Starting phenix.real_space_refine on Fri Jul 3 04:15:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dmx_27548/07_2026/8dmx_27548.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dmx_27548/07_2026/8dmx_27548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dmx_27548/07_2026/8dmx_27548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dmx_27548/07_2026/8dmx_27548.map" model { file = "/net/cci-nas-00/data/ceres_data/8dmx_27548/07_2026/8dmx_27548.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dmx_27548/07_2026/8dmx_27548.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dmx_27548/07_2026/8dmx_27548.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dmx_27548/07_2026/8dmx_27548.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.032 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 7408 2.51 5 N 1980 2.21 5 O 2264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11748 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.10, per 1000 atoms: 0.18 Number of scatterers: 11748 At special positions: 0 Unit cell: (79.299, 105.138, 170.181, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 84 16.00 P 8 15.00 Mg 4 11.99 O 2264 8.00 N 1980 7.00 C 7408 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 547.5 milliseconds 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 24 sheets defined 48.9% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.743A pdb=" N GLN A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 92 removed outlier: 3.902A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.655A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 128 removed outlier: 3.817A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 146 removed outlier: 4.216A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 4.106A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.559A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.647A pdb=" N PHE A 255 " --> pdb=" O ASN A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 removed outlier: 3.838A pdb=" N PHE A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 268 Processing helix chain 'A' and resid 273 through 284 removed outlier: 3.567A pdb=" N THR A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.233A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.530A pdb=" N ALA A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 337 removed outlier: 3.512A pdb=" N TYR A 337 " --> pdb=" O GLU A 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 334 through 337' Processing helix chain 'A' and resid 338 through 348 removed outlier: 3.513A pdb=" N SER A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.768A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.743A pdb=" N GLN B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 92 removed outlier: 3.902A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.655A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 128 removed outlier: 3.817A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 146 removed outlier: 4.216A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 4.106A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.559A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 216 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 251 through 255 removed outlier: 3.647A pdb=" N PHE B 255 " --> pdb=" O ASN B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 removed outlier: 3.839A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 268 Processing helix chain 'B' and resid 273 through 284 removed outlier: 3.567A pdb=" N THR B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.232A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.530A pdb=" N ALA B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 337 removed outlier: 3.512A pdb=" N TYR B 337 " --> pdb=" O GLU B 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 334 through 337' Processing helix chain 'B' and resid 338 through 348 removed outlier: 3.513A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 366 Processing helix chain 'B' and resid 367 through 373 removed outlier: 3.768A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS B 373 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.743A pdb=" N GLN C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 92 removed outlier: 3.903A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.655A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 128 removed outlier: 3.817A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE C 127 " --> pdb=" O MET C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 146 removed outlier: 4.215A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 4.106A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.558A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 216 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 251 through 255 removed outlier: 3.647A pdb=" N PHE C 255 " --> pdb=" O ASN C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 removed outlier: 3.838A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 268 Processing helix chain 'C' and resid 273 through 284 removed outlier: 3.568A pdb=" N THR C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.233A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.530A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 337 removed outlier: 3.511A pdb=" N TYR C 337 " --> pdb=" O GLU C 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 334 through 337' Processing helix chain 'C' and resid 338 through 348 removed outlier: 3.513A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 366 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.769A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.743A pdb=" N GLN D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 92 removed outlier: 3.902A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.656A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 128 removed outlier: 3.816A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE D 127 " --> pdb=" O MET D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 146 removed outlier: 4.216A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 4.106A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.559A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 216 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 251 through 255 removed outlier: 3.647A pdb=" N PHE D 255 " --> pdb=" O ASN D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 removed outlier: 3.839A pdb=" N PHE D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 268 Processing helix chain 'D' and resid 273 through 284 removed outlier: 3.567A pdb=" N THR D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 301 through 306 removed outlier: 4.233A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.530A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 337 removed outlier: 3.513A pdb=" N TYR D 337 " --> pdb=" O GLU D 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 334 through 337' Processing helix chain 'D' and resid 338 through 348 removed outlier: 3.513A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 366 Processing helix chain 'D' and resid 367 through 373 removed outlier: 3.767A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS D 371 " --> pdb=" O SER D 368 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS D 373 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.569A pdb=" N LYS A 18 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR A 133 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.624A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 removed outlier: 3.608A pdb=" N TYR A 166 " --> pdb=" O TYR A 169 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 160 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 3.608A pdb=" N TYR A 166 " --> pdb=" O TYR A 169 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS A 161 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP A 154 " --> pdb=" O HIS A 161 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 163 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 152 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A 165 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.851A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR B 133 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.623A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.608A pdb=" N TYR B 166 " --> pdb=" O TYR B 169 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR B 160 " --> pdb=" O LEU B 178 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.608A pdb=" N TYR B 166 " --> pdb=" O TYR B 169 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS B 161 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP B 154 " --> pdb=" O HIS B 161 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 163 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B 152 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE B 165 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 31 removed outlier: 6.851A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR C 133 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.624A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.608A pdb=" N TYR C 166 " --> pdb=" O TYR C 169 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR C 160 " --> pdb=" O LEU C 178 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.608A pdb=" N TYR C 166 " --> pdb=" O TYR C 169 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS C 161 " --> pdb=" O ASP C 154 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP C 154 " --> pdb=" O HIS C 161 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C 163 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL C 152 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE C 165 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 31 removed outlier: 6.851A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR D 133 " --> pdb=" O THR D 103 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.624A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.608A pdb=" N TYR D 166 " --> pdb=" O TYR D 169 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR D 160 " --> pdb=" O LEU D 178 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.608A pdb=" N TYR D 166 " --> pdb=" O TYR D 169 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS D 161 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP D 154 " --> pdb=" O HIS D 161 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 163 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL D 152 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE D 165 " --> pdb=" O GLY D 150 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 475 hydrogen bonds defined for protein. 1221 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.70 Time building geometry restraints manager: 1.16 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: 3824 1.34 - 1.46: 2391 1.46 - 1.58: 5629 1.58 - 1.69: 12 1.69 - 1.81: 148 Bond restraints: 12004 Sorted by residual: bond pdb=" N HIS B 40 " pdb=" CA HIS B 40 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.15e-02 7.56e+03 8.84e+00 bond pdb=" N ILE B 71 " pdb=" CA ILE B 71 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.26e-02 6.30e+03 7.96e+00 bond pdb=" N ILE C 71 " pdb=" CA ILE C 71 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.26e-02 6.30e+03 7.85e+00 bond pdb=" N ILE A 71 " pdb=" CA ILE A 71 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.26e-02 6.30e+03 7.79e+00 bond pdb=" N ILE D 71 " pdb=" CA ILE D 71 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.26e-02 6.30e+03 7.78e+00 ... (remaining 11999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 15536 1.14 - 2.29: 530 2.29 - 3.43: 151 3.43 - 4.57: 43 4.57 - 5.72: 32 Bond angle restraints: 16292 Sorted by residual: angle pdb=" CA ASN A 12 " pdb=" C ASN A 12 " pdb=" N GLY A 13 " ideal model delta sigma weight residual 115.51 120.24 -4.73 1.27e+00 6.20e-01 1.39e+01 angle pdb=" CA ASN D 296 " pdb=" C ASN D 296 " pdb=" O ASN D 296 " ideal model delta sigma weight residual 121.20 117.51 3.69 1.04e+00 9.25e-01 1.26e+01 angle pdb=" CA ASN A 296 " pdb=" C ASN A 296 " pdb=" O ASN A 296 " ideal model delta sigma weight residual 121.20 117.52 3.68 1.04e+00 9.25e-01 1.25e+01 angle pdb=" CA ASN B 296 " pdb=" C ASN B 296 " pdb=" O ASN B 296 " ideal model delta sigma weight residual 121.20 117.52 3.68 1.04e+00 9.25e-01 1.25e+01 angle pdb=" CA ASN C 296 " pdb=" C ASN C 296 " pdb=" O ASN C 296 " ideal model delta sigma weight residual 121.20 117.56 3.64 1.04e+00 9.25e-01 1.22e+01 ... (remaining 16287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.12: 6744 21.12 - 42.25: 404 42.25 - 63.37: 52 63.37 - 84.49: 12 84.49 - 105.62: 8 Dihedral angle restraints: 7220 sinusoidal: 2920 harmonic: 4300 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 -165.62 105.62 1 2.00e+01 2.50e-03 3.05e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 -165.61 105.61 1 2.00e+01 2.50e-03 3.05e+01 dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 -165.60 105.59 1 2.00e+01 2.50e-03 3.05e+01 ... (remaining 7217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1127 0.032 - 0.065: 447 0.065 - 0.097: 136 0.097 - 0.130: 86 0.130 - 0.162: 12 Chirality restraints: 1808 Sorted by residual: chirality pdb=" CA ILE B 71 " pdb=" N ILE B 71 " pdb=" C ILE B 71 " pdb=" CB ILE B 71 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.56e-01 chirality pdb=" CA ILE A 71 " pdb=" N ILE A 71 " pdb=" C ILE A 71 " pdb=" CB ILE A 71 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA ILE D 71 " pdb=" N ILE D 71 " pdb=" C ILE D 71 " pdb=" CB ILE D 71 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 1805 not shown) Planarity restraints: 2084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 12 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.74e+00 pdb=" C ASN A 12 " -0.051 2.00e-02 2.50e+03 pdb=" O ASN A 12 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY A 13 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 70 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C PRO D 70 " -0.033 2.00e-02 2.50e+03 pdb=" O PRO D 70 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE D 71 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 70 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C PRO B 70 " -0.033 2.00e-02 2.50e+03 pdb=" O PRO B 70 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE B 71 " 0.011 2.00e-02 2.50e+03 ... (remaining 2081 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 121 2.66 - 3.22: 10249 3.22 - 3.78: 16075 3.78 - 4.34: 22709 4.34 - 4.90: 38454 Nonbonded interactions: 87608 Sorted by model distance: nonbonded pdb="MG MG D 400 " pdb=" O1B ADP D 401 " model vdw 2.105 2.170 nonbonded pdb="MG MG B 400 " pdb=" O1B ADP B 401 " model vdw 2.105 2.170 nonbonded pdb="MG MG A 400 " pdb=" O1B ADP A 401 " model vdw 2.105 2.170 nonbonded pdb="MG MG C 400 " pdb=" O1B ADP C 401 " model vdw 2.106 2.170 nonbonded pdb=" O ASP C 51 " pdb=" OD1 ASP C 51 " model vdw 2.144 3.040 ... (remaining 87603 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.970 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.520 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 : 0.003 0.036 12004 Z= 0.182 Angle : 0.585 5.718 16292 Z= 0.328 Chirality : 0.044 0.162 1808 Planarity : 0.005 0.052 2084 Dihedral : 13.993 105.617 4468 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.23), residues: 1468 helix: 1.05 (0.24), residues: 524 sheet: -0.19 (0.32), residues: 276 loop : -0.42 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 372 TYR 0.009 0.001 TYR A 294 PHE 0.009 0.001 PHE B 124 TRP 0.005 0.001 TRP D 356 HIS 0.002 0.000 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.18 (12004) covalent geometry : angle 0.58511 / 0.33 (16292) hydrogen bonds : bond 0.18646 / 13.06 ( 471) hydrogen bonds : angle 6.77205 / 4.69 ( 1221) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.484 Fit side-chains REVERT: A 326 LYS cc_start: 0.8167 (pttt) cc_final: 0.7755 (mttm) REVERT: B 47 MET cc_start: 0.4355 (ptm) cc_final: 0.4129 (ptp) REVERT: B 143 TYR cc_start: 0.7886 (m-10) cc_final: 0.7299 (m-80) REVERT: B 184 ASP cc_start: 0.8015 (m-30) cc_final: 0.7745 (m-30) REVERT: C 364 GLU cc_start: 0.8651 (tt0) cc_final: 0.8412 (tm-30) REVERT: D 47 MET cc_start: 0.3966 (ptm) cc_final: 0.3710 (ppp) REVERT: D 91 TYR cc_start: 0.7417 (m-80) cc_final: 0.6901 (m-80) REVERT: D 123 MET cc_start: 0.6921 (tpp) cc_final: 0.6677 (tpt) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.0983 time to fit residues: 30.5089 Evaluate side-chains 129 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.0770 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 275 HIS B 12 ASN B 275 HIS D 275 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.095822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.085484 restraints weight = 17785.822| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 1.39 r_work: 0.2675 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9083 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 12004 Z= 0.245 Angle : 0.717 11.461 16292 Z= 0.359 Chirality : 0.050 0.162 1808 Planarity : 0.006 0.044 2084 Dihedral : 6.185 75.464 1672 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.07 % Allowed : 9.79 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.22), residues: 1468 helix: 0.28 (0.23), residues: 548 sheet: -0.47 (0.34), residues: 232 loop : -0.65 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 372 TYR 0.012 0.002 TYR B 218 PHE 0.011 0.002 PHE C 352 TRP 0.009 0.002 TRP D 340 HIS 0.007 0.002 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.25 (12004) covalent geometry : angle 0.71718 / 0.36 (16292) hydrogen bonds : bond 0.05414 / 3.72 ( 471) hydrogen bonds : angle 5.41216 / 3.73 ( 1221) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.469 Fit side-chains REVERT: A 326 LYS cc_start: 0.8350 (pttt) cc_final: 0.8116 (mttm) REVERT: B 25 ASP cc_start: 0.8428 (p0) cc_final: 0.8156 (p0) outliers start: 26 outliers final: 17 residues processed: 127 average time/residue: 0.0819 time to fit residues: 15.9877 Evaluate side-chains 107 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 176 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN B 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.092822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.078802 restraints weight = 18312.974| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.20 r_work: 0.2738 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 12004 Z= 0.147 Angle : 0.559 6.365 16292 Z= 0.276 Chirality : 0.046 0.151 1808 Planarity : 0.005 0.051 2084 Dihedral : 5.691 59.714 1672 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.67 % Allowed : 12.34 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.22), residues: 1468 helix: 0.41 (0.23), residues: 552 sheet: -0.50 (0.33), residues: 232 loop : -0.51 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 372 TYR 0.010 0.001 TYR D 69 PHE 0.012 0.001 PHE A 31 TRP 0.008 0.001 TRP D 340 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (12004) covalent geometry : angle 0.55943 / 0.28 (16292) hydrogen bonds : bond 0.04106 / 2.82 ( 471) hydrogen bonds : angle 5.06928 / 3.49 ( 1221) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.317 Fit side-chains REVERT: A 326 LYS cc_start: 0.8577 (pttt) cc_final: 0.8352 (ptpp) outliers start: 21 outliers final: 15 residues processed: 114 average time/residue: 0.0885 time to fit residues: 15.1750 Evaluate side-chains 107 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 163 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 10 optimal weight: 0.6980 chunk 118 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN B 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.094051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.084290 restraints weight = 17788.647| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 1.29 r_work: 0.2673 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9112 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 12004 Z= 0.192 Angle : 0.607 6.218 16292 Z= 0.301 Chirality : 0.048 0.159 1808 Planarity : 0.005 0.053 2084 Dihedral : 5.697 64.764 1672 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.95 % Allowed : 12.74 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.22), residues: 1468 helix: 0.12 (0.23), residues: 572 sheet: -0.61 (0.31), residues: 264 loop : -0.73 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 372 TYR 0.011 0.001 TYR B 218 PHE 0.013 0.001 PHE D 31 TRP 0.010 0.001 TRP D 340 HIS 0.005 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.19 (12004) covalent geometry : angle 0.60746 / 0.30 (16292) hydrogen bonds : bond 0.04728 / 3.23 ( 471) hydrogen bonds : angle 5.10236 / 3.51 ( 1221) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 89 time to evaluate : 0.385 Fit side-chains REVERT: A 261 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8838 (mp) REVERT: D 176 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8275 (mtt) outliers start: 37 outliers final: 24 residues processed: 119 average time/residue: 0.0762 time to fit residues: 14.1972 Evaluate side-chains 112 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 216 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 72 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN B 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.092498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.082948 restraints weight = 17872.674| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 1.26 r_work: 0.2678 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9129 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 12004 Z= 0.238 Angle : 0.638 6.546 16292 Z= 0.321 Chirality : 0.050 0.170 1808 Planarity : 0.005 0.054 2084 Dihedral : 5.925 72.624 1672 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.71 % Allowed : 14.17 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.22), residues: 1468 helix: -0.21 (0.22), residues: 596 sheet: -0.82 (0.30), residues: 264 loop : -0.91 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 372 TYR 0.012 0.001 TYR B 218 PHE 0.015 0.002 PHE D 31 TRP 0.010 0.002 TRP D 340 HIS 0.005 0.002 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.24 (12004) covalent geometry : angle 0.63822 / 0.32 (16292) hydrogen bonds : bond 0.05135 / 3.52 ( 471) hydrogen bonds : angle 5.18454 / 3.55 ( 1221) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 81 time to evaluate : 0.338 Fit side-chains REVERT: D 261 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8936 (mp) outliers start: 34 outliers final: 28 residues processed: 109 average time/residue: 0.0735 time to fit residues: 12.4811 Evaluate side-chains 109 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 80 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 261 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 112 optimal weight: 0.9990 chunk 24 optimal weight: 0.0970 chunk 100 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN B 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.096445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.086891 restraints weight = 17597.987| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 1.25 r_work: 0.2771 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12004 Z= 0.106 Angle : 0.528 6.116 16292 Z= 0.258 Chirality : 0.044 0.164 1808 Planarity : 0.005 0.050 2084 Dihedral : 5.517 65.308 1672 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.51 % Allowed : 15.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.22), residues: 1468 helix: 0.03 (0.23), residues: 600 sheet: -0.81 (0.32), residues: 236 loop : -0.62 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 372 TYR 0.009 0.001 TYR D 69 PHE 0.012 0.001 PHE D 31 TRP 0.007 0.001 TRP D 340 HIS 0.003 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (12004) covalent geometry : angle 0.52773 / 0.26 (16292) hydrogen bonds : bond 0.03198 / 2.20 ( 471) hydrogen bonds : angle 4.82481 / 3.34 ( 1221) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.338 Fit side-chains outliers start: 19 outliers final: 13 residues processed: 100 average time/residue: 0.0803 time to fit residues: 12.6278 Evaluate side-chains 98 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 121 optimal weight: 0.9980 chunk 81 optimal weight: 0.0470 chunk 112 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 125 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 overall best weight: 1.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN B 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.094568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.084972 restraints weight = 17713.435| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 1.27 r_work: 0.2709 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9100 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 12004 Z= 0.162 Angle : 0.565 6.790 16292 Z= 0.279 Chirality : 0.046 0.167 1808 Planarity : 0.005 0.056 2084 Dihedral : 5.564 66.492 1672 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.83 % Allowed : 15.21 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.22), residues: 1468 helix: -0.03 (0.22), residues: 600 sheet: -0.85 (0.32), residues: 236 loop : -0.64 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 372 TYR 0.009 0.001 TYR D 69 PHE 0.013 0.001 PHE D 31 TRP 0.009 0.001 TRP D 340 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.16 (12004) covalent geometry : angle 0.56495 / 0.28 (16292) hydrogen bonds : bond 0.04081 / 2.80 ( 471) hydrogen bonds : angle 4.89533 / 3.37 ( 1221) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.396 Fit side-chains REVERT: D 176 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8300 (mtt) outliers start: 23 outliers final: 16 residues processed: 103 average time/residue: 0.0821 time to fit residues: 13.3265 Evaluate side-chains 102 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 70 optimal weight: 4.9990 chunk 137 optimal weight: 0.0970 chunk 47 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN B 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.094948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.085343 restraints weight = 17728.394| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 1.27 r_work: 0.2713 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9097 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 12004 Z= 0.144 Angle : 0.553 7.012 16292 Z= 0.272 Chirality : 0.046 0.172 1808 Planarity : 0.005 0.051 2084 Dihedral : 5.521 65.178 1672 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.15 % Allowed : 14.49 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.22), residues: 1468 helix: -0.02 (0.22), residues: 600 sheet: -0.85 (0.32), residues: 236 loop : -0.62 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 372 TYR 0.009 0.001 TYR D 69 PHE 0.013 0.001 PHE D 31 TRP 0.008 0.001 TRP D 340 HIS 0.003 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.14 (12004) covalent geometry : angle 0.55302 / 0.27 (16292) hydrogen bonds : bond 0.03819 / 2.63 ( 471) hydrogen bonds : angle 4.84283 / 3.34 ( 1221) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.475 Fit side-chains REVERT: C 227 MET cc_start: 0.8221 (mmt) cc_final: 0.7984 (mmt) REVERT: D 176 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8243 (mtt) outliers start: 27 outliers final: 18 residues processed: 106 average time/residue: 0.0782 time to fit residues: 13.0249 Evaluate side-chains 105 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 132 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN B 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.095750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.086209 restraints weight = 17521.374| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 1.25 r_work: 0.2776 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9094 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12004 Z= 0.123 Angle : 0.538 7.292 16292 Z= 0.263 Chirality : 0.045 0.170 1808 Planarity : 0.005 0.053 2084 Dihedral : 5.377 62.456 1672 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.59 % Allowed : 15.05 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.22), residues: 1468 helix: 0.04 (0.23), residues: 600 sheet: -0.79 (0.32), residues: 236 loop : -0.53 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 372 TYR 0.008 0.001 TYR D 69 PHE 0.012 0.001 PHE D 31 TRP 0.007 0.001 TRP D 340 HIS 0.003 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.12 (12004) covalent geometry : angle 0.53795 / 0.26 (16292) hydrogen bonds : bond 0.03489 / 2.40 ( 471) hydrogen bonds : angle 4.75699 / 3.29 ( 1221) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.403 Fit side-chains REVERT: C 227 MET cc_start: 0.8258 (mmt) cc_final: 0.8047 (mmt) REVERT: D 176 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8242 (mtt) outliers start: 20 outliers final: 17 residues processed: 102 average time/residue: 0.0738 time to fit residues: 11.8248 Evaluate side-chains 104 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 65 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 147 optimal weight: 0.1980 chunk 102 optimal weight: 0.0030 chunk 12 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.098590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.087882 restraints weight = 17546.638| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 1.47 r_work: 0.2762 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9057 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12004 Z= 0.086 Angle : 0.503 7.219 16292 Z= 0.242 Chirality : 0.043 0.172 1808 Planarity : 0.004 0.048 2084 Dihedral : 4.986 52.907 1672 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.35 % Allowed : 15.21 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.23), residues: 1468 helix: 0.39 (0.23), residues: 580 sheet: -0.59 (0.33), residues: 236 loop : -0.41 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 372 TYR 0.007 0.001 TYR D 69 PHE 0.011 0.001 PHE D 31 TRP 0.006 0.001 TRP C 356 HIS 0.003 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.09 (12004) covalent geometry : angle 0.50328 / 0.24 (16292) hydrogen bonds : bond 0.02662 / 1.84 ( 471) hydrogen bonds : angle 4.56329 / 3.18 ( 1221) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.298 Fit side-chains outliers start: 17 outliers final: 15 residues processed: 108 average time/residue: 0.0762 time to fit residues: 12.7792 Evaluate side-chains 104 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 130 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 97 optimal weight: 0.0370 chunk 98 optimal weight: 5.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.095015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.084371 restraints weight = 17696.017| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 1.46 r_work: 0.2676 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9097 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 12004 Z= 0.164 Angle : 0.567 7.272 16292 Z= 0.280 Chirality : 0.046 0.159 1808 Planarity : 0.005 0.056 2084 Dihedral : 5.271 61.242 1672 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.59 % Allowed : 15.13 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.22), residues: 1468 helix: 0.07 (0.23), residues: 600 sheet: -0.72 (0.33), residues: 236 loop : -0.45 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 372 TYR 0.009 0.001 TYR B 218 PHE 0.013 0.001 PHE D 31 TRP 0.010 0.001 TRP D 340 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.16 (12004) covalent geometry : angle 0.56701 / 0.28 (16292) hydrogen bonds : bond 0.04130 / 2.84 ( 471) hydrogen bonds : angle 4.78253 / 3.30 ( 1221) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2060.31 seconds wall clock time: 36 minutes 2.94 seconds (2162.94 seconds total)