Starting phenix.real_space_refine on Thu Jul 2 18:17:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i6d_52653/07_2026/9i6d_52653.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i6d_52653/07_2026/9i6d_52653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9i6d_52653/07_2026/9i6d_52653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i6d_52653/07_2026/9i6d_52653.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i6d_52653/07_2026/9i6d_52653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i6d_52653/07_2026/9i6d_52653.map" } resolution = 3.34 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= 0.012 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: 7 Type Number sf(0) Gaussians P 9 5.49 5 S 51 5.16 5 Cl 6 4.86 5 Na 3 4.78 5 C 6165 2.51 5 N 1449 2.21 5 O 1704 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: 9387 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3009 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 16, 'TRANS': 391} Chain: "B" Number of atoms: 3009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3009 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 16, 'TRANS': 391} Chain: "C" Number of atoms: 3009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3009 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 16, 'TRANS': 391} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 104 Ad-hoc single atom residues: {' NA': 1, ' CL': 2} Unusual residues: {'D3D': 1, 'PG8': 1, 'PGM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 104 Ad-hoc single atom residues: {' NA': 1, ' CL': 2} Unusual residues: {'D3D': 1, 'PG8': 1, 'PGM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "C" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 113 Ad-hoc single atom residues: {' NA': 1, ' CL': 2} Unusual residues: {'D3D': 1, 'PG8': 1, 'PGM': 1} Inner-chain residues flagged as termini: ['pdbres="ASP C 502 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 2.08, per 1000 atoms: 0.22 Number of scatterers: 9387 At special positions: 0 Unit cell: (104.161, 115.209, 73.3863, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 6 17.00 S 51 16.00 P 9 15.00 Na 3 11.00 O 1704 8.00 N 1449 7.00 C 6165 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: 1.11 Conformation dependent library (CDL) restraints added in 358.4 milliseconds 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2202 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 86.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 12 through 34 removed outlier: 3.607A pdb=" N ILE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 43 removed outlier: 3.717A pdb=" N TYR A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 56 removed outlier: 3.686A pdb=" N LEU A 49 " --> pdb=" O PRO A 45 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 54 " --> pdb=" O PHE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 71 removed outlier: 3.712A pdb=" N ILE A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.575A pdb=" N LEU A 78 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 107 removed outlier: 3.516A pdb=" N VAL A 83 " --> pdb=" O GLY A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 141 through 149 removed outlier: 3.914A pdb=" N LEU A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 170 Processing helix chain 'A' and resid 173 through 220 removed outlier: 3.504A pdb=" N LYS A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 198 " --> pdb=" O MET A 194 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ARG A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ILE A 207 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 214 " --> pdb=" O PHE A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 254 removed outlier: 4.701A pdb=" N TYR A 247 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N PHE A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 265 Processing helix chain 'A' and resid 265 through 276 removed outlier: 3.515A pdb=" N MET A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 292 removed outlier: 3.509A pdb=" N ALA A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS A 290 " --> pdb=" O MET A 286 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET A 292 " --> pdb=" O VAL A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.513A pdb=" N SER A 300 " --> pdb=" O GLU A 296 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU A 303 " --> pdb=" O TYR A 299 " (cutoff:3.500A) Proline residue: A 304 - end of helix Processing helix chain 'A' and resid 311 through 329 removed outlier: 3.612A pdb=" N ALA A 315 " --> pdb=" O MET A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 351 removed outlier: 3.546A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 370 removed outlier: 3.916A pdb=" N ILE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 389 removed outlier: 4.038A pdb=" N ILE A 389 " --> pdb=" O MET A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 419 removed outlier: 3.639A pdb=" N LEU A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N MET A 399 " --> pdb=" O MET A 395 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 402 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 403 " --> pdb=" O MET A 399 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 34 Processing helix chain 'B' and resid 37 through 43 removed outlier: 3.717A pdb=" N TYR B 42 " --> pdb=" O ALA B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 56 removed outlier: 3.687A pdb=" N LEU B 49 " --> pdb=" O PRO B 45 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE B 50 " --> pdb=" O PHE B 46 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 54 " --> pdb=" O PHE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 71 removed outlier: 3.713A pdb=" N ILE B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 78 removed outlier: 3.575A pdb=" N LEU B 78 " --> pdb=" O PRO B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 107 removed outlier: 3.515A pdb=" N VAL B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 136 Processing helix chain 'B' and resid 141 through 149 removed outlier: 3.914A pdb=" N LEU B 146 " --> pdb=" O PRO B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 170 Processing helix chain 'B' and resid 173 through 220 removed outlier: 3.504A pdb=" N LYS B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE B 197 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 198 " --> pdb=" O MET B 194 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ARG B 206 " --> pdb=" O MET B 202 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ILE B 207 " --> pdb=" O GLN B 203 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B 214 " --> pdb=" O PHE B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 254 removed outlier: 4.700A pdb=" N TYR B 247 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N PHE B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 265 Processing helix chain 'B' and resid 265 through 276 removed outlier: 3.515A pdb=" N MET B 269 " --> pdb=" O ALA B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 292 removed outlier: 3.509A pdb=" N ALA B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS B 290 " --> pdb=" O MET B 286 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET B 292 " --> pdb=" O VAL B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 309 removed outlier: 3.514A pdb=" N SER B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU B 303 " --> pdb=" O TYR B 299 " (cutoff:3.500A) Proline residue: B 304 - end of helix Processing helix chain 'B' and resid 311 through 329 removed outlier: 3.612A pdb=" N ALA B 315 " --> pdb=" O MET B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 351 removed outlier: 3.546A pdb=" N LEU B 347 " --> pdb=" O LEU B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 370 removed outlier: 3.915A pdb=" N ILE B 361 " --> pdb=" O GLY B 357 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET B 365 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU B 368 " --> pdb=" O ALA B 364 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B 370 " --> pdb=" O VAL B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 389 removed outlier: 4.038A pdb=" N ILE B 389 " --> pdb=" O MET B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 419 removed outlier: 3.639A pdb=" N LEU B 393 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET B 399 " --> pdb=" O MET B 395 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL B 400 " --> pdb=" O GLY B 396 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN B 401 " --> pdb=" O ARG B 397 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 402 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B 403 " --> pdb=" O MET B 399 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 34 Processing helix chain 'C' and resid 37 through 43 removed outlier: 3.718A pdb=" N TYR C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 56 removed outlier: 3.686A pdb=" N LEU C 49 " --> pdb=" O PRO C 45 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE C 50 " --> pdb=" O PHE C 46 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 54 " --> pdb=" O PHE C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 71 removed outlier: 3.713A pdb=" N ILE C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 78 removed outlier: 3.575A pdb=" N LEU C 78 " --> pdb=" O PRO C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 107 removed outlier: 3.515A pdb=" N VAL C 83 " --> pdb=" O GLY C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 136 Processing helix chain 'C' and resid 141 through 149 removed outlier: 3.914A pdb=" N LEU C 146 " --> pdb=" O PRO C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 170 Processing helix chain 'C' and resid 173 through 220 removed outlier: 3.503A pdb=" N LYS C 178 " --> pdb=" O GLU C 174 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER C 179 " --> pdb=" O LYS C 175 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE C 197 " --> pdb=" O ALA C 193 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 198 " --> pdb=" O MET C 194 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ARG C 206 " --> pdb=" O MET C 202 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ILE C 207 " --> pdb=" O GLN C 203 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 214 " --> pdb=" O PHE C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 254 removed outlier: 4.700A pdb=" N TYR C 247 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N PHE C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 265 Processing helix chain 'C' and resid 265 through 276 removed outlier: 3.516A pdb=" N MET C 269 " --> pdb=" O ALA C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 292 removed outlier: 3.509A pdb=" N ALA C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS C 290 " --> pdb=" O MET C 286 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU C 291 " --> pdb=" O ARG C 287 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET C 292 " --> pdb=" O VAL C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 309 removed outlier: 3.513A pdb=" N SER C 300 " --> pdb=" O GLU C 296 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU C 303 " --> pdb=" O TYR C 299 " (cutoff:3.500A) Proline residue: C 304 - end of helix Processing helix chain 'C' and resid 311 through 329 removed outlier: 3.612A pdb=" N ALA C 315 " --> pdb=" O MET C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 351 removed outlier: 3.546A pdb=" N LEU C 347 " --> pdb=" O LEU C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 370 removed outlier: 3.916A pdb=" N ILE C 361 " --> pdb=" O GLY C 357 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET C 365 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU C 368 " --> pdb=" O ALA C 364 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 370 " --> pdb=" O VAL C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 389 removed outlier: 4.038A pdb=" N ILE C 389 " --> pdb=" O MET C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 419 removed outlier: 3.639A pdb=" N LEU C 393 " --> pdb=" O ILE C 389 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET C 399 " --> pdb=" O MET C 395 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL C 400 " --> pdb=" O GLY C 396 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN C 401 " --> pdb=" O ARG C 397 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL C 402 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C 403 " --> pdb=" O MET C 399 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) 699 hydrogen bonds defined for protein. 2088 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: 1.47 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1452 1.31 - 1.43: 2184 1.43 - 1.56: 5748 1.56 - 1.68: 18 1.68 - 1.81: 99 Bond restraints: 9501 Sorted by residual: bond pdb=" C16 PG8 B 503 " pdb=" C17 PG8 B 503 " ideal model delta sigma weight residual 1.521 1.430 0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C16 PG8 C 504 " pdb=" C17 PG8 C 504 " ideal model delta sigma weight residual 1.521 1.430 0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C16 PG8 A 503 " pdb=" C17 PG8 A 503 " ideal model delta sigma weight residual 1.521 1.430 0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C GLN A 203 " pdb=" N TYR A 204 " ideal model delta sigma weight residual 1.335 1.388 -0.053 1.38e-02 5.25e+03 1.49e+01 bond pdb=" C GLN B 203 " pdb=" N TYR B 204 " ideal model delta sigma weight residual 1.335 1.388 -0.053 1.38e-02 5.25e+03 1.49e+01 ... (remaining 9496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 11757 1.53 - 3.06: 884 3.06 - 4.59: 173 4.59 - 6.12: 38 6.12 - 7.65: 18 Bond angle restraints: 12870 Sorted by residual: angle pdb=" CA ASP B 405 " pdb=" CB ASP B 405 " pdb=" CG ASP B 405 " ideal model delta sigma weight residual 112.60 118.54 -5.94 1.00e+00 1.00e+00 3.52e+01 angle pdb=" CA ASP A 405 " pdb=" CB ASP A 405 " pdb=" CG ASP A 405 " ideal model delta sigma weight residual 112.60 118.51 -5.91 1.00e+00 1.00e+00 3.49e+01 angle pdb=" CA ASP C 405 " pdb=" CB ASP C 405 " pdb=" CG ASP C 405 " ideal model delta sigma weight residual 112.60 118.49 -5.89 1.00e+00 1.00e+00 3.47e+01 angle pdb=" N GLN A 203 " pdb=" CA GLN A 203 " pdb=" C GLN A 203 " ideal model delta sigma weight residual 112.23 106.72 5.51 1.26e+00 6.30e-01 1.91e+01 angle pdb=" N GLN C 203 " pdb=" CA GLN C 203 " pdb=" C GLN C 203 " ideal model delta sigma weight residual 112.23 106.72 5.51 1.26e+00 6.30e-01 1.91e+01 ... (remaining 12865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.85: 5478 28.85 - 57.70: 222 57.70 - 86.54: 27 86.54 - 115.39: 12 115.39 - 144.24: 12 Dihedral angle restraints: 5751 sinusoidal: 2283 harmonic: 3468 Sorted by residual: dihedral pdb=" C19 D3D A 507 " pdb=" O5 D3D A 507 " pdb=" P D3D A 507 " pdb=" O3 D3D A 507 " ideal model delta sinusoidal sigma weight residual -35.55 -179.79 144.24 1 3.00e+01 1.11e-03 1.93e+01 dihedral pdb=" C19 D3D C 501 " pdb=" O5 D3D C 501 " pdb=" P D3D C 501 " pdb=" O3 D3D C 501 " ideal model delta sinusoidal sigma weight residual -35.55 -179.77 144.22 1 3.00e+01 1.11e-03 1.93e+01 dihedral pdb=" C19 D3D B 507 " pdb=" O5 D3D B 507 " pdb=" P D3D B 507 " pdb=" O3 D3D B 507 " ideal model delta sinusoidal sigma weight residual -35.55 -179.75 144.20 1 3.00e+01 1.11e-03 1.93e+01 ... (remaining 5748 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 866 0.040 - 0.080: 547 0.080 - 0.120: 148 0.120 - 0.160: 29 0.160 - 0.200: 21 Chirality restraints: 1611 Sorted by residual: chirality pdb=" CA PRO C 153 " pdb=" N PRO C 153 " pdb=" C PRO C 153 " pdb=" CB PRO C 153 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA PRO A 60 " pdb=" N PRO A 60 " pdb=" C PRO A 60 " pdb=" CB PRO A 60 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA PRO C 60 " pdb=" N PRO C 60 " pdb=" C PRO C 60 " pdb=" CB PRO C 60 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.94e-01 ... (remaining 1608 not shown) Planarity restraints: 1554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C29 D3D A 507 " -0.201 2.00e-02 2.50e+03 2.01e-01 4.06e+02 pdb=" C30 D3D A 507 " 0.197 2.00e-02 2.50e+03 pdb=" C31 D3D A 507 " 0.205 2.00e-02 2.50e+03 pdb=" C32 D3D A 507 " -0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C29 D3D C 501 " 0.201 2.00e-02 2.50e+03 2.01e-01 4.05e+02 pdb=" C30 D3D C 501 " -0.198 2.00e-02 2.50e+03 pdb=" C31 D3D C 501 " -0.205 2.00e-02 2.50e+03 pdb=" C32 D3D C 501 " 0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C29 D3D B 507 " -0.201 2.00e-02 2.50e+03 2.01e-01 4.05e+02 pdb=" C30 D3D B 507 " 0.198 2.00e-02 2.50e+03 pdb=" C31 D3D B 507 " 0.205 2.00e-02 2.50e+03 pdb=" C32 D3D B 507 " -0.202 2.00e-02 2.50e+03 ... (remaining 1551 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 78 2.67 - 3.23: 9457 3.23 - 3.79: 14195 3.79 - 4.34: 19110 4.34 - 4.90: 32182 Nonbonded interactions: 75022 Sorted by model distance: nonbonded pdb=" O GLY A 306 " pdb="NA NA A 502 " model vdw 2.118 3.210 nonbonded pdb=" O GLY B 306 " pdb="NA NA B 502 " model vdw 2.118 3.210 nonbonded pdb=" O GLY C 306 " pdb="NA NA C 503 " model vdw 2.118 3.210 nonbonded pdb=" O ASP C 405 " pdb=" OD1 ASP C 405 " model vdw 2.465 3.040 nonbonded pdb=" O ASP A 405 " pdb=" OD1 ASP A 405 " model vdw 2.465 3.040 ... (remaining 75017 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 419 or resid 506)) selection = (chain 'B' and (resid 12 through 419 or resid 506)) selection = (chain 'C' and (resid 12 through 419 or resid 506)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.810 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.720 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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 : 0.008 0.091 9501 Z= 0.455 Angle : 0.955 7.648 12870 Z= 0.534 Chirality : 0.055 0.200 1611 Planarity : 0.011 0.201 1554 Dihedral : 18.188 144.238 3549 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.31 % Allowed : 9.43 % Favored : 90.25 % 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: 0.26 (0.25), residues: 1218 helix: 0.29 (0.17), residues: 1026 sheet: None (None), residues: 0 loop : 0.34 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG A 105 TYR 0.018 0.003 TYR C 236 PHE 0.015 0.004 PHE C 248 HIS 0.002 0.001 HIS B 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00796 / 0.45 ( 9501) covalent geometry : angle 0.95479 / 0.53 (12870) hydrogen bonds : bond 0.18337 / 12.17 ( 699) hydrogen bonds : angle 6.03085 / 4.32 ( 2088) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 179 time to evaluate : 0.345 Fit side-chains REVERT: A 103 MET cc_start: 0.6193 (mmm) cc_final: 0.5788 (mmt) REVERT: B 217 MET cc_start: 0.8314 (mmm) cc_final: 0.7790 (mmm) REVERT: B 220 GLN cc_start: 0.8326 (mm-40) cc_final: 0.7949 (mm-40) outliers start: 3 outliers final: 3 residues processed: 182 average time/residue: 0.0836 time to fit residues: 22.1914 Evaluate side-chains 134 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 131 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain C residue 344 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.0870 chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 0.8980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 GLN B 114 HIS B 150 GLN B 338 GLN C 338 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.178211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.140368 restraints weight = 9506.639| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.77 r_work: 0.3421 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9501 Z= 0.125 Angle : 0.546 6.512 12870 Z= 0.274 Chirality : 0.037 0.126 1611 Planarity : 0.004 0.029 1554 Dihedral : 16.799 112.080 1587 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.36 % Allowed : 14.36 % Favored : 84.28 % 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: 1.09 (0.25), residues: 1218 helix: 0.85 (0.17), residues: 1035 sheet: None (None), residues: 0 loop : 0.62 (0.51), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 287 TYR 0.008 0.001 TYR C 299 PHE 0.013 0.001 PHE A 248 HIS 0.001 0.000 HIS B 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 ( 9501) covalent geometry : angle 0.54636 / 0.27 (12870) hydrogen bonds : bond 0.04471 / 2.95 ( 699) hydrogen bonds : angle 4.22871 / 3.02 ( 2088) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.242 Fit side-chains REVERT: A 103 MET cc_start: 0.5580 (mmm) cc_final: 0.5347 (mmt) REVERT: A 368 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7517 (mm-30) REVERT: C 13 LEU cc_start: 0.8384 (mt) cc_final: 0.8082 (mt) REVERT: C 217 MET cc_start: 0.8302 (mmm) cc_final: 0.8046 (tpp) outliers start: 13 outliers final: 9 residues processed: 159 average time/residue: 0.0659 time to fit residues: 16.5060 Evaluate side-chains 145 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 299 TYR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 299 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 47 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 119 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 29 optimal weight: 0.0370 chunk 67 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.181161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.146466 restraints weight = 9663.945| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 1.55 r_work: 0.3492 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9501 Z= 0.125 Angle : 0.531 10.141 12870 Z= 0.262 Chirality : 0.037 0.133 1611 Planarity : 0.003 0.029 1554 Dihedral : 13.986 88.532 1584 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.31 % Allowed : 16.35 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.25), residues: 1218 helix: 1.05 (0.16), residues: 1035 sheet: None (None), residues: 0 loop : 0.89 (0.52), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 287 TYR 0.010 0.001 TYR A 299 PHE 0.023 0.001 PHE C 301 HIS 0.001 0.000 HIS A 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 9501) covalent geometry : angle 0.53137 / 0.26 (12870) hydrogen bonds : bond 0.04237 / 2.78 ( 699) hydrogen bonds : angle 4.09030 / 2.91 ( 2088) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.319 Fit side-chains REVERT: A 170 ASN cc_start: 0.7032 (t0) cc_final: 0.6818 (t0) REVERT: A 271 THR cc_start: 0.8108 (m) cc_final: 0.7903 (m) REVERT: A 368 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7734 (mm-30) REVERT: C 21 ILE cc_start: 0.8366 (mm) cc_final: 0.8158 (mm) REVERT: C 194 MET cc_start: 0.8677 (tpp) cc_final: 0.8381 (mmp) REVERT: C 217 MET cc_start: 0.8390 (mmm) cc_final: 0.8124 (tpp) outliers start: 22 outliers final: 17 residues processed: 153 average time/residue: 0.0645 time to fit residues: 15.8245 Evaluate side-chains 148 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 299 TYR Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 299 TYR Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain C residue 502 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 69 optimal weight: 0.0570 chunk 47 optimal weight: 0.9990 chunk 115 optimal weight: 0.2980 chunk 21 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.181312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.148063 restraints weight = 9730.893| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.82 r_work: 0.3453 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9501 Z= 0.122 Angle : 0.531 10.087 12870 Z= 0.258 Chirality : 0.037 0.154 1611 Planarity : 0.003 0.027 1554 Dihedral : 13.331 119.570 1584 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.89 % Allowed : 17.71 % Favored : 80.40 % 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: 1.63 (0.25), residues: 1218 helix: 1.16 (0.16), residues: 1041 sheet: None (None), residues: 0 loop : 1.19 (0.54), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 287 TYR 0.009 0.001 TYR C 299 PHE 0.012 0.001 PHE C 301 HIS 0.001 0.000 HIS B 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 9501) covalent geometry : angle 0.53092 / 0.26 (12870) hydrogen bonds : bond 0.04048 / 2.65 ( 699) hydrogen bonds : angle 3.98382 / 2.82 ( 2088) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.322 Fit side-chains REVERT: A 368 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7490 (mm-30) REVERT: C 194 MET cc_start: 0.8658 (tpp) cc_final: 0.8260 (mmp) REVERT: C 286 MET cc_start: 0.9086 (mtp) cc_final: 0.8813 (mmm) outliers start: 18 outliers final: 16 residues processed: 140 average time/residue: 0.0646 time to fit residues: 14.5833 Evaluate side-chains 143 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 299 TYR Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 299 TYR Chi-restraints excluded: chain C residue 323 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 67 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.177566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.146339 restraints weight = 9747.786| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.55 r_work: 0.3455 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9501 Z= 0.147 Angle : 0.563 9.884 12870 Z= 0.273 Chirality : 0.038 0.149 1611 Planarity : 0.003 0.026 1554 Dihedral : 12.911 102.387 1584 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.46 % Allowed : 15.83 % Favored : 80.71 % 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: 1.58 (0.25), residues: 1218 helix: 1.14 (0.16), residues: 1038 sheet: None (None), residues: 0 loop : 1.07 (0.53), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 287 TYR 0.009 0.001 TYR C 236 PHE 0.008 0.001 PHE C 301 HIS 0.001 0.000 HIS A 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 9501) covalent geometry : angle 0.56310 / 0.27 (12870) hydrogen bonds : bond 0.04507 / 2.95 ( 699) hydrogen bonds : angle 4.09630 / 2.90 ( 2088) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 146 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7636 (mm-30) REVERT: B 194 MET cc_start: 0.8560 (mmp) cc_final: 0.8359 (mmp) REVERT: C 123 GLN cc_start: 0.7721 (mm-40) cc_final: 0.7464 (mm-40) REVERT: C 125 LYS cc_start: 0.7908 (pttp) cc_final: 0.7661 (ptpp) REVERT: C 194 MET cc_start: 0.8892 (tpp) cc_final: 0.8411 (mmp) REVERT: C 270 LEU cc_start: 0.8429 (mm) cc_final: 0.8176 (mm) REVERT: C 286 MET cc_start: 0.9143 (mtp) cc_final: 0.8818 (mmm) outliers start: 33 outliers final: 24 residues processed: 174 average time/residue: 0.0676 time to fit residues: 18.2673 Evaluate side-chains 160 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 299 TYR Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 299 TYR Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 386 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 86 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 52 optimal weight: 0.0970 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.178666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.144046 restraints weight = 9792.526| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 1.53 r_work: 0.3473 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9501 Z= 0.137 Angle : 0.558 9.050 12870 Z= 0.270 Chirality : 0.038 0.139 1611 Planarity : 0.003 0.025 1554 Dihedral : 12.603 100.653 1584 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.14 % Allowed : 17.09 % Favored : 79.77 % 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: 1.69 (0.25), residues: 1218 helix: 1.22 (0.16), residues: 1038 sheet: None (None), residues: 0 loop : 1.11 (0.53), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 287 TYR 0.009 0.001 TYR C 299 PHE 0.011 0.001 PHE C 248 HIS 0.001 0.000 HIS C 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 9501) covalent geometry : angle 0.55790 / 0.27 (12870) hydrogen bonds : bond 0.04227 / 2.78 ( 699) hydrogen bonds : angle 4.02726 / 2.86 ( 2088) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7525 (mm-30) REVERT: B 269 MET cc_start: 0.7574 (mtp) cc_final: 0.7365 (mtt) REVERT: B 270 LEU cc_start: 0.8516 (mm) cc_final: 0.8255 (mm) REVERT: C 14 GLN cc_start: 0.6887 (mp10) cc_final: 0.6653 (mp10) REVERT: C 125 LYS cc_start: 0.7846 (pttp) cc_final: 0.7630 (ptpp) REVERT: C 148 ASN cc_start: 0.8017 (m-40) cc_final: 0.7767 (m-40) REVERT: C 194 MET cc_start: 0.8863 (tpp) cc_final: 0.8439 (mmp) REVERT: C 270 LEU cc_start: 0.8438 (mm) cc_final: 0.8215 (mm) REVERT: C 286 MET cc_start: 0.9130 (mtp) cc_final: 0.8802 (mmm) outliers start: 30 outliers final: 26 residues processed: 163 average time/residue: 0.0740 time to fit residues: 18.7578 Evaluate side-chains 162 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 299 TYR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 299 TYR Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 386 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 16 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 43 optimal weight: 0.0040 chunk 47 optimal weight: 0.6980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.179688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.145146 restraints weight = 9786.326| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.54 r_work: 0.3457 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9501 Z= 0.127 Angle : 0.560 16.287 12870 Z= 0.267 Chirality : 0.037 0.128 1611 Planarity : 0.003 0.025 1554 Dihedral : 12.220 93.324 1584 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.25 % Allowed : 17.40 % Favored : 79.35 % 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: 1.80 (0.25), residues: 1218 helix: 1.32 (0.16), residues: 1035 sheet: None (None), residues: 0 loop : 0.94 (0.53), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 287 TYR 0.018 0.001 TYR B 215 PHE 0.008 0.001 PHE C 248 HIS 0.001 0.000 HIS C 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 9501) covalent geometry : angle 0.56042 / 0.27 (12870) hydrogen bonds : bond 0.04058 / 2.66 ( 699) hydrogen bonds : angle 3.97345 / 2.82 ( 2088) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 103 MET cc_start: 0.5808 (mmt) cc_final: 0.5524 (mmt) REVERT: A 311 MET cc_start: 0.8816 (mtt) cc_final: 0.8546 (mtt) REVERT: A 368 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7552 (mm-30) REVERT: C 14 GLN cc_start: 0.6874 (mp10) cc_final: 0.6657 (mp10) REVERT: C 123 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7524 (mm-40) REVERT: C 148 ASN cc_start: 0.8038 (m-40) cc_final: 0.7805 (m-40) REVERT: C 194 MET cc_start: 0.8781 (tpp) cc_final: 0.8404 (mmp) REVERT: C 270 LEU cc_start: 0.8470 (mm) cc_final: 0.8262 (mm) REVERT: C 286 MET cc_start: 0.9132 (mtp) cc_final: 0.8804 (mmm) outliers start: 31 outliers final: 25 residues processed: 162 average time/residue: 0.0664 time to fit residues: 16.8458 Evaluate side-chains 159 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 299 TYR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 299 TYR Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 386 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.9990 chunk 62 optimal weight: 0.0980 chunk 84 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.190820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.159413 restraints weight = 9270.354| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 1.39 r_work: 0.3566 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9501 Z= 0.143 Angle : 0.580 16.064 12870 Z= 0.278 Chirality : 0.038 0.137 1611 Planarity : 0.003 0.024 1554 Dihedral : 12.102 86.376 1584 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.25 % Allowed : 18.34 % Favored : 78.41 % 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: 1.79 (0.25), residues: 1218 helix: 1.29 (0.16), residues: 1032 sheet: None (None), residues: 0 loop : 1.08 (0.54), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 287 TYR 0.009 0.001 TYR B 215 PHE 0.008 0.001 PHE C 248 HIS 0.001 0.000 HIS C 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 9501) covalent geometry : angle 0.57987 / 0.28 (12870) hydrogen bonds : bond 0.04346 / 2.86 ( 699) hydrogen bonds : angle 4.05303 / 2.88 ( 2088) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 103 MET cc_start: 0.5971 (mmt) cc_final: 0.5691 (mmt) REVERT: A 368 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7461 (mm-30) REVERT: C 14 GLN cc_start: 0.7020 (mp10) cc_final: 0.6776 (mp10) REVERT: C 148 ASN cc_start: 0.8087 (m-40) cc_final: 0.7857 (m-40) REVERT: C 194 MET cc_start: 0.8898 (tpp) cc_final: 0.8502 (mmp) REVERT: C 270 LEU cc_start: 0.8614 (mm) cc_final: 0.8410 (mm) REVERT: C 286 MET cc_start: 0.9138 (mtp) cc_final: 0.8841 (mmm) outliers start: 31 outliers final: 29 residues processed: 156 average time/residue: 0.0626 time to fit residues: 15.3740 Evaluate side-chains 161 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 299 TYR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 299 TYR Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 386 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 3 optimal weight: 0.3980 chunk 0 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.190392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.160960 restraints weight = 9307.558| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.37 r_work: 0.3561 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9501 Z= 0.142 Angle : 0.583 15.998 12870 Z= 0.281 Chirality : 0.038 0.168 1611 Planarity : 0.003 0.024 1554 Dihedral : 11.513 76.979 1584 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.35 % Allowed : 18.34 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.25), residues: 1218 helix: 1.29 (0.16), residues: 1026 sheet: None (None), residues: 0 loop : 0.92 (0.52), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 287 TYR 0.008 0.001 TYR C 299 PHE 0.008 0.001 PHE C 248 HIS 0.001 0.000 HIS C 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 9501) covalent geometry : angle 0.58278 / 0.28 (12870) hydrogen bonds : bond 0.04328 / 2.86 ( 699) hydrogen bonds : angle 4.05692 / 2.89 ( 2088) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 103 MET cc_start: 0.6088 (mmt) cc_final: 0.5820 (mmt) REVERT: A 311 MET cc_start: 0.8788 (mtt) cc_final: 0.8534 (mtt) REVERT: A 368 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7460 (mm-30) REVERT: C 14 GLN cc_start: 0.7132 (mp10) cc_final: 0.6885 (mp10) REVERT: C 148 ASN cc_start: 0.8097 (m-40) cc_final: 0.7875 (m-40) REVERT: C 194 MET cc_start: 0.8895 (tpp) cc_final: 0.8505 (mmp) REVERT: C 286 MET cc_start: 0.9153 (mtp) cc_final: 0.8863 (mmm) outliers start: 32 outliers final: 30 residues processed: 158 average time/residue: 0.0646 time to fit residues: 16.0596 Evaluate side-chains 161 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 299 TYR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 299 TYR Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 386 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 53 optimal weight: 0.0040 chunk 103 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.191766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.161763 restraints weight = 9340.331| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.43 r_work: 0.3580 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9501 Z= 0.135 Angle : 0.584 15.963 12870 Z= 0.279 Chirality : 0.038 0.218 1611 Planarity : 0.003 0.024 1554 Dihedral : 11.125 68.898 1584 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.35 % Allowed : 18.87 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.25), residues: 1218 helix: 1.31 (0.16), residues: 1026 sheet: None (None), residues: 0 loop : 0.92 (0.52), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 287 TYR 0.009 0.001 TYR B 215 PHE 0.008 0.001 PHE C 248 HIS 0.001 0.000 HIS C 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 9501) covalent geometry : angle 0.58418 / 0.28 (12870) hydrogen bonds : bond 0.04217 / 2.77 ( 699) hydrogen bonds : angle 4.03158 / 2.88 ( 2088) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 103 MET cc_start: 0.6061 (mmt) cc_final: 0.5821 (mmt) REVERT: A 368 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7445 (mm-30) REVERT: C 148 ASN cc_start: 0.8096 (m-40) cc_final: 0.7871 (m-40) REVERT: C 194 MET cc_start: 0.8867 (tpp) cc_final: 0.8485 (mmp) REVERT: C 286 MET cc_start: 0.9133 (mtp) cc_final: 0.8845 (mmm) outliers start: 32 outliers final: 32 residues processed: 154 average time/residue: 0.0602 time to fit residues: 14.6261 Evaluate side-chains 161 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 299 TYR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 299 TYR Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 386 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 103 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 100 optimal weight: 0.0570 chunk 21 optimal weight: 0.9980 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.190407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.159557 restraints weight = 9280.087| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.37 r_work: 0.3573 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9501 Z= 0.147 Angle : 0.599 16.046 12870 Z= 0.289 Chirality : 0.038 0.244 1611 Planarity : 0.003 0.027 1554 Dihedral : 10.812 64.961 1584 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.67 % Allowed : 18.45 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.25), residues: 1218 helix: 1.29 (0.16), residues: 1023 sheet: None (None), residues: 0 loop : 0.74 (0.51), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 287 TYR 0.010 0.001 TYR B 215 PHE 0.008 0.001 PHE C 248 HIS 0.001 0.000 HIS A 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 9501) covalent geometry : angle 0.59884 / 0.29 (12870) hydrogen bonds : bond 0.04425 / 2.91 ( 699) hydrogen bonds : angle 4.07064 / 2.90 ( 2088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2074.51 seconds wall clock time: 36 minutes 15.33 seconds (2175.33 seconds total)