Starting phenix.real_space_refine on Sat Aug 23 14:47:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tup_41628/08_2025/8tup_41628.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tup_41628/08_2025/8tup_41628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tup_41628/08_2025/8tup_41628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tup_41628/08_2025/8tup_41628.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tup_41628/08_2025/8tup_41628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tup_41628/08_2025/8tup_41628.map" } resolution = 3.3 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= 0.031 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 Mg 3 5.21 5 S 65 5.16 5 C 8210 2.51 5 N 2155 2.21 5 O 2436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12869 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2560 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 309} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Restraints were copied for chains: B, C, D, E Time building chain proxies: 2.30, per 1000 atoms: 0.18 Number of scatterers: 12869 At special positions: 0 Unit cell: (107.07, 108.73, 140.27, 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 65 16.00 Mg 3 11.99 O 2436 8.00 N 2155 7.00 C 8210 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 412.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3030 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 5 sheets defined 69.5% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.953A pdb=" N ARG A 119 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE A 120 " --> pdb=" O ASP A 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 120' Processing helix chain 'A' and resid 161 through 166 Processing helix chain 'A' and resid 166 through 172 Processing helix chain 'A' and resid 183 through 219 Proline residue: A 209 - end of helix removed outlier: 3.755A pdb=" N ALA A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 218 " --> pdb=" O THR A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 261 removed outlier: 3.606A pdb=" N LEU A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N HIS A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 268 removed outlier: 3.528A pdb=" N LEU A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 275 Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.168A pdb=" N LYS A 281 " --> pdb=" O GLN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 360 removed outlier: 3.772A pdb=" N MET A 292 " --> pdb=" O HIS A 288 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 334 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET A 335 " --> pdb=" O HIS A 331 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N MET A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 399 removed outlier: 3.610A pdb=" N GLY A 386 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.954A pdb=" N ARG B 119 " --> pdb=" O ARG B 116 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE B 120 " --> pdb=" O ASP B 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 116 through 120' Processing helix chain 'B' and resid 161 through 166 Processing helix chain 'B' and resid 166 through 172 Processing helix chain 'B' and resid 183 through 219 Proline residue: B 209 - end of helix removed outlier: 3.755A pdb=" N ALA B 217 " --> pdb=" O GLU B 213 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 218 " --> pdb=" O THR B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 261 removed outlier: 3.605A pdb=" N LEU B 231 " --> pdb=" O ASP B 227 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N HIS B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE B 233 " --> pdb=" O SER B 229 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 268 removed outlier: 3.528A pdb=" N LEU B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 275 Processing helix chain 'B' and resid 277 through 282 removed outlier: 4.168A pdb=" N LYS B 281 " --> pdb=" O GLN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 360 removed outlier: 3.772A pdb=" N MET B 292 " --> pdb=" O HIS B 288 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP B 329 " --> pdb=" O PHE B 325 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG B 332 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 334 " --> pdb=" O SER B 330 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET B 335 " --> pdb=" O HIS B 331 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N MET B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY B 356 " --> pdb=" O PHE B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 399 removed outlier: 3.611A pdb=" N GLY B 386 " --> pdb=" O PHE B 382 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 116 through 120 removed outlier: 3.954A pdb=" N ARG C 119 " --> pdb=" O ARG C 116 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N PHE C 120 " --> pdb=" O ASP C 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 116 through 120' Processing helix chain 'C' and resid 161 through 166 Processing helix chain 'C' and resid 166 through 172 Processing helix chain 'C' and resid 183 through 219 Proline residue: C 209 - end of helix removed outlier: 3.754A pdb=" N ALA C 217 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 218 " --> pdb=" O THR C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 261 removed outlier: 3.606A pdb=" N LEU C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N HIS C 232 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE C 233 " --> pdb=" O SER C 229 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU C 261 " --> pdb=" O GLU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 268 removed outlier: 3.528A pdb=" N LEU C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 275 Processing helix chain 'C' and resid 277 through 282 removed outlier: 4.168A pdb=" N LYS C 281 " --> pdb=" O GLN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 360 removed outlier: 3.772A pdb=" N MET C 292 " --> pdb=" O HIS C 288 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP C 329 " --> pdb=" O PHE C 325 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG C 332 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET C 335 " --> pdb=" O HIS C 331 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N MET C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY C 356 " --> pdb=" O PHE C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 399 removed outlier: 3.610A pdb=" N GLY C 386 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 112 Processing helix chain 'D' and resid 116 through 120 removed outlier: 3.953A pdb=" N ARG D 119 " --> pdb=" O ARG D 116 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE D 120 " --> pdb=" O ASP D 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 120' Processing helix chain 'D' and resid 161 through 166 Processing helix chain 'D' and resid 166 through 172 Processing helix chain 'D' and resid 183 through 219 Proline residue: D 209 - end of helix removed outlier: 3.755A pdb=" N ALA D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 218 " --> pdb=" O THR D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 261 removed outlier: 3.606A pdb=" N LEU D 231 " --> pdb=" O ASP D 227 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N HIS D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE D 233 " --> pdb=" O SER D 229 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE D 258 " --> pdb=" O SER D 254 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU D 261 " --> pdb=" O GLU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 268 removed outlier: 3.529A pdb=" N LEU D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 275 Processing helix chain 'D' and resid 277 through 282 removed outlier: 4.168A pdb=" N LYS D 281 " --> pdb=" O GLN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 360 removed outlier: 3.772A pdb=" N MET D 292 " --> pdb=" O HIS D 288 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP D 329 " --> pdb=" O PHE D 325 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG D 332 " --> pdb=" O LEU D 328 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL D 334 " --> pdb=" O SER D 330 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET D 335 " --> pdb=" O HIS D 331 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N MET D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY D 356 " --> pdb=" O PHE D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 399 removed outlier: 3.610A pdb=" N GLY D 386 " --> pdb=" O PHE D 382 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU D 396 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY D 397 " --> pdb=" O LEU D 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 112 Processing helix chain 'E' and resid 116 through 120 removed outlier: 3.953A pdb=" N ARG E 119 " --> pdb=" O ARG E 116 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N PHE E 120 " --> pdb=" O ASP E 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 116 through 120' Processing helix chain 'E' and resid 161 through 166 Processing helix chain 'E' and resid 166 through 172 Processing helix chain 'E' and resid 183 through 219 Proline residue: E 209 - end of helix removed outlier: 3.755A pdb=" N ALA E 217 " --> pdb=" O GLU E 213 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E 218 " --> pdb=" O THR E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 261 removed outlier: 3.605A pdb=" N LEU E 231 " --> pdb=" O ASP E 227 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N HIS E 232 " --> pdb=" O ARG E 228 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE E 233 " --> pdb=" O SER E 229 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE E 258 " --> pdb=" O SER E 254 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU E 261 " --> pdb=" O GLU E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 268 removed outlier: 3.528A pdb=" N LEU E 268 " --> pdb=" O LEU E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 275 Processing helix chain 'E' and resid 277 through 282 removed outlier: 4.167A pdb=" N LYS E 281 " --> pdb=" O GLN E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 360 removed outlier: 3.772A pdb=" N MET E 292 " --> pdb=" O HIS E 288 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP E 329 " --> pdb=" O PHE E 325 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG E 332 " --> pdb=" O LEU E 328 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL E 334 " --> pdb=" O SER E 330 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET E 335 " --> pdb=" O HIS E 331 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N MET E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY E 356 " --> pdb=" O PHE E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 399 removed outlier: 3.611A pdb=" N GLY E 386 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU E 396 " --> pdb=" O LEU E 392 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY E 397 " --> pdb=" O LEU E 393 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 103 removed outlier: 3.803A pdb=" N VAL A 88 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 102 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS A 141 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 103 removed outlier: 3.803A pdb=" N VAL B 88 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 102 " --> pdb=" O PHE B 86 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS B 141 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 97 through 103 removed outlier: 3.803A pdb=" N VAL C 88 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG C 102 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS C 141 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 97 through 103 removed outlier: 3.803A pdb=" N VAL D 88 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D 102 " --> pdb=" O PHE D 86 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS D 141 " --> pdb=" O LEU D 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 97 through 103 removed outlier: 3.803A pdb=" N VAL E 88 " --> pdb=" O PHE E 100 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG E 102 " --> pdb=" O PHE E 86 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS E 141 " --> pdb=" O LEU E 152 " (cutoff:3.500A) 885 hydrogen bonds defined for protein. 2625 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: 1.71 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4230 1.34 - 1.46: 2607 1.46 - 1.58: 6068 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 13025 Sorted by residual: bond pdb=" CB PRO A 221 " pdb=" CG PRO A 221 " ideal model delta sigma weight residual 1.492 1.533 -0.041 5.00e-02 4.00e+02 6.67e-01 bond pdb=" CB PRO D 221 " pdb=" CG PRO D 221 " ideal model delta sigma weight residual 1.492 1.532 -0.040 5.00e-02 4.00e+02 6.55e-01 bond pdb=" CB PRO E 221 " pdb=" CG PRO E 221 " ideal model delta sigma weight residual 1.492 1.532 -0.040 5.00e-02 4.00e+02 6.50e-01 bond pdb=" CB PRO C 221 " pdb=" CG PRO C 221 " ideal model delta sigma weight residual 1.492 1.532 -0.040 5.00e-02 4.00e+02 6.46e-01 bond pdb=" CB PRO B 221 " pdb=" CG PRO B 221 " ideal model delta sigma weight residual 1.492 1.532 -0.040 5.00e-02 4.00e+02 6.33e-01 ... (remaining 13020 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 17270 1.10 - 2.21: 261 2.21 - 3.31: 44 3.31 - 4.41: 5 4.41 - 5.51: 15 Bond angle restraints: 17595 Sorted by residual: angle pdb=" CA GLU D 101 " pdb=" CB GLU D 101 " pdb=" CG GLU D 101 " ideal model delta sigma weight residual 114.10 118.23 -4.13 2.00e+00 2.50e-01 4.27e+00 angle pdb=" CA GLU B 101 " pdb=" CB GLU B 101 " pdb=" CG GLU B 101 " ideal model delta sigma weight residual 114.10 118.23 -4.13 2.00e+00 2.50e-01 4.26e+00 angle pdb=" CA GLU C 101 " pdb=" CB GLU C 101 " pdb=" CG GLU C 101 " ideal model delta sigma weight residual 114.10 118.23 -4.13 2.00e+00 2.50e-01 4.26e+00 angle pdb=" CA GLU A 101 " pdb=" CB GLU A 101 " pdb=" CG GLU A 101 " ideal model delta sigma weight residual 114.10 118.19 -4.09 2.00e+00 2.50e-01 4.18e+00 angle pdb=" CA GLU E 101 " pdb=" CB GLU E 101 " pdb=" CG GLU E 101 " ideal model delta sigma weight residual 114.10 118.18 -4.08 2.00e+00 2.50e-01 4.17e+00 ... (remaining 17590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 6905 16.14 - 32.27: 721 32.27 - 48.41: 229 48.41 - 64.54: 50 64.54 - 80.68: 10 Dihedral angle restraints: 7915 sinusoidal: 3270 harmonic: 4645 Sorted by residual: dihedral pdb=" CB MET D 381 " pdb=" CG MET D 381 " pdb=" SD MET D 381 " pdb=" CE MET D 381 " ideal model delta sinusoidal sigma weight residual 60.00 2.99 57.01 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CB MET C 381 " pdb=" CG MET C 381 " pdb=" SD MET C 381 " pdb=" CE MET C 381 " ideal model delta sinusoidal sigma weight residual 60.00 3.00 57.00 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CB MET E 381 " pdb=" CG MET E 381 " pdb=" SD MET E 381 " pdb=" CE MET E 381 " ideal model delta sinusoidal sigma weight residual 60.00 3.01 56.99 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 7912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1224 0.026 - 0.052: 545 0.052 - 0.078: 150 0.078 - 0.104: 77 0.104 - 0.130: 29 Chirality restraints: 2025 Sorted by residual: chirality pdb=" CA ILE A 126 " pdb=" N ILE A 126 " pdb=" C ILE A 126 " pdb=" CB ILE A 126 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA ILE C 126 " pdb=" N ILE C 126 " pdb=" C ILE C 126 " pdb=" CB ILE C 126 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA ILE E 126 " pdb=" N ILE E 126 " pdb=" C ILE E 126 " pdb=" CB ILE E 126 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 2022 not shown) Planarity restraints: 2240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 145 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO B 146 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 145 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO D 146 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 146 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 146 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 145 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.70e+00 pdb=" N PRO C 146 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 146 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 146 " -0.030 5.00e-02 4.00e+02 ... (remaining 2237 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3065 2.80 - 3.33: 12153 3.33 - 3.85: 21004 3.85 - 4.38: 24334 4.38 - 4.90: 43627 Nonbonded interactions: 104183 Sorted by model distance: nonbonded pdb=" OG SER D 125 " pdb=" O HOH D 501 " model vdw 2.277 3.040 nonbonded pdb=" OG SER E 125 " pdb=" O HOH E 501 " model vdw 2.278 3.040 nonbonded pdb=" OG SER C 125 " pdb=" O HOH C 501 " model vdw 2.278 3.040 nonbonded pdb=" OG SER B 125 " pdb=" O HOH B 601 " model vdw 2.278 3.040 nonbonded pdb=" OG SER A 125 " pdb=" O HOH A 601 " model vdw 2.278 3.040 ... (remaining 104178 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 83 through 400) selection = (chain 'B' and resid 83 through 400) selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 2.840 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.290 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13025 Z= 0.099 Angle : 0.406 5.513 17595 Z= 0.235 Chirality : 0.036 0.130 2025 Planarity : 0.003 0.054 2240 Dihedral : 14.814 80.680 4885 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 15.66 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.22), residues: 1580 helix: 2.00 (0.16), residues: 1025 sheet: 1.87 (0.43), residues: 135 loop : -0.50 (0.36), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 228 TYR 0.006 0.001 TYR C 299 PHE 0.012 0.001 PHE A 352 TRP 0.008 0.001 TRP D 196 HIS 0.003 0.001 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00206 (13025) covalent geometry : angle 0.40553 (17595) hydrogen bonds : bond 0.13917 ( 885) hydrogen bonds : angle 5.19141 ( 2625) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.323 Fit side-chains REVERT: A 336 MET cc_start: 0.8142 (mmt) cc_final: 0.7517 (mmt) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0912 time to fit residues: 10.2483 Evaluate side-chains 70 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0870 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 0.6980 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN B 131 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN C 131 ASN ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN D 122 HIS D 131 ASN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 ASN E 122 HIS ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.197598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.135191 restraints weight = 12228.575| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.38 r_work: 0.3006 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13025 Z= 0.217 Angle : 0.558 5.896 17595 Z= 0.294 Chirality : 0.042 0.144 2025 Planarity : 0.003 0.036 2240 Dihedral : 3.636 14.647 1710 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.63 % Allowed : 14.09 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.22), residues: 1580 helix: 1.77 (0.15), residues: 1030 sheet: 2.23 (0.43), residues: 145 loop : -0.13 (0.38), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 116 TYR 0.020 0.002 TYR A 299 PHE 0.016 0.002 PHE A 352 TRP 0.010 0.001 TRP C 196 HIS 0.003 0.001 HIS B 331 Details of bonding type rmsd covalent geometry : bond 0.00537 (13025) covalent geometry : angle 0.55810 (17595) hydrogen bonds : bond 0.05099 ( 885) hydrogen bonds : angle 4.18820 ( 2625) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 90 time to evaluate : 0.292 Fit side-chains REVERT: B 292 MET cc_start: 0.6251 (mtt) cc_final: 0.6007 (mtt) REVERT: D 228 ARG cc_start: 0.7065 (mtm-85) cc_final: 0.6863 (mtm-85) outliers start: 37 outliers final: 19 residues processed: 126 average time/residue: 0.1106 time to fit residues: 19.7185 Evaluate side-chains 105 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 274 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 92 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 11 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 137 optimal weight: 0.0870 chunk 75 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.200833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.141257 restraints weight = 12229.965| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.45 r_work: 0.3067 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13025 Z= 0.131 Angle : 0.460 6.318 17595 Z= 0.244 Chirality : 0.039 0.138 2025 Planarity : 0.003 0.037 2240 Dihedral : 3.452 12.925 1710 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.99 % Allowed : 14.09 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.22), residues: 1580 helix: 2.01 (0.15), residues: 1035 sheet: 2.08 (0.44), residues: 145 loop : -0.29 (0.38), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 102 TYR 0.014 0.001 TYR E 299 PHE 0.014 0.001 PHE A 352 TRP 0.010 0.001 TRP C 196 HIS 0.003 0.001 HIS B 331 Details of bonding type rmsd covalent geometry : bond 0.00316 (13025) covalent geometry : angle 0.45964 (17595) hydrogen bonds : bond 0.04207 ( 885) hydrogen bonds : angle 3.89493 ( 2625) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: B 130 ASN cc_start: 0.8755 (t0) cc_final: 0.8195 (t0) REVERT: B 136 ARG cc_start: 0.9165 (ttt-90) cc_final: 0.8957 (ttt90) REVERT: B 292 MET cc_start: 0.6118 (mtt) cc_final: 0.5546 (mtt) REVERT: D 130 ASN cc_start: 0.8743 (t0) cc_final: 0.8142 (t0) outliers start: 28 outliers final: 20 residues processed: 124 average time/residue: 0.0865 time to fit residues: 16.7788 Evaluate side-chains 106 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 265 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 61 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 45 optimal weight: 0.0770 chunk 1 optimal weight: 7.9990 chunk 144 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 HIS B 122 HIS B 399 GLN C 122 HIS ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 399 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.193880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.131341 restraints weight = 12353.926| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.87 r_work: 0.2954 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 13025 Z= 0.310 Angle : 0.662 8.614 17595 Z= 0.341 Chirality : 0.046 0.155 2025 Planarity : 0.004 0.039 2240 Dihedral : 3.955 13.465 1710 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.84 % Allowed : 13.02 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.21), residues: 1580 helix: 1.39 (0.15), residues: 1030 sheet: 1.82 (0.47), residues: 135 loop : -0.14 (0.36), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 136 TYR 0.022 0.002 TYR E 299 PHE 0.019 0.002 PHE D 352 TRP 0.013 0.002 TRP E 196 HIS 0.003 0.001 HIS B 331 Details of bonding type rmsd covalent geometry : bond 0.00784 (13025) covalent geometry : angle 0.66231 (17595) hydrogen bonds : bond 0.05649 ( 885) hydrogen bonds : angle 4.16555 ( 2625) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 86 time to evaluate : 0.549 Fit side-chains REVERT: B 292 MET cc_start: 0.6315 (mtt) cc_final: 0.5983 (mtt) REVERT: D 101 GLU cc_start: 0.7680 (tp30) cc_final: 0.7388 (tp30) outliers start: 54 outliers final: 44 residues processed: 135 average time/residue: 0.1038 time to fit residues: 21.9747 Evaluate side-chains 125 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 81 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain E residue 86 PHE Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 342 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 108 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.199616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.143764 restraints weight = 12266.728| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.52 r_work: 0.3048 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13025 Z= 0.133 Angle : 0.479 7.023 17595 Z= 0.252 Chirality : 0.039 0.141 2025 Planarity : 0.003 0.038 2240 Dihedral : 3.581 13.072 1710 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.99 % Allowed : 14.23 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.22), residues: 1580 helix: 1.90 (0.15), residues: 1030 sheet: 2.06 (0.44), residues: 145 loop : -0.21 (0.37), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 102 TYR 0.014 0.001 TYR A 299 PHE 0.013 0.001 PHE B 352 TRP 0.012 0.001 TRP C 196 HIS 0.004 0.001 HIS B 331 Details of bonding type rmsd covalent geometry : bond 0.00322 (13025) covalent geometry : angle 0.47942 (17595) hydrogen bonds : bond 0.04171 ( 885) hydrogen bonds : angle 3.85026 ( 2625) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 83 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 262 GLU cc_start: 0.7030 (tp30) cc_final: 0.6809 (tp30) REVERT: B 292 MET cc_start: 0.6564 (mtt) cc_final: 0.6228 (mtt) REVERT: C 336 MET cc_start: 0.7645 (mmt) cc_final: 0.6856 (mtp) outliers start: 42 outliers final: 37 residues processed: 120 average time/residue: 0.1082 time to fit residues: 19.9936 Evaluate side-chains 116 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 79 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain E residue 86 PHE Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 274 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 55 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 152 optimal weight: 20.0000 chunk 111 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.202171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.132680 restraints weight = 11997.963| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.33 r_work: 0.3159 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13025 Z= 0.131 Angle : 0.478 7.188 17595 Z= 0.250 Chirality : 0.039 0.140 2025 Planarity : 0.003 0.039 2240 Dihedral : 3.497 13.231 1710 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.35 % Allowed : 14.09 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.27 (0.22), residues: 1580 helix: 2.08 (0.15), residues: 1030 sheet: 2.05 (0.44), residues: 145 loop : -0.20 (0.37), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 136 TYR 0.015 0.001 TYR E 299 PHE 0.013 0.001 PHE D 352 TRP 0.010 0.001 TRP A 196 HIS 0.003 0.001 HIS B 331 Details of bonding type rmsd covalent geometry : bond 0.00318 (13025) covalent geometry : angle 0.47756 (17595) hydrogen bonds : bond 0.04099 ( 885) hydrogen bonds : angle 3.78437 ( 2625) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 80 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: A 124 MET cc_start: 0.8494 (tpt) cc_final: 0.8063 (tpt) REVERT: B 101 GLU cc_start: 0.7282 (tp30) cc_final: 0.7070 (tp30) REVERT: B 292 MET cc_start: 0.6301 (mtt) cc_final: 0.5970 (mtt) REVERT: C 336 MET cc_start: 0.7307 (mmt) cc_final: 0.6890 (mtp) REVERT: D 101 GLU cc_start: 0.7584 (tp30) cc_final: 0.7318 (tp30) REVERT: E 103 LYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6457 (mtmt) outliers start: 47 outliers final: 41 residues processed: 121 average time/residue: 0.1060 time to fit residues: 19.7495 Evaluate side-chains 121 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 79 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain E residue 86 PHE Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 274 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 50 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.200081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.144859 restraints weight = 12198.157| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.36 r_work: 0.3148 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13025 Z= 0.130 Angle : 0.481 8.654 17595 Z= 0.249 Chirality : 0.039 0.141 2025 Planarity : 0.003 0.039 2240 Dihedral : 3.468 12.906 1710 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.63 % Allowed : 14.09 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.22), residues: 1580 helix: 2.16 (0.15), residues: 1030 sheet: 2.03 (0.44), residues: 145 loop : -0.21 (0.37), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 136 TYR 0.014 0.001 TYR E 299 PHE 0.013 0.001 PHE A 352 TRP 0.010 0.001 TRP C 196 HIS 0.003 0.001 HIS B 331 Details of bonding type rmsd covalent geometry : bond 0.00315 (13025) covalent geometry : angle 0.48056 (17595) hydrogen bonds : bond 0.04051 ( 885) hydrogen bonds : angle 3.76239 ( 2625) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 77 time to evaluate : 0.495 Fit side-chains REVERT: A 124 MET cc_start: 0.8607 (tpt) cc_final: 0.8219 (tpt) REVERT: B 292 MET cc_start: 0.6650 (mtt) cc_final: 0.6333 (mtt) REVERT: C 228 ARG cc_start: 0.7468 (mtm-85) cc_final: 0.7242 (mtm-85) REVERT: C 336 MET cc_start: 0.7592 (mmt) cc_final: 0.7335 (mtp) REVERT: E 103 LYS cc_start: 0.7029 (OUTLIER) cc_final: 0.6488 (mtmt) REVERT: E 228 ARG cc_start: 0.7624 (mtm-85) cc_final: 0.7331 (mtm180) outliers start: 51 outliers final: 46 residues processed: 123 average time/residue: 0.1097 time to fit residues: 20.8094 Evaluate side-chains 123 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 76 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain E residue 86 PHE Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 274 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 54 optimal weight: 2.9990 chunk 128 optimal weight: 0.4980 chunk 110 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 129 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 114 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.201635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.142646 restraints weight = 12027.745| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.56 r_work: 0.3083 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13025 Z= 0.113 Angle : 0.458 7.835 17595 Z= 0.238 Chirality : 0.038 0.138 2025 Planarity : 0.003 0.041 2240 Dihedral : 3.378 12.902 1710 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.27 % Allowed : 14.59 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.50 (0.22), residues: 1580 helix: 2.31 (0.15), residues: 1030 sheet: 1.99 (0.44), residues: 145 loop : -0.20 (0.37), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 228 TYR 0.012 0.001 TYR E 299 PHE 0.012 0.001 PHE D 352 TRP 0.011 0.001 TRP A 196 HIS 0.003 0.001 HIS B 331 Details of bonding type rmsd covalent geometry : bond 0.00267 (13025) covalent geometry : angle 0.45780 (17595) hydrogen bonds : bond 0.03809 ( 885) hydrogen bonds : angle 3.69022 ( 2625) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 82 time to evaluate : 0.500 Fit side-chains REVERT: A 124 MET cc_start: 0.8566 (tpt) cc_final: 0.8263 (tpt) REVERT: B 292 MET cc_start: 0.6105 (mtt) cc_final: 0.5789 (mtt) REVERT: C 336 MET cc_start: 0.7114 (mmt) cc_final: 0.6904 (mtp) outliers start: 46 outliers final: 42 residues processed: 123 average time/residue: 0.1086 time to fit residues: 20.8510 Evaluate side-chains 122 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 80 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain E residue 86 PHE Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 274 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 1 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 150 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 149 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.198547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.136746 restraints weight = 12058.953| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.24 r_work: 0.3012 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13025 Z= 0.190 Angle : 0.538 7.317 17595 Z= 0.278 Chirality : 0.041 0.147 2025 Planarity : 0.003 0.039 2240 Dihedral : 3.631 13.049 1710 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.56 % Allowed : 14.45 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.22), residues: 1580 helix: 1.99 (0.15), residues: 1030 sheet: 2.07 (0.45), residues: 145 loop : -0.17 (0.37), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 136 TYR 0.020 0.002 TYR B 299 PHE 0.015 0.002 PHE C 352 TRP 0.010 0.001 TRP C 196 HIS 0.003 0.001 HIS B 331 Details of bonding type rmsd covalent geometry : bond 0.00475 (13025) covalent geometry : angle 0.53765 (17595) hydrogen bonds : bond 0.04596 ( 885) hydrogen bonds : angle 3.84191 ( 2625) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 79 time to evaluate : 0.542 Fit side-chains REVERT: A 124 MET cc_start: 0.8643 (tpt) cc_final: 0.8134 (tpt) REVERT: B 292 MET cc_start: 0.6368 (mtt) cc_final: 0.6017 (mtt) REVERT: C 336 MET cc_start: 0.7417 (mmt) cc_final: 0.6974 (mtp) REVERT: E 103 LYS cc_start: 0.6905 (OUTLIER) cc_final: 0.6376 (mtmt) outliers start: 50 outliers final: 46 residues processed: 125 average time/residue: 0.1071 time to fit residues: 20.8597 Evaluate side-chains 126 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 79 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain E residue 86 PHE Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 342 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 71 optimal weight: 50.0000 chunk 19 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 137 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 102 optimal weight: 0.0970 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.196654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.135121 restraints weight = 12173.183| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 3.17 r_work: 0.3025 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13025 Z= 0.200 Angle : 0.555 7.231 17595 Z= 0.287 Chirality : 0.041 0.150 2025 Planarity : 0.003 0.040 2240 Dihedral : 3.741 13.814 1710 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.35 % Allowed : 14.66 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.22), residues: 1580 helix: 1.85 (0.15), residues: 1030 sheet: 2.05 (0.45), residues: 145 loop : -0.14 (0.37), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 136 TYR 0.019 0.002 TYR A 299 PHE 0.015 0.002 PHE C 352 TRP 0.011 0.001 TRP C 196 HIS 0.003 0.001 HIS B 331 Details of bonding type rmsd covalent geometry : bond 0.00503 (13025) covalent geometry : angle 0.55494 (17595) hydrogen bonds : bond 0.04695 ( 885) hydrogen bonds : angle 3.89715 ( 2625) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 79 time to evaluate : 0.519 Fit side-chains REVERT: A 124 MET cc_start: 0.8596 (tpt) cc_final: 0.8055 (tpt) REVERT: B 292 MET cc_start: 0.6234 (mtt) cc_final: 0.5877 (mtt) REVERT: C 336 MET cc_start: 0.7257 (mmt) cc_final: 0.6810 (mtp) outliers start: 47 outliers final: 45 residues processed: 122 average time/residue: 0.1063 time to fit residues: 20.2376 Evaluate side-chains 122 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 77 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain E residue 86 PHE Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 342 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 60 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 131 optimal weight: 0.0040 chunk 57 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.201629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.133056 restraints weight = 12108.396| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.33 r_work: 0.3136 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13025 Z= 0.111 Angle : 0.468 7.504 17595 Z= 0.244 Chirality : 0.038 0.136 2025 Planarity : 0.003 0.042 2240 Dihedral : 3.482 14.121 1710 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.78 % Allowed : 15.30 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.22), residues: 1580 helix: 2.24 (0.15), residues: 1030 sheet: 1.99 (0.44), residues: 145 loop : -0.16 (0.37), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 228 TYR 0.011 0.001 TYR D 299 PHE 0.012 0.001 PHE A 352 TRP 0.013 0.001 TRP C 196 HIS 0.003 0.001 HIS B 331 Details of bonding type rmsd covalent geometry : bond 0.00261 (13025) covalent geometry : angle 0.46766 (17595) hydrogen bonds : bond 0.03813 ( 885) hydrogen bonds : angle 3.71628 ( 2625) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2746.37 seconds wall clock time: 47 minutes 54.25 seconds (2874.25 seconds total)