Starting phenix.real_space_refine on Fri Aug 7 05:12:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e64_47549/08_2026/9e64_47549.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e64_47549/08_2026/9e64_47549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e64_47549/08_2026/9e64_47549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e64_47549/08_2026/9e64_47549.map" model { file = "/net/cci-nas-00/data/ceres_data/9e64_47549/08_2026/9e64_47549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e64_47549/08_2026/9e64_47549.cif" } resolution = 3.0 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= 0.001 sd= 0.030 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-2.2rc3-6140/lib/python3.11/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: 4.09, per 1000 atoms: 0.22 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: 1.95 Conformation dependent library (CDL) restraints added in 851.6 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: 0.59 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: 3.17 Time building geometry restraints manager: 2.52 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: 0.07 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: 5.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.590 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0058 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/Z covalent geometry : bond 0.00447 / 0.23 (19320) covalent geometry : angle 0.75401 / 0.36 (25914) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.13836 / 9.50 ( 1229) hydrogen bonds : angle 4.74627 / 3.39 ( 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 235 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 227 time to evaluate : 1.122 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: -0.0235 (tpp) cc_final: -0.1519 (ptt) REVERT: A 140 MET cc_start: -0.1097 (mmt) cc_final: -0.2680 (mmt) REVERT: B 118 MET cc_start: -0.0370 (tpp) cc_final: -0.1574 (ptt) REVERT: B 140 MET cc_start: -0.1375 (mmt) cc_final: -0.2693 (mmt) REVERT: C 118 MET cc_start: -0.0744 (tpp) cc_final: -0.1687 (ptt) REVERT: C 140 MET cc_start: -0.1531 (mmt) cc_final: -0.2846 (mmt) REVERT: D 118 MET cc_start: -0.0478 (tpp) cc_final: -0.1694 (ptt) REVERT: D 140 MET cc_start: -0.1767 (mmt) cc_final: -0.2948 (mmt) REVERT: E 140 MET cc_start: -0.1546 (mmt) cc_final: -0.2848 (mmt) REVERT: F 118 MET cc_start: -0.0735 (tpp) cc_final: -0.1699 (ptt) REVERT: F 140 MET cc_start: -0.1155 (mmt) cc_final: -0.2564 (mmt) REVERT: G 118 MET cc_start: -0.0274 (tpp) cc_final: -0.1489 (ptt) REVERT: G 140 MET cc_start: -0.1317 (mmt) cc_final: -0.2690 (mmt) outliers start: 8 outliers final: 1 residues processed: 235 average time/residue: 0.5409 time to fit residues: 144.4167 Evaluate side-chains 154 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 220 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 59.1128 > 50:) chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 0.5980 chunk 227 optimal weight: 0.4980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 50.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 HIS A 306 GLN B 265 HIS B 306 GLN C 265 HIS C 306 GLN D 265 HIS D 306 GLN E 265 HIS E 306 GLN F 265 HIS F 306 GLN ** G 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 HIS G 306 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5409 r_free = 0.5409 target = 0.302621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.5285 r_free = 0.5285 target = 0.286965 restraints weight = 62576.554| |-----------------------------------------------------------------------------| r_work (start): 0.5255 rms_B_bonded: 5.06 r_work (final): 0.5255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0717 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19320 Z= 0.141 Angle : 0.594 7.503 25916 Z= 0.306 Chirality : 0.042 0.190 2933 Planarity : 0.004 0.046 3122 Dihedral : 15.750 73.528 3663 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.13 % Favored : 97.57 % Rotamer: Outliers : 1.86 % Allowed : 21.65 % 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: 1.09 (0.16), residues: 2303 helix: 2.24 (0.13), residues: 1295 sheet: 0.20 (0.30), residues: 273 loop : -1.97 (0.18), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 177 TYR 0.014 0.002 TYR A 291 PHE 0.016 0.001 PHE F 175 TRP 0.010 0.002 TRP A 184 HIS 0.003 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.14 (19320) covalent geometry : angle 0.59370 / 0.31 (25914) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03845 / 2.67 ( 1229) hydrogen bonds : angle 3.85829 / 2.79 ( 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 211 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 0.625 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ARG cc_start: -0.2826 (tpt170) cc_final: -0.3317 (tpt170) REVERT: A 118 MET cc_start: -0.0767 (tpp) cc_final: -0.1548 (ptt) REVERT: A 140 MET cc_start: -0.4556 (mmt) cc_final: -0.5284 (mmt) REVERT: A 174 TYR cc_start: 0.2825 (t80) cc_final: 0.2305 (t80) REVERT: A 231 ARG cc_start: 0.2399 (mtt180) cc_final: 0.0344 (mtt180) REVERT: B 110 ARG cc_start: -0.1680 (tpt170) cc_final: -0.2065 (tpt170) REVERT: B 118 MET cc_start: 0.0164 (tpp) cc_final: -0.0923 (ptt) REVERT: B 140 MET cc_start: -0.4164 (mmt) cc_final: -0.4904 (mmt) REVERT: B 174 TYR cc_start: 0.3159 (t80) cc_final: 0.2558 (t80) REVERT: B 231 ARG cc_start: 0.2689 (mtt180) cc_final: 0.1478 (mtt180) REVERT: C 110 ARG cc_start: -0.1535 (tpt170) cc_final: -0.1868 (tpt170) REVERT: C 118 MET cc_start: -0.0137 (tpp) cc_final: -0.1210 (ptt) REVERT: C 140 MET cc_start: -0.5004 (mmt) cc_final: -0.5535 (mmt) REVERT: C 174 TYR cc_start: 0.3294 (t80) cc_final: 0.2641 (t80) REVERT: C 231 ARG cc_start: 0.2531 (mtt180) cc_final: 0.0190 (mtt-85) REVERT: D 110 ARG cc_start: -0.2171 (tpt170) cc_final: -0.2626 (tpt170) REVERT: D 118 MET cc_start: -0.0270 (tpp) cc_final: -0.1259 (ptt) REVERT: D 140 MET cc_start: -0.4656 (mmt) cc_final: -0.5249 (mmt) REVERT: D 174 TYR cc_start: 0.3304 (t80) cc_final: 0.2726 (t80) REVERT: D 231 ARG cc_start: 0.2332 (mtt180) cc_final: 0.0062 (mtt-85) REVERT: E 140 MET cc_start: -0.4576 (mmt) cc_final: -0.5362 (mmt) REVERT: E 174 TYR cc_start: 0.3443 (t80) cc_final: 0.2827 (t80) REVERT: E 231 ARG cc_start: 0.2591 (mtt180) cc_final: 0.0603 (ttm170) REVERT: F 118 MET cc_start: -0.0682 (tpp) cc_final: -0.1219 (ptt) REVERT: F 140 MET cc_start: -0.4351 (mmt) cc_final: -0.4912 (mmt) REVERT: F 231 ARG cc_start: 0.2303 (mtt180) cc_final: 0.0255 (ttm170) REVERT: G 118 MET cc_start: -0.0112 (tpp) cc_final: -0.1268 (ptt) REVERT: G 140 MET cc_start: -0.3999 (mmt) cc_final: -0.4860 (mmt) REVERT: G 174 TYR cc_start: 0.3186 (t80) cc_final: 0.2502 (t80) REVERT: G 231 ARG cc_start: 0.2598 (mtt180) cc_final: 0.0714 (mtt90) outliers start: 33 outliers final: 16 residues processed: 193 average time/residue: 0.5740 time to fit residues: 124.8068 Evaluate side-chains 179 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain G residue 254 ILE Chi-restraints excluded: chain G residue 289 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 171 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 18 optimal weight: 0.0870 chunk 205 optimal weight: 40.0000 chunk 57 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 67 optimal weight: 50.0000 chunk 145 optimal weight: 0.0020 chunk 165 optimal weight: 60.0000 overall best weight: 1.3970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 ASN B 211 ASN C 211 ASN ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 228 ASN ** F 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5385 r_free = 0.5385 target = 0.299437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.5266 r_free = 0.5266 target = 0.284276 restraints weight = 63801.298| |-----------------------------------------------------------------------------| r_work (start): 0.5223 rms_B_bonded: 4.86 r_work (final): 0.5223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1109 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19320 Z= 0.132 Angle : 0.599 8.323 25916 Z= 0.307 Chirality : 0.042 0.183 2933 Planarity : 0.003 0.027 3122 Dihedral : 14.886 75.416 3661 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.31 % Allowed : 20.64 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.02 (0.16), residues: 2303 helix: 2.15 (0.13), residues: 1302 sheet: 0.20 (0.32), residues: 273 loop : -1.99 (0.19), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 212 TYR 0.012 0.001 TYR F 291 PHE 0.011 0.001 PHE A 148 TRP 0.030 0.004 TRP B 184 HIS 0.003 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (19320) covalent geometry : angle 0.59883 / 0.31 (25914) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03590 / 2.50 ( 1229) hydrogen bonds : angle 4.05184 / 2.92 ( 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 196 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 155 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: -0.0735 (tpp) cc_final: -0.1649 (ppp) REVERT: A 140 MET cc_start: -0.5189 (mmt) cc_final: -0.5629 (mmt) REVERT: A 174 TYR cc_start: 0.2935 (t80) cc_final: 0.2467 (t80) REVERT: A 231 ARG cc_start: 0.2852 (mtt180) cc_final: 0.2629 (mtm180) REVERT: B 79 ASP cc_start: 0.5805 (m-30) cc_final: 0.5441 (m-30) REVERT: B 118 MET cc_start: -0.0026 (tpp) cc_final: -0.1214 (ptt) REVERT: B 140 MET cc_start: -0.4759 (mmt) cc_final: -0.5067 (mmt) REVERT: C 118 MET cc_start: -0.0034 (tpp) cc_final: -0.0436 (mmm) REVERT: C 140 MET cc_start: -0.5424 (mmt) cc_final: -0.5804 (mmt) REVERT: C 142 LEU cc_start: 0.0870 (OUTLIER) cc_final: 0.0506 (mm) REVERT: C 174 TYR cc_start: 0.3446 (t80) cc_final: 0.2938 (t80) REVERT: D 110 ARG cc_start: -0.2198 (tpt170) cc_final: -0.2591 (tpt170) REVERT: D 118 MET cc_start: -0.0158 (tpp) cc_final: -0.1450 (ptt) REVERT: D 140 MET cc_start: -0.4683 (mmt) cc_final: -0.5052 (mmt) REVERT: E 140 MET cc_start: -0.5309 (mmt) cc_final: -0.5672 (mmt) REVERT: E 174 TYR cc_start: 0.3231 (t80) cc_final: 0.2466 (t80) REVERT: F 140 MET cc_start: -0.5658 (mmt) cc_final: -0.5995 (mmt) REVERT: G 118 MET cc_start: 0.0034 (tpp) cc_final: -0.1131 (ptt) REVERT: G 140 MET cc_start: -0.4935 (mmt) cc_final: -0.5364 (mmt) REVERT: G 142 LEU cc_start: 0.0663 (OUTLIER) cc_final: 0.0308 (mm) outliers start: 41 outliers final: 9 residues processed: 186 average time/residue: 0.5498 time to fit residues: 115.7631 Evaluate side-chains 147 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain E residue 228 ASN Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain F residue 333 MET Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 254 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 181 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 chunk 187 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 219 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 228 ASN F 234 ASN ** G 211 ASN ** 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 = 0.5423 r_free = 0.5423 target = 0.307592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5475 r_free = 0.5475 target = 0.295935 restraints weight = 69457.353| |-----------------------------------------------------------------------------| r_work (start): 0.5227 rms_B_bonded: 2.65 r_work: 0.5147 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.5147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1978 moved from start: 0.7728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 19320 Z= 0.253 Angle : 0.867 11.895 25916 Z= 0.457 Chirality : 0.051 0.284 2933 Planarity : 0.005 0.052 3122 Dihedral : 16.589 76.101 3661 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 21.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.16 % Allowed : 20.87 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.02 (0.17), residues: 2303 helix: 1.33 (0.13), residues: 1323 sheet: -0.96 (0.33), residues: 266 loop : -2.25 (0.18), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 231 TYR 0.031 0.002 TYR D 215 PHE 0.023 0.002 PHE F 179 TRP 0.023 0.004 TRP B 299 HIS 0.015 0.003 HIS E 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.25 (19320) covalent geometry : angle 0.86731 / 0.46 (25914) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.05072 / 3.52 ( 1229) hydrogen bonds : angle 5.16774 / 3.74 ( 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 214 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 140 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: A 140 MET cc_start: -0.4624 (mmt) cc_final: -0.4953 (mmt) REVERT: B 118 MET cc_start: -0.0271 (tpp) cc_final: -0.0690 (mmm) REVERT: B 140 MET cc_start: -0.3968 (mmt) cc_final: -0.4221 (mmt) REVERT: C 118 MET cc_start: -0.0036 (tpp) cc_final: -0.0370 (mmm) REVERT: C 140 MET cc_start: -0.4694 (mmt) cc_final: -0.5103 (mmt) REVERT: C 142 LEU cc_start: 0.0824 (OUTLIER) cc_final: 0.0497 (mm) REVERT: D 140 MET cc_start: -0.4341 (mmt) cc_final: -0.4627 (mmt) REVERT: D 254 ILE cc_start: 0.3631 (OUTLIER) cc_final: 0.1531 (pt) REVERT: E 140 MET cc_start: -0.4915 (mmt) cc_final: -0.5210 (mmt) REVERT: F 110 ARG cc_start: -0.1192 (tpt170) cc_final: -0.1437 (mmt180) REVERT: F 140 MET cc_start: -0.4974 (mmt) cc_final: -0.5209 (mmt) REVERT: F 161 LYS cc_start: 0.1538 (OUTLIER) cc_final: 0.0388 (tttm) REVERT: G 118 MET cc_start: -0.0265 (tpp) cc_final: -0.0726 (mmm) REVERT: G 140 MET cc_start: -0.4385 (mmt) cc_final: -0.4785 (mmt) REVERT: G 142 LEU cc_start: 0.0147 (OUTLIER) cc_final: -0.0182 (mm) REVERT: G 154 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6425 (tm) REVERT: G 158 MET cc_start: 0.1546 (mtm) cc_final: 0.1175 (ttt) REVERT: G 161 LYS cc_start: 0.1324 (OUTLIER) cc_final: -0.0182 (tttm) outliers start: 74 outliers final: 39 residues processed: 198 average time/residue: 0.5758 time to fit residues: 129.6247 Evaluate side-chains 178 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 133 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain F residue 161 LYS Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 228 ASN Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 254 ILE Chi-restraints excluded: chain G residue 289 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 100 optimal weight: 10.0000 chunk 188 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 59 optimal weight: 0.4980 chunk 206 optimal weight: 5.9990 chunk 168 optimal weight: 50.0000 chunk 133 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 132 optimal weight: 50.0000 chunk 176 optimal weight: 7.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 105 GLN E 137 HIS ** G 211 ASN ** 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 = 0.5415 r_free = 0.5415 target = 0.304981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5462 r_free = 0.5462 target = 0.293247 restraints weight = 67690.084| |-----------------------------------------------------------------------------| r_work (start): 0.5216 rms_B_bonded: 2.73 r_work: 0.5133 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.5133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2189 moved from start: 0.9359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 19320 Z= 0.241 Angle : 0.797 9.286 25916 Z= 0.416 Chirality : 0.049 0.215 2933 Planarity : 0.005 0.062 3122 Dihedral : 15.695 72.214 3661 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 21.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.06 % Allowed : 20.64 % Favored : 74.30 % 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: -0.42 (0.16), residues: 2303 helix: 1.07 (0.13), residues: 1323 sheet: -0.35 (0.37), residues: 196 loop : -2.71 (0.17), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG F 231 TYR 0.027 0.002 TYR G 215 PHE 0.024 0.002 PHE E 293 TRP 0.029 0.004 TRP E 302 HIS 0.010 0.003 HIS G 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.24 (19320) covalent geometry : angle 0.79734 / 0.42 (25914) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.05591 / 3.77 ( 1229) hydrogen bonds : angle 5.49869 / 3.94 ( 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 227 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 137 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ARG cc_start: 0.0225 (mmt180) cc_final: -0.0049 (tpt170) REVERT: A 140 MET cc_start: -0.4762 (mmt) cc_final: -0.5063 (mmt) REVERT: A 238 THR cc_start: 0.2638 (OUTLIER) cc_final: 0.2383 (p) REVERT: B 239 THR cc_start: 0.4330 (OUTLIER) cc_final: 0.3204 (t) REVERT: C 140 MET cc_start: -0.4855 (mmt) cc_final: -0.5259 (mmt) REVERT: C 142 LEU cc_start: 0.1186 (OUTLIER) cc_final: 0.0865 (mm) REVERT: C 158 MET cc_start: 0.2254 (ptt) cc_final: 0.2022 (ptt) REVERT: C 239 THR cc_start: 0.4336 (OUTLIER) cc_final: 0.3196 (t) REVERT: D 110 ARG cc_start: -0.0025 (mmt180) cc_final: -0.0260 (tpt170) REVERT: D 140 MET cc_start: -0.4873 (mmt) cc_final: -0.5198 (mmt) REVERT: E 140 MET cc_start: -0.5238 (mmt) cc_final: -0.5533 (mmt) REVERT: E 158 MET cc_start: 0.0705 (ttt) cc_final: 0.0444 (ptm) REVERT: F 140 MET cc_start: -0.4770 (mmt) cc_final: -0.5055 (mmt) REVERT: G 140 MET cc_start: -0.5063 (mmt) cc_final: -0.5321 (mmt) outliers start: 90 outliers final: 46 residues processed: 217 average time/residue: 0.4534 time to fit residues: 114.7777 Evaluate side-chains 173 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 123 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain G residue 254 ILE Chi-restraints excluded: chain G residue 289 MET Chi-restraints excluded: chain G residue 309 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 94 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 212 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 214 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 50.0000 chunk 55 optimal weight: 0.9980 chunk 217 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 136 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 ASN B 211 ASN C 211 ASN ** F 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5406 r_free = 0.5406 target = 0.304118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5452 r_free = 0.5452 target = 0.292790 restraints weight = 68216.432| |-----------------------------------------------------------------------------| r_work (start): 0.5209 rms_B_bonded: 2.75 r_work: 0.5129 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.5129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2027 moved from start: 0.9657 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= 0.146 Angle : 0.610 8.398 25916 Z= 0.321 Chirality : 0.044 0.195 2933 Planarity : 0.004 0.039 3122 Dihedral : 14.819 68.007 3661 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.50 % Allowed : 20.98 % Favored : 74.52 % 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: 0.06 (0.16), residues: 2303 helix: 1.48 (0.13), residues: 1330 sheet: -0.50 (0.37), residues: 196 loop : -2.47 (0.18), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 231 TYR 0.016 0.001 TYR B 174 PHE 0.016 0.001 PHE F 47 TRP 0.015 0.002 TRP B 299 HIS 0.004 0.001 HIS D 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (19320) covalent geometry : angle 0.61039 / 0.32 (25914) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.04030 / 2.75 ( 1229) hydrogen bonds : angle 4.84147 / 3.47 ( 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 211 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 131 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASP cc_start: 0.5575 (m-30) cc_final: 0.5349 (m-30) REVERT: A 140 MET cc_start: -0.4626 (mmt) cc_final: -0.4924 (mmt) REVERT: C 158 MET cc_start: 0.2090 (ptt) cc_final: 0.1829 (ptt) REVERT: C 239 THR cc_start: 0.4200 (OUTLIER) cc_final: 0.3919 (p) REVERT: D 140 MET cc_start: -0.4870 (mmt) cc_final: -0.5194 (mmt) REVERT: D 158 MET cc_start: 0.2157 (ttt) cc_final: 0.1342 (ptt) REVERT: E 140 MET cc_start: -0.5005 (mmt) cc_final: -0.5262 (mmt) REVERT: E 158 MET cc_start: 0.1698 (ttt) cc_final: 0.0824 (mtm) REVERT: F 140 MET cc_start: -0.4522 (mmt) cc_final: -0.4822 (mmt) REVERT: F 239 THR cc_start: 0.4380 (OUTLIER) cc_final: 0.3954 (p) REVERT: G 140 MET cc_start: -0.4944 (mmt) cc_final: -0.5189 (mmt) outliers start: 80 outliers final: 46 residues processed: 195 average time/residue: 0.4794 time to fit residues: 107.6490 Evaluate side-chains 173 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 125 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 232 MET Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 254 ILE Chi-restraints excluded: chain G residue 289 MET Chi-restraints excluded: chain G residue 309 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 226 optimal weight: 5.9990 chunk 156 optimal weight: 0.4980 chunk 114 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 199 optimal weight: 7.9990 chunk 213 optimal weight: 7.9990 chunk 67 optimal weight: 30.0000 chunk 22 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 184 optimal weight: 8.9990 chunk 141 optimal weight: 6.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 HIS B 137 HIS ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 HIS ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 HIS F 137 HIS ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5380 r_free = 0.5380 target = 0.296168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.5425 r_free = 0.5425 target = 0.282785 restraints weight = 67316.893| |-----------------------------------------------------------------------------| r_work (start): 0.5134 rms_B_bonded: 3.07 r_work: 0.5045 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.5045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2824 moved from start: 1.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 19320 Z= 0.348 Angle : 1.059 12.437 25916 Z= 0.557 Chirality : 0.058 0.328 2933 Planarity : 0.008 0.104 3122 Dihedral : 17.618 87.005 3661 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 32.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.82 % Favored : 93.05 % Rotamer: Outliers : 5.29 % Allowed : 21.32 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % 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: -1.24 (0.17), residues: 2303 helix: 0.62 (0.14), residues: 1295 sheet: -1.17 (0.41), residues: 182 loop : -3.17 (0.17), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG A 236 TYR 0.037 0.003 TYR E 215 PHE 0.032 0.003 PHE G 175 TRP 0.051 0.006 TRP D 302 HIS 0.013 0.004 HIS F 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00766 / 0.35 (19320) covalent geometry : angle 1.05885 / 0.56 (25914) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.06732 / 4.60 ( 1229) hydrogen bonds : angle 6.98772 / 4.99 ( 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 247 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 153 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LEU cc_start: 0.6906 (tm) cc_final: 0.6636 (tt) REVERT: A 158 MET cc_start: 0.2506 (OUTLIER) cc_final: -0.0218 (ttt) REVERT: C 158 MET cc_start: 0.2477 (ptt) cc_final: 0.2252 (ptt) REVERT: C 231 ARG cc_start: 0.3818 (mtt180) cc_final: 0.3107 (mtt90) REVERT: D 317 VAL cc_start: 0.7934 (t) cc_final: 0.7247 (p) REVERT: F 110 ARG cc_start: 0.2117 (mmt180) cc_final: 0.1870 (mmt180) REVERT: F 158 MET cc_start: 0.2073 (ptp) cc_final: 0.1808 (ttp) REVERT: G 154 LEU cc_start: 0.5991 (OUTLIER) cc_final: 0.5690 (tt) REVERT: G 158 MET cc_start: 0.1524 (mtm) cc_final: 0.1112 (ttt) outliers start: 94 outliers final: 64 residues processed: 228 average time/residue: 0.4548 time to fit residues: 120.1000 Evaluate side-chains 197 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 131 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 232 MET Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 254 ILE Chi-restraints excluded: chain G residue 289 MET Chi-restraints excluded: chain G residue 309 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 132 optimal weight: 40.0000 chunk 216 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 211 ASN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 ASN ** 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 = 0.5388 r_free = 0.5388 target = 0.297823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5437 r_free = 0.5437 target = 0.284899 restraints weight = 67794.459| |-----------------------------------------------------------------------------| r_work (start): 0.5164 rms_B_bonded: 2.98 r_work: 0.5079 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.5079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2534 moved from start: 1.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19320 Z= 0.193 Angle : 0.720 9.882 25916 Z= 0.384 Chirality : 0.046 0.205 2933 Planarity : 0.005 0.058 3122 Dihedral : 15.701 80.349 3661 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 21.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.27 % Allowed : 23.23 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.76 (0.17), residues: 2303 helix: 0.89 (0.14), residues: 1337 sheet: -1.07 (0.42), residues: 182 loop : -2.89 (0.18), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 231 TYR 0.021 0.002 TYR B 215 PHE 0.019 0.002 PHE G 175 TRP 0.030 0.003 TRP A 302 HIS 0.006 0.001 HIS D 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 (19320) covalent geometry : angle 0.72047 / 0.38 (25914) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.04687 / 3.22 ( 1229) hydrogen bonds : angle 5.84242 / 4.17 ( 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 220 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 144 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LEU cc_start: 0.6515 (tm) cc_final: 0.6266 (tt) REVERT: A 158 MET cc_start: 0.2194 (OUTLIER) cc_final: -0.0470 (mmm) REVERT: C 158 MET cc_start: 0.2189 (ptt) cc_final: 0.1976 (ptt) REVERT: D 317 VAL cc_start: 0.7740 (t) cc_final: 0.7194 (p) REVERT: F 110 ARG cc_start: 0.1756 (mmt180) cc_final: 0.1485 (mmt180) REVERT: F 158 MET cc_start: 0.1899 (ptp) cc_final: 0.1476 (ttt) outliers start: 76 outliers final: 58 residues processed: 194 average time/residue: 0.4373 time to fit residues: 97.9944 Evaluate side-chains 198 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 139 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 316 ILE Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 254 ILE Chi-restraints excluded: chain G residue 289 MET Chi-restraints excluded: chain G residue 309 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 1 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 120 optimal weight: 0.0270 chunk 119 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 221 optimal weight: 0.4980 chunk 63 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 132 optimal weight: 50.0000 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5395 r_free = 0.5395 target = 0.299201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.5439 r_free = 0.5439 target = 0.287854 restraints weight = 68714.826| |-----------------------------------------------------------------------------| r_work (start): 0.5192 rms_B_bonded: 2.85 r_work: 0.5119 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.5119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2090 moved from start: 1.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19320 Z= 0.119 Angle : 0.588 12.251 25916 Z= 0.309 Chirality : 0.042 0.181 2933 Planarity : 0.005 0.073 3122 Dihedral : 14.004 74.506 3661 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.25 % Allowed : 25.76 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.17), residues: 2303 helix: 1.37 (0.14), residues: 1344 sheet: -1.75 (0.31), residues: 294 loop : -2.63 (0.20), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 212 TYR 0.018 0.001 TYR A 245 PHE 0.015 0.001 PHE B 175 TRP 0.009 0.001 TRP C 201 HIS 0.003 0.001 HIS C 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (19320) covalent geometry : angle 0.58836 / 0.31 (25914) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03494 / 2.41 ( 1229) hydrogen bonds : angle 4.86857 / 3.46 ( 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 203 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: -0.0153 (pp-130) cc_final: -0.3824 (tpt) REVERT: A 154 LEU cc_start: 0.6420 (tm) cc_final: 0.6085 (tt) REVERT: A 158 MET cc_start: 0.1759 (OUTLIER) cc_final: -0.0524 (tpt) REVERT: C 158 MET cc_start: 0.2176 (ptt) cc_final: 0.1946 (ptt) REVERT: F 158 MET cc_start: 0.1741 (OUTLIER) cc_final: 0.1480 (ttt) REVERT: G 158 MET cc_start: 0.1084 (mtm) cc_final: 0.0499 (mtm) outliers start: 40 outliers final: 26 residues processed: 191 average time/residue: 0.4791 time to fit residues: 105.0773 Evaluate side-chains 185 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain G residue 254 ILE 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: 7.9990 chunk 91 optimal weight: 0.6980 chunk 186 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 211 optimal weight: 3.9990 chunk 102 optimal weight: 50.0000 chunk 136 optimal weight: 5.9990 chunk 132 optimal weight: 50.0000 chunk 7 optimal weight: 30.0000 chunk 180 optimal weight: 2.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 211 ASN C 211 ASN F 211 ASN G 211 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5387 r_free = 0.5387 target = 0.296960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5441 r_free = 0.5441 target = 0.284950 restraints weight = 68315.409| |-----------------------------------------------------------------------------| r_work (start): 0.5167 rms_B_bonded: 3.03 r_work: 0.5090 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.5090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2394 moved from start: 1.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 19320 Z= 0.161 Angle : 0.663 11.207 25916 Z= 0.347 Chirality : 0.044 0.191 2933 Planarity : 0.005 0.066 3122 Dihedral : 14.144 76.387 3661 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.25 % Allowed : 26.32 % Favored : 71.43 % 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: -0.04 (0.17), residues: 2303 helix: 1.43 (0.14), residues: 1337 sheet: -0.90 (0.40), residues: 196 loop : -2.50 (0.18), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 212 TYR 0.018 0.002 TYR A 215 PHE 0.022 0.001 PHE A 293 TRP 0.018 0.003 TRP B 302 HIS 0.004 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (19320) covalent geometry : angle 0.66310 / 0.35 (25914) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03904 / 2.67 ( 1229) hydrogen bonds : angle 5.05802 / 3.61 ( 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 184 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASP cc_start: 0.5096 (m-30) cc_final: 0.4836 (m-30) REVERT: A 118 MET cc_start: 0.0182 (pp-130) cc_final: -0.3595 (mmm) REVERT: A 154 LEU cc_start: 0.6324 (tm) cc_final: 0.6022 (tt) REVERT: A 158 MET cc_start: 0.2181 (OUTLIER) cc_final: -0.0495 (mmm) REVERT: A 333 MET cc_start: 0.1903 (ptt) cc_final: 0.1483 (ptm) REVERT: B 158 MET cc_start: 0.2163 (mtm) cc_final: 0.1927 (mtm) REVERT: D 317 VAL cc_start: 0.7630 (t) cc_final: 0.6976 (p) REVERT: G 158 MET cc_start: 0.1148 (mtm) cc_final: 0.0485 (mtm) outliers start: 40 outliers final: 34 residues processed: 168 average time/residue: 0.5242 time to fit residues: 100.3864 Evaluate side-chains 173 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 316 ILE Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 254 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 110 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 194 optimal weight: 0.9980 chunk 218 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 196 optimal weight: 0.6980 chunk 227 optimal weight: 0.7980 chunk 174 optimal weight: 5.9990 chunk 40 optimal weight: 0.0370 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5385 r_free = 0.5385 target = 0.296871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5436 r_free = 0.5436 target = 0.284580 restraints weight = 68301.129| |-----------------------------------------------------------------------------| r_work (start): 0.5162 rms_B_bonded: 3.18 r_work: 0.5089 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.5089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2388 moved from start: 1.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.208 19320 Z= 0.254 Angle : 1.044 59.199 25916 Z= 0.635 Chirality : 0.049 0.732 2933 Planarity : 0.005 0.064 3122 Dihedral : 14.139 76.389 3661 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 21.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.42 % Allowed : 26.49 % Favored : 71.09 % Cbeta Deviations : 0.14 % 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: -0.03 (0.17), residues: 2303 helix: 1.43 (0.14), residues: 1337 sheet: -0.90 (0.40), residues: 196 loop : -2.50 (0.18), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 212 TYR 0.057 0.002 TYR F 310 PHE 0.018 0.001 PHE A 293 TRP 0.016 0.003 TRP B 302 HIS 0.003 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.25 (19320) covalent geometry : angle 1.04412 / 0.64 (25914) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03886 / 2.66 ( 1229) hydrogen bonds : angle 5.05716 / 3.61 ( 3540) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5949.35 seconds wall clock time: 102 minutes 9.68 seconds (6129.68 seconds total)