLN 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 59 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain 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 132 GLN 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 132 GLN 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 100 LEU Chi-restraints excluded: chain F residue 127 LEU 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 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 100 LEU 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 196 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 chunk 169 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 184 optimal weight: 0.9980 chunk 77 optimal weight: 0.2980 chunk 189 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN C 268 GLN F 268 GLN G 268 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.139045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.095203 restraints weight = 34173.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.098485 restraints weight = 20380.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.100812 restraints weight = 14985.428| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 17376 Z= 0.316 Angle : 0.588 9.222 23672 Z= 0.297 Chirality : 0.038 0.141 2792 Planarity : 0.004 0.040 3016 Dihedral : 4.297 15.869 2496 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 5.51 % Allowed : 32.25 % Favored : 62.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.18), residues: 2360 helix: 1.34 (0.16), residues: 1192 sheet: -3.38 (0.35), residues: 160 loop : -2.09 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 95 HIS 0.003 0.001 HIS B 229 PHE 0.016 0.001 PHE H 117 TYR 0.026 0.002 TYR F 189 ARG 0.003 0.000 ARG C 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3317.48 seconds wall clock time: 61 minutes 32.06 seconds (3692.06 seconds total)