Starting phenix.real_space_refine on Thu Feb 5 18:42:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e62_47547/02_2026/9e62_47547.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e62_47547/02_2026/9e62_47547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e62_47547/02_2026/9e62_47547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e62_47547/02_2026/9e62_47547.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e62_47547/02_2026/9e62_47547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e62_47547/02_2026/9e62_47547.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.037 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: 5 Type Number sf(0) Gaussians P 35 5.49 5 S 70 5.16 5 C 12488 2.51 5 N 2982 2.21 5 O 3444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19019 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2509 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 8, 'TRANS': 322} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "G" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2509 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 8, 'TRANS': 322} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "A" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 208 Unusual residues: {'PTY': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Chain: "G" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 208 Unusual residues: {'PTY': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 3.38, per 1000 atoms: 0.18 Number of scatterers: 19019 At special positions: 0 Unit cell: (109.22, 107.5, 141.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 P 35 15.00 O 3444 8.00 N 2982 7.00 C 12488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 82 " - pdb=" SG CYS B 82 " distance=0.00 Simple disulfide: pdb=" SG CYS B 292 " - pdb=" SG CYS B 292 " distance=0.00 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 768.6 milliseconds 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4312 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 15 sheets defined 62.2% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.542A pdb=" N LEU A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 32 removed outlier: 4.538A pdb=" N PHE A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N CYS A 20 " --> pdb=" O ILE A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 68 removed outlier: 3.564A pdb=" N ILE A 65 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 109 removed outlier: 4.151A pdb=" N ILE A 78 " --> pdb=" O THR A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 134 Processing helix chain 'A' and resid 143 through 160 Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 219 through 223 Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 244 through 249 removed outlier: 3.746A pdb=" N ALA A 248 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ALA A 249 " --> pdb=" O GLU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 264 Processing helix chain 'A' and resid 298 through 320 removed outlier: 3.579A pdb=" N HIS A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 13 removed outlier: 3.542A pdb=" N LEU B 13 " --> pdb=" O ASN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 32 removed outlier: 4.539A pdb=" N PHE B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N CYS B 20 " --> pdb=" O ILE B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 68 removed outlier: 3.564A pdb=" N ILE B 65 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 109 removed outlier: 4.151A pdb=" N ILE B 78 " --> pdb=" O THR B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 134 Processing helix chain 'B' and resid 143 through 160 Processing helix chain 'B' and resid 160 through 176 Processing helix chain 'B' and resid 219 through 223 Processing helix chain 'B' and resid 229 through 232 Processing helix chain 'B' and resid 244 through 249 removed outlier: 3.746A pdb=" N ALA B 248 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ALA B 249 " --> pdb=" O GLU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 264 Processing helix chain 'B' and resid 298 through 320 removed outlier: 3.579A pdb=" N HIS B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 13 removed outlier: 3.543A pdb=" N LEU C 13 " --> pdb=" O ASN C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 32 removed outlier: 4.538A pdb=" N PHE C 17 " --> pdb=" O LEU C 13 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N CYS C 20 " --> pdb=" O ILE C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 68 removed outlier: 3.564A pdb=" N ILE C 65 " --> pdb=" O ILE C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 109 removed outlier: 4.150A pdb=" N ILE C 78 " --> pdb=" O THR C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 134 Processing helix chain 'C' and resid 143 through 160 Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 219 through 223 Processing helix chain 'C' and resid 229 through 232 Processing helix chain 'C' and resid 244 through 249 removed outlier: 3.746A pdb=" N ALA C 248 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ALA C 249 " --> pdb=" O GLU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 264 Processing helix chain 'C' and resid 298 through 320 removed outlier: 3.579A pdb=" N HIS C 320 " --> pdb=" O ILE C 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 13 removed outlier: 3.543A pdb=" N LEU D 13 " --> pdb=" O ASN D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 32 removed outlier: 4.538A pdb=" N PHE D 17 " --> pdb=" O LEU D 13 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N CYS D 20 " --> pdb=" O ILE D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 68 removed outlier: 3.564A pdb=" N ILE D 65 " --> pdb=" O ILE D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 109 removed outlier: 4.150A pdb=" N ILE D 78 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 134 Processing helix chain 'D' and resid 143 through 160 Processing helix chain 'D' and resid 160 through 176 Processing helix chain 'D' and resid 219 through 223 Processing helix chain 'D' and resid 229 through 232 Processing helix chain 'D' and resid 244 through 249 removed outlier: 3.747A pdb=" N ALA D 248 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ALA D 249 " --> pdb=" O GLU D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 264 Processing helix chain 'D' and resid 298 through 320 removed outlier: 3.579A pdb=" N HIS D 320 " --> pdb=" O ILE D 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 13 removed outlier: 3.542A pdb=" N LEU E 13 " --> pdb=" O ASN E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 32 removed outlier: 4.539A pdb=" N PHE E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N CYS E 20 " --> pdb=" O ILE E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 68 removed outlier: 3.564A pdb=" N ILE E 65 " --> pdb=" O ILE E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 109 removed outlier: 4.151A pdb=" N ILE E 78 " --> pdb=" O THR E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 134 Processing helix chain 'E' and resid 143 through 160 Processing helix chain 'E' and resid 160 through 176 Processing helix chain 'E' and resid 219 through 223 Processing helix chain 'E' and resid 229 through 232 Processing helix chain 'E' and resid 244 through 249 removed outlier: 3.746A pdb=" N ALA E 248 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ALA E 249 " --> pdb=" O GLU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 264 Processing helix chain 'E' and resid 298 through 320 removed outlier: 3.579A pdb=" N HIS E 320 " --> pdb=" O ILE E 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 13 removed outlier: 3.542A pdb=" N LEU F 13 " --> pdb=" O ASN F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 32 removed outlier: 4.539A pdb=" N PHE F 17 " --> pdb=" O LEU F 13 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N CYS F 20 " --> pdb=" O ILE F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 68 removed outlier: 3.564A pdb=" N ILE F 65 " --> pdb=" O ILE F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 109 removed outlier: 4.151A pdb=" N ILE F 78 " --> pdb=" O THR F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 134 Processing helix chain 'F' and resid 143 through 160 Processing helix chain 'F' and resid 160 through 176 Processing helix chain 'F' and resid 219 through 223 Processing helix chain 'F' and resid 229 through 232 Processing helix chain 'F' and resid 244 through 249 removed outlier: 3.746A pdb=" N ALA F 248 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ALA F 249 " --> pdb=" O GLU F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 264 Processing helix chain 'F' and resid 298 through 320 removed outlier: 3.579A pdb=" N HIS F 320 " --> pdb=" O ILE F 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 13 removed outlier: 3.543A pdb=" N LEU G 13 " --> pdb=" O ASN G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 32 removed outlier: 4.538A pdb=" N PHE G 17 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N CYS G 20 " --> pdb=" O ILE G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 68 removed outlier: 3.564A pdb=" N ILE G 65 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 109 removed outlier: 4.151A pdb=" N ILE G 78 " --> pdb=" O THR G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 134 Processing helix chain 'G' and resid 143 through 160 Processing helix chain 'G' and resid 160 through 176 Processing helix chain 'G' and resid 219 through 223 Processing helix chain 'G' and resid 229 through 232 Processing helix chain 'G' and resid 244 through 249 removed outlier: 3.746A pdb=" N ALA G 248 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ALA G 249 " --> pdb=" O GLU G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 264 Processing helix chain 'G' and resid 298 through 320 removed outlier: 3.579A pdb=" N HIS G 320 " --> pdb=" O ILE G 316 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 185 removed outlier: 6.608A pdb=" N LYS A 205 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ILE A 199 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 removed outlier: 7.393A pdb=" N ILE G 203 " --> pdb=" O ILE G 199 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ILE G 199 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS G 205 " --> pdb=" O ALA G 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 235 through 243 removed outlier: 3.861A pdb=" N ARG A 235 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN A 280 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET A 289 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N PHE A 278 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N TYR A 291 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N VAL A 276 " --> pdb=" O TYR A 291 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 333 removed outlier: 8.503A pdb=" N GLN G 329 " --> pdb=" O SER A 328 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR A 330 " --> pdb=" O GLN G 329 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU G 331 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TYR A 332 " --> pdb=" O LEU G 331 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N MET G 333 " --> pdb=" O TYR A 332 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 184 through 185 removed outlier: 6.608A pdb=" N LYS B 205 " --> pdb=" O ALA B 197 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ILE B 199 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 235 through 243 removed outlier: 3.862A pdb=" N ARG B 235 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN B 280 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET B 289 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N PHE B 278 " --> pdb=" O MET B 289 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N TYR B 291 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL B 276 " --> pdb=" O TYR B 291 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 184 through 185 removed outlier: 6.608A pdb=" N LYS C 205 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ILE C 199 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 235 through 243 removed outlier: 3.861A pdb=" N ARG C 235 " --> pdb=" O THR C 294 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN C 280 " --> pdb=" O ASN C 287 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET C 289 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N PHE C 278 " --> pdb=" O MET C 289 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N TYR C 291 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N VAL C 276 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 184 through 185 removed outlier: 6.608A pdb=" N LYS D 205 " --> pdb=" O ALA D 197 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ILE D 199 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE D 203 " --> pdb=" O ILE D 199 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 235 through 243 removed outlier: 3.862A pdb=" N ARG D 235 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN D 280 " --> pdb=" O ASN D 287 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET D 289 " --> pdb=" O PHE D 278 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N PHE D 278 " --> pdb=" O MET D 289 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N TYR D 291 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N VAL D 276 " --> pdb=" O TYR D 291 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 184 through 185 removed outlier: 6.608A pdb=" N LYS E 205 " --> pdb=" O ALA E 197 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ILE E 199 " --> pdb=" O ILE E 203 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE E 203 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 235 through 243 removed outlier: 3.862A pdb=" N ARG E 235 " --> pdb=" O THR E 294 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN E 280 " --> pdb=" O ASN E 287 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET E 289 " --> pdb=" O PHE E 278 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N PHE E 278 " --> pdb=" O MET E 289 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N TYR E 291 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N VAL E 276 " --> pdb=" O TYR E 291 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 184 through 185 removed outlier: 6.609A pdb=" N LYS F 205 " --> pdb=" O ALA F 197 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ILE F 199 " --> pdb=" O ILE F 203 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE F 203 " --> pdb=" O ILE F 199 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 235 through 243 removed outlier: 3.862A pdb=" N ARG F 235 " --> pdb=" O THR F 294 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN F 280 " --> pdb=" O ASN F 287 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET F 289 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N PHE F 278 " --> pdb=" O MET F 289 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N TYR F 291 " --> pdb=" O VAL F 276 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N VAL F 276 " --> pdb=" O TYR F 291 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 235 through 243 removed outlier: 3.861A pdb=" N ARG G 235 " --> pdb=" O THR G 294 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN G 280 " --> pdb=" O ASN G 287 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET G 289 " --> pdb=" O PHE G 278 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N PHE G 278 " --> pdb=" O MET G 289 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N TYR G 291 " --> pdb=" O VAL G 276 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL G 276 " --> pdb=" O TYR G 291 " (cutoff:3.500A) 1229 hydrogen bonds defined for protein. 3540 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: 3.38 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3172 1.33 - 1.45: 4688 1.45 - 1.57: 11264 1.57 - 1.69: 70 1.69 - 1.81: 126 Bond restraints: 19320 Sorted by residual: bond pdb=" C8 PTY B 403 " pdb=" O7 PTY B 403 " ideal model delta sigma weight residual 1.331 1.455 -0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" C8 PTY F 403 " pdb=" O7 PTY F 403 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" C8 PTY G 401 " pdb=" O7 PTY G 401 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" C8 PTY E 403 " pdb=" O7 PTY E 403 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" C8 PTY D 403 " pdb=" O7 PTY D 403 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.76e+01 ... (remaining 19315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 25425 2.30 - 4.59: 375 4.59 - 6.89: 58 6.89 - 9.18: 35 9.18 - 11.48: 21 Bond angle restraints: 25914 Sorted by residual: angle pdb=" CA LYS F 103 " pdb=" CB LYS F 103 " pdb=" CG LYS F 103 " ideal model delta sigma weight residual 114.10 121.63 -7.53 2.00e+00 2.50e-01 1.42e+01 angle pdb=" CA LYS D 103 " pdb=" CB LYS D 103 " pdb=" CG LYS D 103 " ideal model delta sigma weight residual 114.10 121.63 -7.53 2.00e+00 2.50e-01 1.42e+01 angle pdb=" CA LYS A 103 " pdb=" CB LYS A 103 " pdb=" CG LYS A 103 " ideal model delta sigma weight residual 114.10 121.61 -7.51 2.00e+00 2.50e-01 1.41e+01 angle pdb=" CA LYS B 103 " pdb=" CB LYS B 103 " pdb=" CG LYS B 103 " ideal model delta sigma weight residual 114.10 121.61 -7.51 2.00e+00 2.50e-01 1.41e+01 angle pdb=" CA LYS E 103 " pdb=" CB LYS E 103 " pdb=" CG LYS E 103 " ideal model delta sigma weight residual 114.10 121.60 -7.50 2.00e+00 2.50e-01 1.41e+01 ... (remaining 25909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.77: 10409 19.77 - 39.53: 973 39.53 - 59.30: 298 59.30 - 79.07: 42 79.07 - 98.83: 14 Dihedral angle restraints: 11736 sinusoidal: 5037 harmonic: 6699 Sorted by residual: dihedral pdb=" CB CYS B 82 " pdb=" SG CYS B 82 " pdb=" SG CYS B 82 " pdb=" CB CYS B 82 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 dihedral pdb=" CB CYS B 292 " pdb=" SG CYS B 292 " pdb=" SG CYS B 292 " pdb=" CB CYS B 292 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 dihedral pdb=" CA PHE B 138 " pdb=" C PHE B 138 " pdb=" N GLY B 139 " pdb=" CA GLY B 139 " ideal model delta harmonic sigma weight residual -180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 11733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1884 0.030 - 0.060: 560 0.060 - 0.090: 341 0.090 - 0.120: 90 0.120 - 0.150: 58 Chirality restraints: 2933 Sorted by residual: chirality pdb=" CG LEU G 145 " pdb=" CB LEU G 145 " pdb=" CD1 LEU G 145 " pdb=" CD2 LEU G 145 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CG LEU B 145 " pdb=" CB LEU B 145 " pdb=" CD1 LEU B 145 " pdb=" CD2 LEU B 145 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CG LEU E 145 " pdb=" CB LEU E 145 " pdb=" CD1 LEU E 145 " pdb=" CD2 LEU E 145 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.45e-01 ... (remaining 2930 not shown) Planarity restraints: 3122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 102 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" CD GLU C 102 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU C 102 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU C 102 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 102 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" CD GLU E 102 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU E 102 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU E 102 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU F 102 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.13e+00 pdb=" CD GLU F 102 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU F 102 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU F 102 " 0.014 2.00e-02 2.50e+03 ... (remaining 3119 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4584 2.80 - 3.33: 18099 3.33 - 3.85: 30550 3.85 - 4.38: 36350 4.38 - 4.90: 61927 Nonbonded interactions: 151510 Sorted by model distance: nonbonded pdb=" O LEU A 48 " pdb=" OG1 THR A 51 " model vdw 2.278 3.040 nonbonded pdb=" O LEU B 48 " pdb=" OG1 THR B 51 " model vdw 2.278 3.040 nonbonded pdb=" O LEU E 48 " pdb=" OG1 THR E 51 " model vdw 2.278 3.040 nonbonded pdb=" O LEU D 48 " pdb=" OG1 THR D 51 " model vdw 2.278 3.040 nonbonded pdb=" O LEU F 48 " pdb=" OG1 THR F 51 " model vdw 2.278 3.040 ... (remaining 151505 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 401 or (resid 402 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C40 or name C41 or name C5 or name C6 or name C8 or nam \ e N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or \ name O4 or name O7 or name P1 )) or (resid 403 and (name C1 or name C11 or name \ C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or n \ ame C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C3 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C3 \ 6 or name C37 or name C38 or name C39 or name C5 or name C6 or name C8 or name N \ 1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or nam \ e O4 or name O7 or name P1 )) or (resid 404 and (name C1 or name C11 or name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 or na \ me C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 o \ r name C39 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 o \ r name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 \ )) or resid 405)) selection = (chain 'B' and (resid 4 through 401 or (resid 402 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C40 or name C41 or name C5 or name C6 or name C8 or nam \ e N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or \ name O4 or name O7 or name P1 )) or (resid 403 and (name C1 or name C11 or name \ C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or n \ ame C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C3 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C3 \ 6 or name C37 or name C38 or name C39 or name C5 or name C6 or name C8 or name N \ 1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or nam \ e O4 or name O7 or name P1 )) or (resid 404 and (name C1 or name C11 or name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 or na \ me C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 o \ r name C39 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 o \ r name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 \ )) or resid 405)) selection = (chain 'C' and (resid 4 through 401 or (resid 402 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C40 or name C41 or name C5 or name C6 or name C8 or nam \ e N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or \ name O4 or name O7 or name P1 )) or (resid 403 and (name C1 or name C11 or name \ C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or n \ ame C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C3 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C3 \ 6 or name C37 or name C38 or name C39 or name C5 or name C6 or name C8 or name N \ 1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or nam \ e O4 or name O7 or name P1 )) or (resid 404 and (name C1 or name C11 or name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 or na \ me C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 o \ r name C39 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 o \ r name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 \ )) or resid 405)) selection = (chain 'D' and (resid 4 through 401 or (resid 402 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C40 or name C41 or name C5 or name C6 or name C8 or nam \ e N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or \ name O4 or name O7 or name P1 )) or (resid 403 and (name C1 or name C11 or name \ C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or n \ ame C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C3 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C3 \ 6 or name C37 or name C38 or name C39 or name C5 or name C6 or name C8 or name N \ 1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or nam \ e O4 or name O7 or name P1 )) or (resid 404 and (name C1 or name C11 or name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 or na \ me C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 o \ r name C39 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 o \ r name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 \ )) or resid 405)) selection = (chain 'E' and (resid 4 through 401 or (resid 402 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C40 or name C41 or name C5 or name C6 or name C8 or nam \ e N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or \ name O4 or name O7 or name P1 )) or (resid 403 and (name C1 or name C11 or name \ C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or n \ ame C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C3 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C3 \ 6 or name C37 or name C38 or name C39 or name C5 or name C6 or name C8 or name N \ 1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or nam \ e O4 or name O7 or name P1 )) or (resid 404 and (name C1 or name C11 or name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 or na \ me C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 o \ r name C39 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 o \ r name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 \ )) or resid 405)) selection = (chain 'F' and (resid 4 through 401 or (resid 402 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C40 or name C41 or name C5 or name C6 or name C8 or nam \ e N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or \ name O4 or name O7 or name P1 )) or (resid 403 and (name C1 or name C11 or name \ C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or n \ ame C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C3 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C3 \ 6 or name C37 or name C38 or name C39 or name C5 or name C6 or name C8 or name N \ 1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or nam \ e O4 or name O7 or name P1 )) or (resid 404 and (name C1 or name C11 or name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 or na \ me C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 o \ r name C39 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 o \ r name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 \ )) or resid 405)) selection = (chain 'G' and (resid 4 through 334 or (resid 401 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C3 or name C30 or name C31 or name C32 or name C33 or name \ C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C5 or n \ ame C6 or name C8 or name N1 or name O10 or name O11 or name O12 or name O13 or \ name O14 or name O30 or name O4 or name O7 or name P1 )) or resid 402 through 40 \ 3 or (resid 404 and (name C1 or name C11 or name C12 or name C13 or name C14 or \ name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C20 \ or name C21 or name C3 or name C30 or name C31 or name C32 or name C33 or name C \ 34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C5 or nam \ e C6 or name C8 or name N1 or name O10 or name O11 or name O12 or name O13 or na \ me O14 or name O30 or name O4 or name O7 or name P1 )) or (resid 405 and (name C \ 1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or nam \ e C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name C22 or \ name C23 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 \ or name C35 or name C36 or name C37 or name C38 or name C39 or name C5 or name C \ 6 or name C8 or name N1 or name O10 or name O11 or name O12 or name O13 or name \ O14 or name O30 or name O4 or name O7 or name P1 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.840 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.020 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:8.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 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 : 0.004 0.124 19320 Z= 0.230 Angle : 0.754 11.478 25916 Z= 0.357 Chirality : 0.043 0.150 2933 Planarity : 0.003 0.030 3122 Dihedral : 16.864 98.834 7420 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.45 % Allowed : 19.24 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.17), residues: 2303 helix: 2.21 (0.14), residues: 1274 sheet: -0.77 (0.26), residues: 357 loop : -1.97 (0.19), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 271 TYR 0.011 0.001 TYR F 291 PHE 0.009 0.001 PHE D 101 TRP 0.006 0.001 TRP C 184 HIS 0.001 0.000 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00447 (19320) covalent geometry : angle 0.75401 (25914) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.13836 ( 1229) hydrogen bonds : angle 4.74627 ( 3540) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 349 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ILE cc_start: 0.9230 (mm) cc_final: 0.8992 (pp) REVERT: A 158 MET cc_start: 0.8885 (mtm) cc_final: 0.8570 (mtm) REVERT: B 126 ILE cc_start: 0.9249 (mm) cc_final: 0.8993 (pp) REVERT: C 126 ILE cc_start: 0.9210 (mm) cc_final: 0.8962 (pp) REVERT: C 158 MET cc_start: 0.8881 (mtm) cc_final: 0.8608 (mtm) REVERT: C 176 ASP cc_start: 0.7892 (t0) cc_final: 0.7553 (t0) REVERT: D 126 ILE cc_start: 0.9202 (mm) cc_final: 0.8960 (pp) REVERT: D 158 MET cc_start: 0.8821 (mtm) cc_final: 0.8212 (mtm) REVERT: E 126 ILE cc_start: 0.9233 (mm) cc_final: 0.9024 (pp) REVERT: E 158 MET cc_start: 0.8863 (mtm) cc_final: 0.8499 (mtm) REVERT: E 176 ASP cc_start: 0.7903 (t0) cc_final: 0.7510 (t0) REVERT: F 126 ILE cc_start: 0.9214 (mm) cc_final: 0.8985 (pp) REVERT: F 158 MET cc_start: 0.8836 (mtm) cc_final: 0.8480 (mtp) REVERT: G 158 MET cc_start: 0.8846 (mtm) cc_final: 0.8496 (mtm) REVERT: G 176 ASP cc_start: 0.7936 (t0) cc_final: 0.7598 (OUTLIER) outliers start: 8 outliers final: 1 residues processed: 349 average time/residue: 0.6588 time to fit residues: 256.7835 Evaluate side-chains 310 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 20.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.129291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.064916 restraints weight = 31442.547| |-----------------------------------------------------------------------------| r_work (start): 0.2648 rms_B_bonded: 2.21 r_work: 0.2457 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work: 0.2325 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 19320 Z= 0.242 Angle : 0.638 9.630 25916 Z= 0.333 Chirality : 0.046 0.149 2933 Planarity : 0.004 0.037 3122 Dihedral : 15.372 82.495 3661 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.31 % Allowed : 19.40 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.16), residues: 2303 helix: 2.00 (0.13), residues: 1344 sheet: -0.01 (0.30), residues: 259 loop : -2.15 (0.17), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 271 TYR 0.030 0.002 TYR B 50 PHE 0.026 0.002 PHE A 148 TRP 0.009 0.001 TRP G 184 HIS 0.003 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00564 (19320) covalent geometry : angle 0.63848 (25914) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.05660 ( 1229) hydrogen bonds : angle 4.17181 ( 3540) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 319 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 158 MET cc_start: 0.9280 (mtm) cc_final: 0.9043 (mtm) REVERT: A 176 ASP cc_start: 0.8389 (t0) cc_final: 0.8160 (t0) REVERT: B 176 ASP cc_start: 0.8447 (t0) cc_final: 0.8170 (t0) REVERT: B 333 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8621 (mpp) REVERT: C 120 ARG cc_start: 0.7948 (mmm-85) cc_final: 0.7719 (mtt180) REVERT: C 176 ASP cc_start: 0.8509 (t0) cc_final: 0.8280 (t0) REVERT: D 120 ARG cc_start: 0.8410 (mmt90) cc_final: 0.7915 (mtt180) REVERT: D 158 MET cc_start: 0.9309 (mtm) cc_final: 0.9039 (mtm) REVERT: E 50 TYR cc_start: 0.8626 (m-80) cc_final: 0.8390 (m-80) REVERT: E 176 ASP cc_start: 0.8438 (t0) cc_final: 0.8210 (t0) REVERT: F 104 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8547 (tp40) REVERT: F 120 ARG cc_start: 0.8486 (mmt90) cc_final: 0.8010 (mtt180) REVERT: F 333 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8680 (mpp) REVERT: G 50 TYR cc_start: 0.8682 (m-80) cc_final: 0.8467 (m-80) REVERT: G 93 LYS cc_start: 0.8767 (mmtt) cc_final: 0.8548 (tppp) REVERT: G 120 ARG cc_start: 0.7975 (mmm-85) cc_final: 0.7679 (mtt180) REVERT: G 176 ASP cc_start: 0.8507 (t0) cc_final: 0.8298 (OUTLIER) outliers start: 41 outliers final: 7 residues processed: 334 average time/residue: 0.6707 time to fit residues: 250.6727 Evaluate side-chains 325 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 317 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 333 MET Chi-restraints excluded: chain G residue 154 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 171 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 26 optimal weight: 0.0870 chunk 18 optimal weight: 8.9990 chunk 205 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 67 optimal weight: 40.0000 chunk 145 optimal weight: 20.0000 chunk 165 optimal weight: 30.0000 overall best weight: 2.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 HIS F 46 GLN F 137 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.127774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.064280 restraints weight = 31526.686| |-----------------------------------------------------------------------------| r_work (start): 0.2646 rms_B_bonded: 2.24 r_work: 0.2447 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work: 0.2314 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9027 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 19320 Z= 0.235 Angle : 0.621 7.546 25916 Z= 0.326 Chirality : 0.045 0.142 2933 Planarity : 0.003 0.033 3122 Dihedral : 14.905 88.532 3661 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.21 % Allowed : 19.07 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.17), residues: 2303 helix: 2.19 (0.14), residues: 1358 sheet: -0.15 (0.30), residues: 259 loop : -2.11 (0.17), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 271 TYR 0.046 0.001 TYR A 50 PHE 0.024 0.002 PHE C 148 TRP 0.008 0.001 TRP G 184 HIS 0.004 0.001 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00556 (19320) covalent geometry : angle 0.62102 (25914) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.05378 ( 1229) hydrogen bonds : angle 3.96937 ( 3540) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 319 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.9377 (tm-30) cc_final: 0.8857 (tm-30) REVERT: A 176 ASP cc_start: 0.8537 (t0) cc_final: 0.8337 (t0) REVERT: A 280 GLN cc_start: 0.9449 (OUTLIER) cc_final: 0.9192 (tt0) REVERT: B 176 ASP cc_start: 0.8489 (t0) cc_final: 0.8262 (t0) REVERT: C 102 GLU cc_start: 0.9379 (tm-30) cc_final: 0.8758 (tm-30) REVERT: C 140 MET cc_start: 0.8398 (mmt) cc_final: 0.8143 (mmp) REVERT: C 333 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8792 (mpp) REVERT: D 50 TYR cc_start: 0.8748 (m-80) cc_final: 0.8253 (m-80) REVERT: D 102 GLU cc_start: 0.9354 (tm-30) cc_final: 0.8562 (tm-30) REVERT: D 116 ARG cc_start: 0.8846 (mmm160) cc_final: 0.8484 (mmp80) REVERT: D 120 ARG cc_start: 0.8432 (mmt90) cc_final: 0.8046 (mtt180) REVERT: D 158 MET cc_start: 0.9462 (mtm) cc_final: 0.9198 (mtm) REVERT: E 50 TYR cc_start: 0.8880 (m-80) cc_final: 0.8474 (m-80) REVERT: E 93 LYS cc_start: 0.8825 (tppt) cc_final: 0.8440 (mmtp) REVERT: F 104 GLN cc_start: 0.8986 (tm-30) cc_final: 0.8631 (tm-30) REVERT: F 120 ARG cc_start: 0.8575 (mmt90) cc_final: 0.8150 (mtt180) REVERT: G 50 TYR cc_start: 0.8928 (m-80) cc_final: 0.8623 (m-80) REVERT: G 93 LYS cc_start: 0.9082 (mmtt) cc_final: 0.8841 (mmtp) outliers start: 57 outliers final: 25 residues processed: 345 average time/residue: 0.6288 time to fit residues: 242.8920 Evaluate side-chains 339 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 312 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 176 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 181 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 156 optimal weight: 0.9980 chunk 187 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 HIS ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.130489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.066938 restraints weight = 31575.665| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 2.22 r_work: 0.2519 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work: 0.2386 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19320 Z= 0.113 Angle : 0.563 10.863 25916 Z= 0.286 Chirality : 0.042 0.141 2933 Planarity : 0.003 0.040 3122 Dihedral : 13.778 79.310 3661 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.15 % Allowed : 20.36 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.17), residues: 2303 helix: 2.67 (0.14), residues: 1316 sheet: 0.04 (0.29), residues: 273 loop : -1.80 (0.18), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 271 TYR 0.034 0.001 TYR A 50 PHE 0.025 0.001 PHE A 148 TRP 0.005 0.001 TRP B 184 HIS 0.003 0.001 HIS G 137 Details of bonding type rmsd covalent geometry : bond 0.00235 (19320) covalent geometry : angle 0.56265 (25914) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03844 ( 1229) hydrogen bonds : angle 3.64103 ( 3540) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 315 time to evaluate : 0.832 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 280 GLN cc_start: 0.9392 (OUTLIER) cc_final: 0.9167 (tp40) REVERT: B 82 CYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6603 (p) REVERT: B 85 LEU cc_start: 0.9556 (mm) cc_final: 0.9297 (pp) REVERT: B 176 ASP cc_start: 0.8278 (t0) cc_final: 0.7999 (t0) REVERT: C 85 LEU cc_start: 0.9557 (mm) cc_final: 0.9330 (pp) REVERT: D 85 LEU cc_start: 0.9565 (mm) cc_final: 0.9346 (pt) REVERT: D 102 GLU cc_start: 0.9320 (tm-30) cc_final: 0.8833 (tm-30) REVERT: D 116 ARG cc_start: 0.8751 (mmm160) cc_final: 0.8494 (mmp80) REVERT: D 120 ARG cc_start: 0.8411 (mmt90) cc_final: 0.8162 (mtt180) REVERT: E 50 TYR cc_start: 0.8955 (m-80) cc_final: 0.8597 (m-80) REVERT: E 85 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9332 (pp) REVERT: E 93 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8533 (mmtp) REVERT: E 140 MET cc_start: 0.7974 (mmp) cc_final: 0.7627 (tpp) REVERT: F 85 LEU cc_start: 0.9567 (mm) cc_final: 0.9324 (pp) REVERT: F 104 GLN cc_start: 0.9028 (tm-30) cc_final: 0.8663 (tm-30) REVERT: G 93 LYS cc_start: 0.9135 (mmtt) cc_final: 0.8772 (mmmm) REVERT: G 116 ARG cc_start: 0.8973 (mmm160) cc_final: 0.8679 (mmp80) outliers start: 56 outliers final: 12 residues processed: 341 average time/residue: 0.6533 time to fit residues: 248.9473 Evaluate side-chains 327 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 311 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 100 optimal weight: 40.0000 chunk 188 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 215 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 206 optimal weight: 9.9990 chunk 168 optimal weight: 50.0000 chunk 133 optimal weight: 50.0000 chunk 146 optimal weight: 4.9990 chunk 132 optimal weight: 50.0000 chunk 176 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 HIS ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.127287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.062626 restraints weight = 31707.874| |-----------------------------------------------------------------------------| r_work (start): 0.2625 rms_B_bonded: 2.25 r_work: 0.2435 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 19320 Z= 0.200 Angle : 0.619 11.508 25916 Z= 0.315 Chirality : 0.045 0.158 2933 Planarity : 0.003 0.037 3122 Dihedral : 13.836 86.429 3661 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.43 % Allowed : 19.97 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.17), residues: 2303 helix: 2.39 (0.14), residues: 1365 sheet: -0.14 (0.30), residues: 259 loop : -1.97 (0.18), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 271 TYR 0.054 0.001 TYR D 50 PHE 0.025 0.002 PHE G 148 TRP 0.008 0.001 TRP G 184 HIS 0.003 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00472 (19320) covalent geometry : angle 0.61889 (25914) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.04965 ( 1229) hydrogen bonds : angle 3.79541 ( 3540) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 307 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 CYS cc_start: 0.7328 (OUTLIER) cc_final: 0.6672 (p) REVERT: A 85 LEU cc_start: 0.9612 (mm) cc_final: 0.9379 (pp) REVERT: B 85 LEU cc_start: 0.9572 (OUTLIER) cc_final: 0.9312 (pp) REVERT: B 120 ARG cc_start: 0.8223 (mmt90) cc_final: 0.7890 (mtt180) REVERT: C 85 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9301 (pp) REVERT: C 96 LEU cc_start: 0.9711 (OUTLIER) cc_final: 0.9443 (pp) REVERT: C 116 ARG cc_start: 0.9010 (mmp80) cc_final: 0.8728 (mmm160) REVERT: C 120 ARG cc_start: 0.8346 (mtm180) cc_final: 0.8091 (mtm180) REVERT: C 140 MET cc_start: 0.8324 (mmm) cc_final: 0.7952 (mmm) REVERT: D 85 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9308 (pp) REVERT: D 102 GLU cc_start: 0.9289 (tm-30) cc_final: 0.8460 (tm-30) REVERT: D 116 ARG cc_start: 0.8667 (mmm160) cc_final: 0.8463 (mmp80) REVERT: D 120 ARG cc_start: 0.8155 (mmt90) cc_final: 0.7853 (mtt180) REVERT: E 43 HIS cc_start: 0.7778 (m90) cc_final: 0.7377 (m-70) REVERT: E 50 TYR cc_start: 0.9013 (m-10) cc_final: 0.8691 (m-80) REVERT: E 85 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9367 (pp) REVERT: E 93 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8618 (tptm) REVERT: E 102 GLU cc_start: 0.9242 (tm-30) cc_final: 0.8138 (tm-30) REVERT: E 140 MET cc_start: 0.7982 (mmp) cc_final: 0.7646 (tpp) REVERT: F 85 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9336 (pp) REVERT: F 104 GLN cc_start: 0.9046 (tm-30) cc_final: 0.8683 (tm-30) REVERT: F 120 ARG cc_start: 0.8289 (mmt90) cc_final: 0.7974 (mtt180) REVERT: G 93 LYS cc_start: 0.9111 (mmtt) cc_final: 0.8812 (tppp) REVERT: G 102 GLU cc_start: 0.9304 (tm-30) cc_final: 0.8715 (tm-30) REVERT: G 116 ARG cc_start: 0.8837 (mmm160) cc_final: 0.8398 (mmp80) outliers start: 61 outliers final: 19 residues processed: 329 average time/residue: 0.6128 time to fit residues: 225.8607 Evaluate side-chains 330 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 303 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 46 GLN Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 176 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 94 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 212 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 214 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 0 optimal weight: 80.0000 chunk 55 optimal weight: 0.8980 chunk 217 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 136 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 HIS E 280 GLN ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.129549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.065113 restraints weight = 31613.885| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 2.27 r_work: 0.2505 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work: 0.2374 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19320 Z= 0.112 Angle : 0.578 9.334 25916 Z= 0.290 Chirality : 0.043 0.161 2933 Planarity : 0.003 0.056 3122 Dihedral : 13.236 78.795 3661 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.04 % Allowed : 20.75 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.17), residues: 2303 helix: 2.78 (0.14), residues: 1309 sheet: 0.04 (0.30), residues: 273 loop : -1.83 (0.18), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 271 TYR 0.047 0.001 TYR D 50 PHE 0.027 0.001 PHE A 148 TRP 0.006 0.001 TRP D 201 HIS 0.002 0.001 HIS E 137 Details of bonding type rmsd covalent geometry : bond 0.00241 (19320) covalent geometry : angle 0.57825 (25914) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03659 ( 1229) hydrogen bonds : angle 3.57630 ( 3540) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 313 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 CYS cc_start: 0.7245 (OUTLIER) cc_final: 0.6512 (p) REVERT: A 93 LYS cc_start: 0.8819 (mmtt) cc_final: 0.8425 (mmtt) REVERT: A 96 LEU cc_start: 0.9707 (tm) cc_final: 0.9492 (pp) REVERT: A 116 ARG cc_start: 0.8971 (mmm160) cc_final: 0.8661 (mmm160) REVERT: A 140 MET cc_start: 0.8007 (mmp) cc_final: 0.7586 (tpp) REVERT: A 280 GLN cc_start: 0.9377 (OUTLIER) cc_final: 0.9134 (tp40) REVERT: B 82 CYS cc_start: 0.7249 (OUTLIER) cc_final: 0.6560 (p) REVERT: B 85 LEU cc_start: 0.9556 (OUTLIER) cc_final: 0.9339 (pp) REVERT: B 96 LEU cc_start: 0.9700 (tm) cc_final: 0.9488 (pp) REVERT: B 102 GLU cc_start: 0.9273 (tm-30) cc_final: 0.8913 (tm-30) REVERT: B 116 ARG cc_start: 0.8978 (mmm160) cc_final: 0.8553 (mmp80) REVERT: B 120 ARG cc_start: 0.8415 (mmt90) cc_final: 0.8002 (mtp180) REVERT: B 140 MET cc_start: 0.7990 (mmp) cc_final: 0.7669 (mmp) REVERT: C 50 TYR cc_start: 0.8801 (m-80) cc_final: 0.8356 (m-80) REVERT: C 93 LYS cc_start: 0.8977 (mmtp) cc_final: 0.8734 (mmtt) REVERT: C 96 LEU cc_start: 0.9707 (tm) cc_final: 0.9469 (pp) REVERT: C 102 GLU cc_start: 0.9335 (tm-30) cc_final: 0.8805 (tm-30) REVERT: C 116 ARG cc_start: 0.8955 (mmp80) cc_final: 0.8386 (mmp80) REVERT: C 120 ARG cc_start: 0.8500 (mtm180) cc_final: 0.8262 (mtm180) REVERT: D 85 LEU cc_start: 0.9562 (OUTLIER) cc_final: 0.9359 (pp) REVERT: D 93 LYS cc_start: 0.8965 (mmtp) cc_final: 0.8659 (tptm) REVERT: D 96 LEU cc_start: 0.9735 (tm) cc_final: 0.9522 (pp) REVERT: D 102 GLU cc_start: 0.9261 (tm-30) cc_final: 0.8334 (tm-30) REVERT: E 43 HIS cc_start: 0.7845 (m90) cc_final: 0.7521 (m-70) REVERT: E 50 TYR cc_start: 0.9051 (m-10) cc_final: 0.8716 (m-80) REVERT: E 85 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9358 (pp) REVERT: E 93 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8421 (tptm) REVERT: E 96 LEU cc_start: 0.9737 (tm) cc_final: 0.9502 (pp) REVERT: E 140 MET cc_start: 0.7914 (mmp) cc_final: 0.7578 (tpp) REVERT: F 85 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9373 (pp) REVERT: F 104 GLN cc_start: 0.9108 (tm-30) cc_final: 0.8695 (tm-30) REVERT: F 120 ARG cc_start: 0.8527 (mmt90) cc_final: 0.8325 (mtt180) REVERT: F 140 MET cc_start: 0.8080 (mmp) cc_final: 0.7474 (tpp) REVERT: G 85 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9333 (pp) REVERT: G 93 LYS cc_start: 0.9126 (mmtt) cc_final: 0.8792 (mmmm) REVERT: G 102 GLU cc_start: 0.9337 (tm-30) cc_final: 0.8743 (tm-30) REVERT: G 116 ARG cc_start: 0.8830 (mmm160) cc_final: 0.8487 (mmp80) REVERT: G 176 ASP cc_start: 0.8003 (t0) cc_final: 0.7599 (OUTLIER) REVERT: G 333 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8772 (mmm) outliers start: 54 outliers final: 17 residues processed: 335 average time/residue: 0.5645 time to fit residues: 212.1248 Evaluate side-chains 335 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 309 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 46 GLN Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 333 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 226 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 199 optimal weight: 50.0000 chunk 213 optimal weight: 0.8980 chunk 67 optimal weight: 50.0000 chunk 22 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 184 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN F 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.129595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.066403 restraints weight = 31749.114| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 2.28 r_work: 0.2514 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work: 0.2384 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19320 Z= 0.112 Angle : 0.596 11.593 25916 Z= 0.298 Chirality : 0.043 0.171 2933 Planarity : 0.003 0.050 3122 Dihedral : 12.925 72.836 3661 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.81 % Allowed : 21.03 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.17), residues: 2303 helix: 2.82 (0.14), residues: 1309 sheet: 0.12 (0.30), residues: 273 loop : -1.81 (0.18), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 271 TYR 0.012 0.001 TYR G 50 PHE 0.027 0.001 PHE A 148 TRP 0.006 0.001 TRP F 201 HIS 0.002 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00239 (19320) covalent geometry : angle 0.59647 (25914) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03515 ( 1229) hydrogen bonds : angle 3.51047 ( 3540) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 309 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.8789 (mmtt) cc_final: 0.8429 (mmtt) REVERT: A 96 LEU cc_start: 0.9728 (tm) cc_final: 0.9505 (pp) REVERT: A 102 GLU cc_start: 0.9350 (tm-30) cc_final: 0.8593 (tm-30) REVERT: A 116 ARG cc_start: 0.8895 (mmm160) cc_final: 0.8331 (mmp80) REVERT: A 140 MET cc_start: 0.8004 (mmp) cc_final: 0.7711 (tpp) REVERT: A 280 GLN cc_start: 0.9362 (OUTLIER) cc_final: 0.9140 (tp40) REVERT: B 82 CYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6446 (p) REVERT: B 120 ARG cc_start: 0.8459 (mmt90) cc_final: 0.8056 (mtp180) REVERT: B 140 MET cc_start: 0.7915 (mmp) cc_final: 0.7617 (mmp) REVERT: C 50 TYR cc_start: 0.8858 (m-80) cc_final: 0.8520 (m-80) REVERT: C 96 LEU cc_start: 0.9724 (tm) cc_final: 0.9491 (pp) REVERT: C 120 ARG cc_start: 0.8464 (mtm180) cc_final: 0.8233 (mtm180) REVERT: D 93 LYS cc_start: 0.8931 (mmtp) cc_final: 0.8588 (mmtp) REVERT: D 96 LEU cc_start: 0.9737 (tm) cc_final: 0.9511 (pp) REVERT: D 120 ARG cc_start: 0.8462 (mtt180) cc_final: 0.8150 (mtm180) REVERT: E 50 TYR cc_start: 0.9122 (m-10) cc_final: 0.8862 (m-80) REVERT: E 93 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8416 (mmtp) REVERT: E 96 LEU cc_start: 0.9740 (tm) cc_final: 0.9494 (pp) REVERT: E 116 ARG cc_start: 0.8889 (mmp80) cc_final: 0.8572 (mmp80) REVERT: E 140 MET cc_start: 0.7853 (mmp) cc_final: 0.7524 (mtp) REVERT: F 82 CYS cc_start: 0.7264 (OUTLIER) cc_final: 0.6471 (p) REVERT: F 93 LYS cc_start: 0.8925 (mmtt) cc_final: 0.8494 (mmtp) REVERT: F 96 LEU cc_start: 0.9755 (tm) cc_final: 0.9534 (pp) REVERT: F 104 GLN cc_start: 0.9143 (tm-30) cc_final: 0.8733 (tm-30) REVERT: F 116 ARG cc_start: 0.9044 (mmm160) cc_final: 0.8839 (mmm160) REVERT: F 120 ARG cc_start: 0.8516 (mmt90) cc_final: 0.8144 (mtp180) REVERT: G 85 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9360 (pp) REVERT: G 93 LYS cc_start: 0.9089 (mmtt) cc_final: 0.8605 (mmmm) REVERT: G 96 LEU cc_start: 0.9708 (tm) cc_final: 0.9480 (pp) REVERT: G 102 GLU cc_start: 0.9333 (tm-30) cc_final: 0.8730 (tm-30) REVERT: G 116 ARG cc_start: 0.8724 (mmm160) cc_final: 0.8509 (mmp80) REVERT: G 176 ASP cc_start: 0.8092 (t0) cc_final: 0.7862 (OUTLIER) outliers start: 50 outliers final: 13 residues processed: 331 average time/residue: 0.6274 time to fit residues: 232.5463 Evaluate side-chains 322 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 305 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain G residue 85 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 132 optimal weight: 9.9990 chunk 216 optimal weight: 0.0050 chunk 95 optimal weight: 3.9990 chunk 228 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 34 optimal weight: 50.0000 chunk 131 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.130377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.066114 restraints weight = 31765.052| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 2.32 r_work: 0.2532 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work: 0.2403 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19320 Z= 0.111 Angle : 0.618 14.258 25916 Z= 0.304 Chirality : 0.044 0.205 2933 Planarity : 0.004 0.050 3122 Dihedral : 12.650 70.980 3661 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.86 % Allowed : 22.67 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.17), residues: 2303 helix: 2.80 (0.14), residues: 1309 sheet: 0.14 (0.30), residues: 273 loop : -1.78 (0.18), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 271 TYR 0.013 0.001 TYR G 50 PHE 0.027 0.001 PHE D 148 TRP 0.006 0.001 TRP C 201 HIS 0.002 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00238 (19320) covalent geometry : angle 0.61842 (25914) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03348 ( 1229) hydrogen bonds : angle 3.50395 ( 3540) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 316 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.8895 (mmtt) cc_final: 0.8551 (mmtt) REVERT: A 96 LEU cc_start: 0.9740 (tm) cc_final: 0.9529 (pp) REVERT: A 102 GLU cc_start: 0.9327 (tm-30) cc_final: 0.9046 (tm-30) REVERT: A 116 ARG cc_start: 0.8833 (mmm160) cc_final: 0.8492 (mmp80) REVERT: A 140 MET cc_start: 0.8063 (mmp) cc_final: 0.7699 (tpp) REVERT: A 280 GLN cc_start: 0.9336 (OUTLIER) cc_final: 0.9116 (tp40) REVERT: B 50 TYR cc_start: 0.8986 (m-80) cc_final: 0.8630 (m-80) REVERT: B 120 ARG cc_start: 0.8440 (mmt90) cc_final: 0.8044 (mtp180) REVERT: C 50 TYR cc_start: 0.8912 (m-80) cc_final: 0.8696 (m-80) REVERT: C 93 LYS cc_start: 0.9070 (mmtp) cc_final: 0.8758 (tptm) REVERT: C 120 ARG cc_start: 0.8412 (mtm180) cc_final: 0.8154 (mtm180) REVERT: C 140 MET cc_start: 0.8277 (mmp) cc_final: 0.7859 (tpp) REVERT: C 158 MET cc_start: 0.9275 (mtm) cc_final: 0.8938 (mtm) REVERT: D 93 LYS cc_start: 0.9014 (mmtp) cc_final: 0.8756 (mmtp) REVERT: D 96 LEU cc_start: 0.9746 (tm) cc_final: 0.9537 (pp) REVERT: D 120 ARG cc_start: 0.8484 (mtt180) cc_final: 0.8228 (mtm180) REVERT: D 140 MET cc_start: 0.7986 (mmp) cc_final: 0.7490 (tpp) REVERT: E 50 TYR cc_start: 0.9145 (m-10) cc_final: 0.8864 (m-80) REVERT: E 93 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8418 (mmtp) REVERT: E 96 LEU cc_start: 0.9749 (tm) cc_final: 0.9502 (pp) REVERT: E 116 ARG cc_start: 0.8939 (mmp80) cc_final: 0.8610 (mmp80) REVERT: E 140 MET cc_start: 0.7753 (mmp) cc_final: 0.7542 (tpp) REVERT: F 102 GLU cc_start: 0.9301 (tm-30) cc_final: 0.8770 (tm-30) REVERT: F 104 GLN cc_start: 0.9139 (tm-30) cc_final: 0.8740 (tm-30) REVERT: F 116 ARG cc_start: 0.8978 (mmm160) cc_final: 0.8389 (mmp80) REVERT: F 120 ARG cc_start: 0.8459 (mmt90) cc_final: 0.8121 (mtt180) REVERT: F 140 MET cc_start: 0.7958 (mmp) cc_final: 0.7548 (tpp) REVERT: G 93 LYS cc_start: 0.9164 (mmtt) cc_final: 0.8727 (mmmm) REVERT: G 96 LEU cc_start: 0.9721 (tm) cc_final: 0.9507 (pp) REVERT: G 102 GLU cc_start: 0.9342 (tm-30) cc_final: 0.8680 (tm-30) outliers start: 33 outliers final: 14 residues processed: 331 average time/residue: 0.6061 time to fit residues: 225.0986 Evaluate side-chains 327 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 311 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain G residue 145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 1 optimal weight: 30.0000 chunk 4 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 132 optimal weight: 20.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.129800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.065543 restraints weight = 31527.610| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 2.29 r_work: 0.2517 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.2395 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19320 Z= 0.118 Angle : 0.649 13.927 25916 Z= 0.316 Chirality : 0.045 0.376 2933 Planarity : 0.004 0.055 3122 Dihedral : 12.537 70.925 3661 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.46 % Allowed : 22.89 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.17), residues: 2303 helix: 2.75 (0.14), residues: 1309 sheet: 0.17 (0.30), residues: 273 loop : -1.75 (0.18), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 271 TYR 0.062 0.001 TYR D 50 PHE 0.027 0.001 PHE A 148 TRP 0.006 0.001 TRP C 201 HIS 0.001 0.000 HIS E 43 Details of bonding type rmsd covalent geometry : bond 0.00264 (19320) covalent geometry : angle 0.64924 (25914) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03524 ( 1229) hydrogen bonds : angle 3.54848 ( 3540) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 315 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.8903 (mmtt) cc_final: 0.8574 (mmtp) REVERT: A 140 MET cc_start: 0.8060 (mmp) cc_final: 0.7633 (tpp) REVERT: A 280 GLN cc_start: 0.9311 (OUTLIER) cc_final: 0.9081 (tp40) REVERT: B 50 TYR cc_start: 0.9038 (m-10) cc_final: 0.8724 (m-80) REVERT: B 120 ARG cc_start: 0.8347 (mmt90) cc_final: 0.7901 (mtp180) REVERT: B 140 MET cc_start: 0.7696 (mmp) cc_final: 0.7387 (tpp) REVERT: C 50 TYR cc_start: 0.8960 (m-10) cc_final: 0.8713 (m-80) REVERT: C 116 ARG cc_start: 0.8897 (mmp80) cc_final: 0.8595 (mmp80) REVERT: C 120 ARG cc_start: 0.8315 (mtm180) cc_final: 0.8039 (mtm180) REVERT: C 140 MET cc_start: 0.8078 (mmp) cc_final: 0.7768 (tpp) REVERT: D 116 ARG cc_start: 0.8929 (mmp80) cc_final: 0.8691 (mmm160) REVERT: D 120 ARG cc_start: 0.8381 (mtt180) cc_final: 0.8091 (mtm180) REVERT: E 50 TYR cc_start: 0.9162 (m-10) cc_final: 0.8854 (m-80) REVERT: E 93 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8665 (mmtp) REVERT: E 96 LEU cc_start: 0.9741 (tm) cc_final: 0.9520 (pp) REVERT: E 103 LYS cc_start: 0.9206 (mmtt) cc_final: 0.9005 (mmtm) REVERT: F 102 GLU cc_start: 0.9284 (tm-30) cc_final: 0.8761 (tm-30) REVERT: F 104 GLN cc_start: 0.9128 (tm-30) cc_final: 0.8726 (tm-30) REVERT: F 116 ARG cc_start: 0.8944 (mmm160) cc_final: 0.8425 (mmp80) REVERT: F 120 ARG cc_start: 0.8343 (mmt90) cc_final: 0.7995 (mtt180) REVERT: F 140 MET cc_start: 0.7940 (mmp) cc_final: 0.7544 (tpp) REVERT: G 93 LYS cc_start: 0.9167 (mmtt) cc_final: 0.8713 (mmmm) REVERT: G 96 LEU cc_start: 0.9714 (tm) cc_final: 0.9502 (pp) outliers start: 26 outliers final: 16 residues processed: 323 average time/residue: 0.6213 time to fit residues: 223.9397 Evaluate side-chains 332 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 314 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain G residue 145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 135 optimal weight: 50.0000 chunk 59 optimal weight: 2.9990 chunk 91 optimal weight: 0.0980 chunk 186 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 211 optimal weight: 6.9990 chunk 102 optimal weight: 50.0000 chunk 136 optimal weight: 9.9990 chunk 132 optimal weight: 40.0000 chunk 7 optimal weight: 8.9990 chunk 180 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.127590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.064807 restraints weight = 31854.588| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 2.19 r_work: 0.2460 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work: 0.2330 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19320 Z= 0.184 Angle : 0.713 16.615 25916 Z= 0.347 Chirality : 0.046 0.216 2933 Planarity : 0.004 0.058 3122 Dihedral : 12.969 73.158 3661 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.26 % Favored : 97.70 % Rotamer: Outliers : 1.07 % Allowed : 23.62 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.17), residues: 2303 helix: 2.44 (0.14), residues: 1351 sheet: 0.05 (0.30), residues: 259 loop : -1.98 (0.18), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 271 TYR 0.014 0.001 TYR F 291 PHE 0.028 0.002 PHE A 148 TRP 0.010 0.001 TRP B 184 HIS 0.003 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00436 (19320) covalent geometry : angle 0.71332 (25914) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.04467 ( 1229) hydrogen bonds : angle 3.78154 ( 3540) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 310 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.9247 (tm-30) cc_final: 0.8571 (tm-30) REVERT: A 116 ARG cc_start: 0.8908 (mmm160) cc_final: 0.8251 (mmp80) REVERT: A 140 MET cc_start: 0.8088 (mmp) cc_final: 0.7690 (tpp) REVERT: A 280 GLN cc_start: 0.9373 (OUTLIER) cc_final: 0.9112 (tp40) REVERT: B 50 TYR cc_start: 0.9052 (m-10) cc_final: 0.8754 (m-80) REVERT: B 116 ARG cc_start: 0.8960 (mmm160) cc_final: 0.8613 (mmp80) REVERT: B 120 ARG cc_start: 0.8471 (mmt90) cc_final: 0.8095 (mtt180) REVERT: B 140 MET cc_start: 0.7762 (mmp) cc_final: 0.7433 (tpp) REVERT: C 50 TYR cc_start: 0.8950 (m-10) cc_final: 0.8667 (m-80) REVERT: C 102 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8867 (tm-30) REVERT: C 116 ARG cc_start: 0.8913 (mmp80) cc_final: 0.8390 (mmp80) REVERT: C 120 ARG cc_start: 0.8431 (mtm180) cc_final: 0.8177 (mtm180) REVERT: C 140 MET cc_start: 0.8046 (mmp) cc_final: 0.7811 (tpp) REVERT: D 120 ARG cc_start: 0.8486 (mtt180) cc_final: 0.8210 (mtm180) REVERT: E 50 TYR cc_start: 0.9166 (m-10) cc_final: 0.8858 (m-80) REVERT: E 93 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8454 (mmtp) REVERT: E 96 LEU cc_start: 0.9743 (tm) cc_final: 0.9511 (pp) REVERT: E 116 ARG cc_start: 0.8873 (mmp80) cc_final: 0.8597 (mmp80) REVERT: F 102 GLU cc_start: 0.9296 (tm-30) cc_final: 0.8720 (tm-30) REVERT: F 104 GLN cc_start: 0.9136 (tm-30) cc_final: 0.8746 (tm-30) REVERT: F 116 ARG cc_start: 0.8934 (mmm160) cc_final: 0.8437 (mmp80) REVERT: F 120 ARG cc_start: 0.8478 (mmt90) cc_final: 0.8127 (mtt180) REVERT: F 140 MET cc_start: 0.8004 (mmp) cc_final: 0.7582 (tpp) REVERT: G 93 LYS cc_start: 0.9171 (mmtt) cc_final: 0.8750 (mmmt) outliers start: 19 outliers final: 13 residues processed: 316 average time/residue: 0.6691 time to fit residues: 236.3652 Evaluate side-chains 322 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 307 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 127 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 110 optimal weight: 5.9990 chunk 94 optimal weight: 0.4980 chunk 38 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 134 optimal weight: 40.0000 chunk 196 optimal weight: 0.8980 chunk 227 optimal weight: 0.7980 chunk 174 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.128902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.064731 restraints weight = 31857.862| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 2.28 r_work: 0.2500 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work: 0.2370 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19320 Z= 0.129 Angle : 0.695 17.297 25916 Z= 0.334 Chirality : 0.046 0.351 2933 Planarity : 0.004 0.058 3122 Dihedral : 12.709 73.114 3661 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.13 % Favored : 97.83 % Rotamer: Outliers : 1.12 % Allowed : 24.30 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.17), residues: 2303 helix: 2.62 (0.14), residues: 1309 sheet: 0.15 (0.30), residues: 273 loop : -1.82 (0.18), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 271 TYR 0.057 0.001 TYR D 50 PHE 0.029 0.001 PHE A 148 TRP 0.007 0.001 TRP F 201 HIS 0.005 0.000 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00293 (19320) covalent geometry : angle 0.69461 (25914) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03767 ( 1229) hydrogen bonds : angle 3.68921 ( 3540) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10671.68 seconds wall clock time: 181 minutes 36.15 seconds (10896.15 seconds total)