Starting phenix.real_space_refine on Wed Jul 30 21:29:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tup_41628/07_2025/8tup_41628.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tup_41628/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tup_41628/07_2025/8tup_41628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tup_41628/07_2025/8tup_41628.map" model { file = "/net/cci-nas-00/data/ceres_data/8tup_41628/07_2025/8tup_41628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tup_41628/07_2025/8tup_41628.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.36, per 1000 atoms: 0.49 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: 3.36 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.05 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: 4.01 Time building geometry restraints manager: 3.99 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: 8.310 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.300 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.040 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.040 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.008 0.001 TRP D 196 HIS 0.003 0.001 HIS C 288 PHE 0.012 0.001 PHE A 352 TYR 0.006 0.001 TYR C 299 ARG 0.003 0.000 ARG B 228 Details of bonding type rmsd hydrogen bonds : bond 0.13917 ( 885) hydrogen bonds : angle 5.19141 ( 2625) covalent geometry : bond 0.00206 (13025) covalent geometry : angle 0.40553 (17595) *********************** 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 : 1.751 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: 0.2404 time to fit residues: 28.5334 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 : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 40 optimal weight: 20.0000 chunk 79 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 121 optimal weight: 30.0000 chunk 47 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 131 ASN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 ASN E 131 ASN ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.198027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.137955 restraints weight = 12049.203| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.17 r_work: 0.3048 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13025 Z= 0.171 Angle : 0.515 5.791 17595 Z= 0.272 Chirality : 0.041 0.140 2025 Planarity : 0.003 0.034 2240 Dihedral : 3.542 15.026 1710 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.28 % Allowed : 13.59 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.22), residues: 1580 helix: 1.93 (0.15), residues: 1030 sheet: 2.21 (0.43), residues: 145 loop : -0.14 (0.38), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 196 HIS 0.003 0.001 HIS B 331 PHE 0.015 0.002 PHE A 352 TYR 0.019 0.002 TYR A 299 ARG 0.003 0.000 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.04698 ( 885) hydrogen bonds : angle 4.08651 ( 2625) covalent geometry : bond 0.00417 (13025) covalent geometry : angle 0.51502 (17595) *********************** 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 135 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 2.238 Fit side-chains REVERT: B 130 ASN cc_start: 0.8713 (t0) cc_final: 0.8155 (t0) REVERT: B 292 MET cc_start: 0.6170 (mtt) cc_final: 0.5934 (mtt) REVERT: D 130 ASN cc_start: 0.8724 (t0) cc_final: 0.8116 (t0) outliers start: 32 outliers final: 19 residues processed: 132 average time/residue: 0.3129 time to fit residues: 59.4608 Evaluate side-chains 107 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 1.689 ------------------------------------------------------------------------------- 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 135 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4090 r_free = 0.4090 target = 0.200486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.139870 restraints weight = 12264.017| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 3.14 r_work: 0.3080 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1363 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= 0.125 Angle : 0.455 6.483 17595 Z= 0.240 Chirality : 0.038 0.138 2025 Planarity : 0.003 0.036 2240 Dihedral : 3.397 12.658 1710 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.28 % Allowed : 13.45 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.22), residues: 1580 helix: 2.11 (0.15), residues: 1035 sheet: 2.09 (0.43), residues: 145 loop : -0.28 (0.38), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 196 HIS 0.003 0.001 HIS B 331 PHE 0.014 0.001 PHE A 352 TYR 0.013 0.001 TYR E 299 ARG 0.006 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.04117 ( 885) hydrogen bonds : angle 3.86077 ( 2625) covalent geometry : bond 0.00296 (13025) covalent geometry : angle 0.45470 (17595) *********************** 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 133 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 1.600 Fit side-chains revert: symmetry clash REVERT: A 130 ASN cc_start: 0.8712 (t0) cc_final: 0.8438 (t0) REVERT: B 130 ASN cc_start: 0.8749 (t0) cc_final: 0.8215 (t0) REVERT: B 136 ARG cc_start: 0.9132 (ttt-90) cc_final: 0.8922 (ttt90) REVERT: B 292 MET cc_start: 0.6060 (mtt) cc_final: 0.5527 (mtt) REVERT: C 130 ASN cc_start: 0.8728 (t0) cc_final: 0.8252 (t0) REVERT: D 130 ASN cc_start: 0.8763 (t0) cc_final: 0.8193 (t0) REVERT: E 130 ASN cc_start: 0.8725 (t0) cc_final: 0.8192 (t0) outliers start: 32 outliers final: 24 residues processed: 129 average time/residue: 0.3566 time to fit residues: 69.5067 Evaluate side-chains 114 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 3.514 ------------------------------------------------------------------------------- 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 149 LEU 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 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 206 ILE Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 197 ILE 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 274 SER Chi-restraints excluded: chain E residue 342 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 12 optimal weight: 0.8980 chunk 151 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 109 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 63 optimal weight: 0.0050 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 chunk 145 optimal weight: 0.8980 overall best weight: 0.7594 ------------------------------------------------------------------------------- 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 = 0.4103 r_free = 0.4103 target = 0.201144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.141939 restraints weight = 12056.546| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.71 r_work: 0.3064 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1481 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= 0.121 Angle : 0.457 6.697 17595 Z= 0.240 Chirality : 0.038 0.140 2025 Planarity : 0.003 0.041 2240 Dihedral : 3.358 12.478 1710 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.56 % Allowed : 13.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.22), residues: 1580 helix: 2.19 (0.15), residues: 1035 sheet: 1.72 (0.46), residues: 135 loop : -0.20 (0.37), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 196 HIS 0.003 0.001 HIS B 331 PHE 0.014 0.001 PHE B 352 TYR 0.014 0.001 TYR E 299 ARG 0.004 0.000 ARG E 136 Details of bonding type rmsd hydrogen bonds : bond 0.03970 ( 885) hydrogen bonds : angle 3.77372 ( 2625) covalent geometry : bond 0.00291 (13025) covalent geometry : angle 0.45662 (17595) *********************** 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 125 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 89 time to evaluate : 1.486 Fit side-chains revert: symmetry clash REVERT: A 124 MET cc_start: 0.8484 (tpt) cc_final: 0.8201 (tpt) REVERT: A 130 ASN cc_start: 0.8662 (t0) cc_final: 0.8398 (t0) REVERT: A 370 ASP cc_start: 0.7035 (OUTLIER) cc_final: 0.6828 (t0) REVERT: B 130 ASN cc_start: 0.8726 (t0) cc_final: 0.8168 (t0) REVERT: B 136 ARG cc_start: 0.9188 (ttt-90) cc_final: 0.8949 (ttt90) REVERT: B 292 MET cc_start: 0.6075 (mtt) cc_final: 0.5480 (mtt) REVERT: D 130 ASN cc_start: 0.8751 (t0) cc_final: 0.8148 (t0) REVERT: D 370 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6892 (t0) outliers start: 36 outliers final: 27 residues processed: 119 average time/residue: 0.2850 time to fit residues: 54.1011 Evaluate side-chains 117 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 2.958 ------------------------------------------------------------------------------- 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 137 MET 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 A residue 370 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 206 ILE 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 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 D residue 370 ASP Chi-restraints excluded: chain E residue 86 PHE 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 Chi-restraints excluded: chain E residue 274 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 116 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.4060 r_free = 0.4060 target = 0.197657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.136719 restraints weight = 12278.001| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.37 r_work: 0.2988 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13025 Z= 0.183 Angle : 0.528 7.095 17595 Z= 0.276 Chirality : 0.041 0.147 2025 Planarity : 0.003 0.038 2240 Dihedral : 3.557 12.869 1710 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.99 % Allowed : 13.45 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.22), residues: 1580 helix: 1.99 (0.15), residues: 1030 sheet: 1.81 (0.46), residues: 135 loop : -0.11 (0.37), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 196 HIS 0.003 0.001 HIS B 331 PHE 0.014 0.002 PHE E 352 TYR 0.019 0.002 TYR B 299 ARG 0.005 0.000 ARG E 136 Details of bonding type rmsd hydrogen bonds : bond 0.04590 ( 885) hydrogen bonds : angle 3.88106 ( 2625) covalent geometry : bond 0.00456 (13025) covalent geometry : angle 0.52839 (17595) *********************** 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 132 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 90 time to evaluate : 1.444 Fit side-chains revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7461 (tp30) cc_final: 0.7240 (tp30) REVERT: A 124 MET cc_start: 0.8576 (tpt) cc_final: 0.8235 (tpt) REVERT: B 292 MET cc_start: 0.6326 (mtt) cc_final: 0.6055 (mtt) outliers start: 42 outliers final: 35 residues processed: 127 average time/residue: 0.2116 time to fit residues: 42.1296 Evaluate side-chains 122 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 87 time to evaluate : 1.323 ------------------------------------------------------------------------------- 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 137 MET Chi-restraints excluded: chain A residue 148 CYS 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 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 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 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 274 SER Chi-restraints excluded: chain E residue 86 PHE 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 274 SER Chi-restraints excluded: chain E residue 342 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 = 0.4075 r_free = 0.4075 target = 0.198694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.137917 restraints weight = 12306.958| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 3.40 r_work: 0.3050 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13025 Z= 0.148 Angle : 0.504 7.717 17595 Z= 0.261 Chirality : 0.039 0.143 2025 Planarity : 0.003 0.040 2240 Dihedral : 3.491 12.769 1710 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.85 % Allowed : 13.74 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.22), residues: 1580 helix: 2.07 (0.15), residues: 1030 sheet: 1.70 (0.46), residues: 135 loop : -0.14 (0.36), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 196 HIS 0.003 0.001 HIS B 331 PHE 0.013 0.001 PHE B 352 TYR 0.016 0.002 TYR A 299 ARG 0.004 0.000 ARG E 136 Details of bonding type rmsd hydrogen bonds : bond 0.04243 ( 885) hydrogen bonds : angle 3.80599 ( 2625) covalent geometry : bond 0.00367 (13025) covalent geometry : angle 0.50354 (17595) *********************** 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 128 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 88 time to evaluate : 1.477 Fit side-chains revert: symmetry clash REVERT: A 124 MET cc_start: 0.8522 (tpt) cc_final: 0.8125 (tpt) REVERT: B 292 MET cc_start: 0.6132 (mtt) cc_final: 0.5839 (mtt) REVERT: C 228 ARG cc_start: 0.7135 (mtm-85) cc_final: 0.6872 (mtm-85) REVERT: D 101 GLU cc_start: 0.7452 (tp30) cc_final: 0.7209 (tp30) outliers start: 40 outliers final: 37 residues processed: 122 average time/residue: 0.2186 time to fit residues: 41.8094 Evaluate side-chains 122 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 85 time to evaluate : 1.361 ------------------------------------------------------------------------------- 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 137 MET Chi-restraints excluded: chain A residue 148 CYS 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 A residue 342 LEU 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 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 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 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 206 ILE Chi-restraints excluded: chain E residue 219 VAL 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 106 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 127 optimal weight: 0.3980 chunk 40 optimal weight: 20.0000 chunk 79 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.4092 r_free = 0.4092 target = 0.199841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.143478 restraints weight = 12112.173| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.41 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13025 Z= 0.142 Angle : 0.497 7.298 17595 Z= 0.257 Chirality : 0.039 0.143 2025 Planarity : 0.003 0.042 2240 Dihedral : 3.465 12.767 1710 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.13 % Allowed : 13.67 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.22), residues: 1580 helix: 2.13 (0.15), residues: 1030 sheet: 2.04 (0.44), residues: 145 loop : -0.19 (0.37), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 196 HIS 0.003 0.001 HIS B 331 PHE 0.014 0.001 PHE A 352 TYR 0.016 0.002 TYR E 299 ARG 0.004 0.000 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.04166 ( 885) hydrogen bonds : angle 3.77447 ( 2625) covalent geometry : bond 0.00350 (13025) covalent geometry : angle 0.49680 (17595) *********************** 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 132 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 88 time to evaluate : 1.316 Fit side-chains REVERT: A 124 MET cc_start: 0.8241 (tpt) cc_final: 0.7839 (tpt) REVERT: B 292 MET cc_start: 0.6565 (mtt) cc_final: 0.6276 (mtt) REVERT: B 336 MET cc_start: 0.7888 (mmt) cc_final: 0.7539 (mmm) REVERT: C 336 MET cc_start: 0.7256 (mmt) cc_final: 0.6840 (mtp) REVERT: D 101 GLU cc_start: 0.7403 (tp30) cc_final: 0.7181 (tp30) REVERT: D 228 ARG cc_start: 0.7587 (mtm-85) cc_final: 0.7349 (mtm-85) REVERT: E 101 GLU cc_start: 0.7327 (tp30) cc_final: 0.7116 (tp30) REVERT: E 228 ARG cc_start: 0.7605 (mtm-85) cc_final: 0.7338 (mtm180) outliers start: 44 outliers final: 41 residues processed: 127 average time/residue: 0.2079 time to fit residues: 41.0655 Evaluate side-chains 128 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 87 time to evaluate : 1.381 ------------------------------------------------------------------------------- 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 137 MET Chi-restraints excluded: chain A residue 148 CYS 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 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 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 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 Chi-restraints excluded: chain E residue 342 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 81 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 142 optimal weight: 0.8980 chunk 120 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.4074 r_free = 0.4074 target = 0.199152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.137221 restraints weight = 12298.591| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.31 r_work: 0.3015 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13025 Z= 0.150 Angle : 0.509 7.701 17595 Z= 0.263 Chirality : 0.039 0.143 2025 Planarity : 0.003 0.043 2240 Dihedral : 3.510 12.833 1710 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.06 % Allowed : 13.88 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.22), residues: 1580 helix: 2.09 (0.15), residues: 1030 sheet: 2.01 (0.44), residues: 145 loop : -0.18 (0.37), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 196 HIS 0.003 0.001 HIS B 331 PHE 0.014 0.001 PHE D 352 TYR 0.016 0.002 TYR E 299 ARG 0.004 0.000 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.04256 ( 885) hydrogen bonds : angle 3.78492 ( 2625) covalent geometry : bond 0.00371 (13025) covalent geometry : angle 0.50892 (17595) *********************** 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: 43 poor density : 85 time to evaluate : 1.331 Fit side-chains REVERT: A 124 MET cc_start: 0.8535 (tpt) cc_final: 0.8107 (tpt) REVERT: B 292 MET cc_start: 0.6112 (mtt) cc_final: 0.5792 (mtt) REVERT: C 228 ARG cc_start: 0.7162 (mtm-85) cc_final: 0.6955 (mtm-85) REVERT: D 101 GLU cc_start: 0.7384 (tp30) cc_final: 0.7165 (tp30) outliers start: 43 outliers final: 40 residues processed: 124 average time/residue: 0.2297 time to fit residues: 44.6279 Evaluate side-chains 123 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 83 time to evaluate : 1.446 ------------------------------------------------------------------------------- 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 137 MET Chi-restraints excluded: chain A residue 148 CYS 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 79 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 125 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 143 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 399 GLN D 399 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.197429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.136283 restraints weight = 12150.758| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.51 r_work: 0.2985 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13025 Z= 0.181 Angle : 0.542 6.688 17595 Z= 0.281 Chirality : 0.041 0.147 2025 Planarity : 0.003 0.042 2240 Dihedral : 3.640 13.976 1710 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.13 % Allowed : 13.81 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.21), residues: 1580 helix: 1.95 (0.15), residues: 1030 sheet: 2.02 (0.44), residues: 145 loop : -0.16 (0.37), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 196 HIS 0.003 0.001 HIS B 331 PHE 0.015 0.002 PHE A 352 TYR 0.019 0.002 TYR B 299 ARG 0.004 0.000 ARG E 136 Details of bonding type rmsd hydrogen bonds : bond 0.04538 ( 885) hydrogen bonds : angle 3.85250 ( 2625) covalent geometry : bond 0.00453 (13025) covalent geometry : angle 0.54150 (17595) *********************** 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 125 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 81 time to evaluate : 1.470 Fit side-chains REVERT: A 124 MET cc_start: 0.8588 (tpt) cc_final: 0.8146 (tpt) REVERT: B 292 MET cc_start: 0.6258 (mtt) cc_final: 0.5938 (mtt) REVERT: C 228 ARG cc_start: 0.7241 (mtm-85) cc_final: 0.6929 (mtm-85) REVERT: D 228 ARG cc_start: 0.7335 (mtm-85) cc_final: 0.7069 (mtm-85) outliers start: 44 outliers final: 41 residues processed: 121 average time/residue: 0.2181 time to fit residues: 41.0300 Evaluate side-chains 121 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 80 time to evaluate : 1.227 ------------------------------------------------------------------------------- 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 148 CYS 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 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 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 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 147 GLU 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 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 116 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 34 optimal weight: 0.2980 chunk 31 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4095 r_free = 0.4095 target = 0.200567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.144197 restraints weight = 12085.201| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.40 r_work: 0.3124 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1938 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= 0.122 Angle : 0.480 6.677 17595 Z= 0.251 Chirality : 0.038 0.140 2025 Planarity : 0.003 0.044 2240 Dihedral : 3.477 13.868 1710 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.42 % Allowed : 14.73 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.22), residues: 1580 helix: 2.23 (0.15), residues: 1030 sheet: 2.01 (0.44), residues: 145 loop : -0.20 (0.36), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 196 HIS 0.003 0.001 HIS B 331 PHE 0.013 0.001 PHE A 352 TYR 0.013 0.001 TYR E 299 ARG 0.005 0.000 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.03920 ( 885) hydrogen bonds : angle 3.72880 ( 2625) covalent geometry : bond 0.00294 (13025) covalent geometry : angle 0.48016 (17595) ********************** 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 119 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 85 time to evaluate : 1.293 Fit side-chains REVERT: A 124 MET cc_start: 0.8534 (tpt) cc_final: 0.8134 (tpt) REVERT: B 136 ARG cc_start: 0.9289 (ttt-90) cc_final: 0.9084 (ttt90) REVERT: B 292 MET cc_start: 0.6586 (mtt) cc_final: 0.6279 (mtt) REVERT: C 228 ARG cc_start: 0.7437 (mtm-85) cc_final: 0.7197 (mtm-85) REVERT: D 228 ARG cc_start: 0.7524 (mtm-85) cc_final: 0.7298 (mtm-85) outliers start: 34 outliers final: 33 residues processed: 115 average time/residue: 0.2310 time to fit residues: 40.6890 Evaluate side-chains 116 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 83 time to evaluate : 1.306 ------------------------------------------------------------------------------- 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 137 MET 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 B residue 86 PHE Chi-restraints excluded: chain B residue 123 VAL 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 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 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 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 148 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 13 optimal weight: 1.9990 chunk 107 optimal weight: 0.1980 chunk 89 optimal weight: 10.0000 chunk 149 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 126 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4090 r_free = 0.4090 target = 0.199970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.143656 restraints weight = 12091.114| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.38 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1978 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 : 0.502 6.746 17595 Z= 0.261 Chirality : 0.039 0.142 2025 Planarity : 0.003 0.043 2240 Dihedral : 3.509 14.080 1710 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.56 % Allowed : 14.73 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.22), residues: 1580 helix: 2.21 (0.15), residues: 1030 sheet: 2.06 (0.44), residues: 145 loop : -0.14 (0.37), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 196 HIS 0.003 0.001 HIS B 331 PHE 0.013 0.001 PHE D 352 TYR 0.015 0.001 TYR A 299 ARG 0.004 0.000 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 885) hydrogen bonds : angle 3.74032 ( 2625) covalent geometry : bond 0.00325 (13025) covalent geometry : angle 0.50157 (17595) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6207.45 seconds wall clock time: 115 minutes 5.32 seconds (6905.32 seconds total)