Starting phenix.real_space_refine on Mon May 19 12:32:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jk6_61545/05_2025/9jk6_61545.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jk6_61545/05_2025/9jk6_61545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jk6_61545/05_2025/9jk6_61545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jk6_61545/05_2025/9jk6_61545.map" model { file = "/net/cci-nas-00/data/ceres_data/9jk6_61545/05_2025/9jk6_61545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jk6_61545/05_2025/9jk6_61545.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.066 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 12120 2.51 5 N 3192 2.21 5 O 3120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 18504 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3084 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 13, 'TRANS': 362} Chain breaks: 2 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 7.67, per 1000 atoms: 0.41 Number of scatterers: 18504 At special positions: 0 Unit cell: (105.56, 93.96, 221.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 3120 8.00 N 3192 7.00 C 12120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 145 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 145 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS F 145 " - pdb=" SG CYS F 149 " distance=2.03 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: 4.27 Conformation dependent library (CDL) restraints added in 2.2 seconds 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4356 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 12 sheets defined 62.8% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 115 through 133 Proline residue: A 127 - end of helix removed outlier: 3.653A pdb=" N LEU A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 172 removed outlier: 4.076A pdb=" N GLU A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU A 152 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 207 removed outlier: 3.525A pdb=" N ALA A 187 " --> pdb=" O PHE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 Processing helix chain 'A' and resid 215 through 243 removed outlier: 3.863A pdb=" N ILE A 219 " --> pdb=" O ASN A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 287 removed outlier: 3.888A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 294 Processing helix chain 'A' and resid 295 through 306 removed outlier: 3.555A pdb=" N LYS A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 337 removed outlier: 3.658A pdb=" N ARG A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 370 removed outlier: 4.359A pdb=" N TYR A 345 " --> pdb=" O ASN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 398 Processing helix chain 'A' and resid 401 through 412 Processing helix chain 'A' and resid 419 through 434 Processing helix chain 'A' and resid 436 through 446 removed outlier: 4.859A pdb=" N ARG A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TYR A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 453 removed outlier: 3.600A pdb=" N GLN A 452 " --> pdb=" O PRO A 449 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR A 453 " --> pdb=" O THR A 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 449 through 453' Processing helix chain 'A' and resid 508 through 513 removed outlier: 3.895A pdb=" N HIS A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS A 513 " --> pdb=" O LYS A 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 133 Proline residue: B 127 - end of helix removed outlier: 3.654A pdb=" N LEU B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 172 removed outlier: 4.076A pdb=" N GLU B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU B 152 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE B 172 " --> pdb=" O TRP B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 207 removed outlier: 3.525A pdb=" N ALA B 187 " --> pdb=" O PHE B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 212 Processing helix chain 'B' and resid 215 through 243 removed outlier: 3.863A pdb=" N ILE B 219 " --> pdb=" O ASN B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 287 removed outlier: 3.888A pdb=" N TYR B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 294 Processing helix chain 'B' and resid 295 through 306 removed outlier: 3.555A pdb=" N LYS B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 337 removed outlier: 3.657A pdb=" N ARG B 335 " --> pdb=" O ALA B 331 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 370 removed outlier: 4.359A pdb=" N TYR B 345 " --> pdb=" O ASN B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 398 Processing helix chain 'B' and resid 401 through 412 Processing helix chain 'B' and resid 419 through 434 Processing helix chain 'B' and resid 436 through 446 removed outlier: 4.859A pdb=" N ARG B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TYR B 444 " --> pdb=" O PHE B 440 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 453 removed outlier: 3.600A pdb=" N GLN B 452 " --> pdb=" O PRO B 449 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR B 453 " --> pdb=" O THR B 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 449 through 453' Processing helix chain 'B' and resid 508 through 513 removed outlier: 3.896A pdb=" N HIS B 512 " --> pdb=" O PRO B 509 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS B 513 " --> pdb=" O LYS B 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 133 Proline residue: C 127 - end of helix removed outlier: 3.654A pdb=" N LEU C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 172 removed outlier: 4.076A pdb=" N GLU C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU C 152 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE C 172 " --> pdb=" O TRP C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 207 removed outlier: 3.524A pdb=" N ALA C 187 " --> pdb=" O PHE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 Processing helix chain 'C' and resid 215 through 243 removed outlier: 3.863A pdb=" N ILE C 219 " --> pdb=" O ASN C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 287 removed outlier: 3.889A pdb=" N TYR C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS C 285 " --> pdb=" O GLU C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 294 Processing helix chain 'C' and resid 295 through 306 removed outlier: 3.555A pdb=" N LYS C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 337 removed outlier: 3.658A pdb=" N ARG C 335 " --> pdb=" O ALA C 331 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP C 337 " --> pdb=" O ALA C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 370 removed outlier: 4.359A pdb=" N TYR C 345 " --> pdb=" O ASN C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 398 Processing helix chain 'C' and resid 401 through 412 Processing helix chain 'C' and resid 419 through 434 Processing helix chain 'C' and resid 436 through 446 removed outlier: 4.859A pdb=" N ARG C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TYR C 444 " --> pdb=" O PHE C 440 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER C 446 " --> pdb=" O GLU C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 453 removed outlier: 3.601A pdb=" N GLN C 452 " --> pdb=" O PRO C 449 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR C 453 " --> pdb=" O THR C 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 449 through 453' Processing helix chain 'C' and resid 508 through 513 removed outlier: 3.895A pdb=" N HIS C 512 " --> pdb=" O PRO C 509 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS C 513 " --> pdb=" O LYS C 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 133 Proline residue: D 127 - end of helix removed outlier: 3.653A pdb=" N LEU D 133 " --> pdb=" O ALA D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 172 removed outlier: 4.076A pdb=" N GLU D 150 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY D 151 " --> pdb=" O THR D 147 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE D 172 " --> pdb=" O TRP D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 207 removed outlier: 3.525A pdb=" N ALA D 187 " --> pdb=" O PHE D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 212 Processing helix chain 'D' and resid 215 through 243 removed outlier: 3.864A pdb=" N ILE D 219 " --> pdb=" O ASN D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 287 removed outlier: 3.887A pdb=" N TYR D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS D 285 " --> pdb=" O GLU D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 294 Processing helix chain 'D' and resid 295 through 306 removed outlier: 3.555A pdb=" N LYS D 299 " --> pdb=" O LEU D 295 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 337 removed outlier: 3.658A pdb=" N ARG D 335 " --> pdb=" O ALA D 331 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP D 337 " --> pdb=" O ALA D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 370 removed outlier: 4.359A pdb=" N TYR D 345 " --> pdb=" O ASN D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 398 Processing helix chain 'D' and resid 401 through 412 Processing helix chain 'D' and resid 419 through 434 Processing helix chain 'D' and resid 436 through 446 removed outlier: 4.859A pdb=" N ARG D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TYR D 444 " --> pdb=" O PHE D 440 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER D 446 " --> pdb=" O GLU D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 453 removed outlier: 3.600A pdb=" N GLN D 452 " --> pdb=" O PRO D 449 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR D 453 " --> pdb=" O THR D 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 449 through 453' Processing helix chain 'D' and resid 508 through 513 removed outlier: 3.895A pdb=" N HIS D 512 " --> pdb=" O PRO D 509 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS D 513 " --> pdb=" O LYS D 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 133 Proline residue: E 127 - end of helix removed outlier: 3.653A pdb=" N LEU E 133 " --> pdb=" O ALA E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 172 removed outlier: 4.076A pdb=" N GLU E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY E 151 " --> pdb=" O THR E 147 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU E 152 " --> pdb=" O ILE E 148 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE E 172 " --> pdb=" O TRP E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 207 removed outlier: 3.525A pdb=" N ALA E 187 " --> pdb=" O PHE E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 212 Processing helix chain 'E' and resid 215 through 243 removed outlier: 3.863A pdb=" N ILE E 219 " --> pdb=" O ASN E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 287 removed outlier: 3.888A pdb=" N TYR E 284 " --> pdb=" O LEU E 280 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 294 Processing helix chain 'E' and resid 295 through 306 removed outlier: 3.555A pdb=" N LYS E 299 " --> pdb=" O LEU E 295 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG E 301 " --> pdb=" O ALA E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 337 removed outlier: 3.658A pdb=" N ARG E 335 " --> pdb=" O ALA E 331 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP E 337 " --> pdb=" O ALA E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 370 removed outlier: 4.358A pdb=" N TYR E 345 " --> pdb=" O ASN E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 398 Processing helix chain 'E' and resid 401 through 412 Processing helix chain 'E' and resid 419 through 434 Processing helix chain 'E' and resid 436 through 446 removed outlier: 4.858A pdb=" N ARG E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N TYR E 444 " --> pdb=" O PHE E 440 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER E 446 " --> pdb=" O GLU E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 453 removed outlier: 3.601A pdb=" N GLN E 452 " --> pdb=" O PRO E 449 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR E 453 " --> pdb=" O THR E 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 449 through 453' Processing helix chain 'E' and resid 508 through 513 removed outlier: 3.895A pdb=" N HIS E 512 " --> pdb=" O PRO E 509 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS E 513 " --> pdb=" O LYS E 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 133 Proline residue: F 127 - end of helix removed outlier: 3.654A pdb=" N LEU F 133 " --> pdb=" O ALA F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 172 removed outlier: 4.075A pdb=" N GLU F 150 " --> pdb=" O GLY F 146 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY F 151 " --> pdb=" O THR F 147 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU F 152 " --> pdb=" O ILE F 148 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE F 172 " --> pdb=" O TRP F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 207 removed outlier: 3.525A pdb=" N ALA F 187 " --> pdb=" O PHE F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 212 Processing helix chain 'F' and resid 215 through 243 removed outlier: 3.864A pdb=" N ILE F 219 " --> pdb=" O ASN F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 287 removed outlier: 3.888A pdb=" N TYR F 284 " --> pdb=" O LEU F 280 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS F 285 " --> pdb=" O GLU F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 294 Processing helix chain 'F' and resid 295 through 306 removed outlier: 3.555A pdb=" N LYS F 299 " --> pdb=" O LEU F 295 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG F 301 " --> pdb=" O ALA F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 337 removed outlier: 3.658A pdb=" N ARG F 335 " --> pdb=" O ALA F 331 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP F 337 " --> pdb=" O ALA F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 370 removed outlier: 4.359A pdb=" N TYR F 345 " --> pdb=" O ASN F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 398 Processing helix chain 'F' and resid 401 through 412 Processing helix chain 'F' and resid 419 through 434 Processing helix chain 'F' and resid 436 through 446 removed outlier: 4.860A pdb=" N ARG F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TYR F 444 " --> pdb=" O PHE F 440 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER F 446 " --> pdb=" O GLU F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 453 removed outlier: 3.600A pdb=" N GLN F 452 " --> pdb=" O PRO F 449 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR F 453 " --> pdb=" O THR F 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 449 through 453' Processing helix chain 'F' and resid 508 through 513 removed outlier: 3.896A pdb=" N HIS F 512 " --> pdb=" O PRO F 509 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS F 513 " --> pdb=" O LYS F 510 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 178 removed outlier: 6.345A pdb=" N ASP A 178 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N GLU B 504 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 373 through 375 removed outlier: 3.503A pdb=" N GLN A 373 " --> pdb=" O VAL C 515 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 515 " --> pdb=" O GLN A 373 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 177 through 178 removed outlier: 6.445A pdb=" N ILE A 501 " --> pdb=" O TRP C 463 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU C 465 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N SER A 503 " --> pdb=" O LEU C 465 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 373 through 375 removed outlier: 3.698A pdb=" N GLN B 373 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 515 " --> pdb=" O GLN B 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 177 through 178 removed outlier: 6.259A pdb=" N ASP B 178 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N GLU C 504 " --> pdb=" O ASP B 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP B 463 " --> pdb=" O ILE C 501 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU C 505 " --> pdb=" O LEU B 465 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 373 through 375 Processing sheet with id=AA7, first strand: chain 'D' and resid 177 through 178 removed outlier: 6.453A pdb=" N ASP D 178 " --> pdb=" O LEU E 502 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N GLU E 504 " --> pdb=" O ASP D 178 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU E 505 " --> pdb=" O LEU D 465 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 373 through 375 removed outlier: 3.522A pdb=" N VAL F 515 " --> pdb=" O GLN D 373 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 177 through 178 removed outlier: 6.545A pdb=" N ILE D 501 " --> pdb=" O TRP F 463 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N LEU F 465 " --> pdb=" O ILE D 501 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER D 503 " --> pdb=" O LEU F 465 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 373 through 375 Processing sheet with id=AB2, first strand: chain 'E' and resid 177 through 178 removed outlier: 6.261A pdb=" N ASP E 178 " --> pdb=" O LEU F 502 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N GLU F 504 " --> pdb=" O ASP E 178 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP E 463 " --> pdb=" O ILE F 501 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU F 505 " --> pdb=" O LEU E 465 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 373 through 375 removed outlier: 3.554A pdb=" N GLN F 373 " --> pdb=" O VAL E 515 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL E 515 " --> pdb=" O GLN F 373 " (cutoff:3.500A) 1057 hydrogen bonds defined for protein. 3084 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: 5.75 Time building geometry restraints manager: 5.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5040 1.34 - 1.45: 3423 1.45 - 1.57: 10341 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 18924 Sorted by residual: bond pdb=" C THR E 126 " pdb=" N PRO E 127 " ideal model delta sigma weight residual 1.336 1.391 -0.055 1.23e-02 6.61e+03 2.02e+01 bond pdb=" C THR C 126 " pdb=" N PRO C 127 " ideal model delta sigma weight residual 1.336 1.391 -0.055 1.23e-02 6.61e+03 2.01e+01 bond pdb=" C THR F 126 " pdb=" N PRO F 127 " ideal model delta sigma weight residual 1.336 1.391 -0.055 1.23e-02 6.61e+03 2.00e+01 bond pdb=" C THR D 126 " pdb=" N PRO D 127 " ideal model delta sigma weight residual 1.336 1.391 -0.055 1.23e-02 6.61e+03 2.00e+01 bond pdb=" C THR A 126 " pdb=" N PRO A 127 " ideal model delta sigma weight residual 1.336 1.390 -0.055 1.23e-02 6.61e+03 1.99e+01 ... (remaining 18919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 24959 2.41 - 4.83: 553 4.83 - 7.24: 75 7.24 - 9.66: 9 9.66 - 12.07: 6 Bond angle restraints: 25602 Sorted by residual: angle pdb=" CA PRO C 134 " pdb=" C PRO C 134 " pdb=" N PRO C 135 " ideal model delta sigma weight residual 117.93 122.49 -4.56 1.20e+00 6.94e-01 1.44e+01 angle pdb=" CA PRO B 134 " pdb=" C PRO B 134 " pdb=" N PRO B 135 " ideal model delta sigma weight residual 117.93 122.48 -4.55 1.20e+00 6.94e-01 1.44e+01 angle pdb=" CA PRO A 134 " pdb=" C PRO A 134 " pdb=" N PRO A 135 " ideal model delta sigma weight residual 117.93 122.46 -4.53 1.20e+00 6.94e-01 1.43e+01 angle pdb=" CA PRO F 134 " pdb=" C PRO F 134 " pdb=" N PRO F 135 " ideal model delta sigma weight residual 117.93 122.45 -4.52 1.20e+00 6.94e-01 1.42e+01 angle pdb=" CA PRO E 134 " pdb=" C PRO E 134 " pdb=" N PRO E 135 " ideal model delta sigma weight residual 117.93 122.43 -4.50 1.20e+00 6.94e-01 1.40e+01 ... (remaining 25597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.86: 10280 10.86 - 21.73: 886 21.73 - 32.59: 138 32.59 - 43.45: 36 43.45 - 54.32: 12 Dihedral angle restraints: 11352 sinusoidal: 4668 harmonic: 6684 Sorted by residual: dihedral pdb=" CB CYS D 145 " pdb=" SG CYS D 145 " pdb=" SG CYS D 149 " pdb=" CB CYS D 149 " ideal model delta sinusoidal sigma weight residual 93.00 38.68 54.32 1 1.00e+01 1.00e-02 4.00e+01 dihedral pdb=" CB CYS B 145 " pdb=" SG CYS B 145 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 38.69 54.31 1 1.00e+01 1.00e-02 4.00e+01 dihedral pdb=" CB CYS E 145 " pdb=" SG CYS E 145 " pdb=" SG CYS E 149 " pdb=" CB CYS E 149 " ideal model delta sinusoidal sigma weight residual 93.00 38.70 54.30 1 1.00e+01 1.00e-02 4.00e+01 ... (remaining 11349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1553 0.033 - 0.066: 908 0.066 - 0.099: 278 0.099 - 0.132: 152 0.132 - 0.166: 31 Chirality restraints: 2922 Sorted by residual: chirality pdb=" CB ILE D 431 " pdb=" CA ILE D 431 " pdb=" CG1 ILE D 431 " pdb=" CG2 ILE D 431 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.85e-01 chirality pdb=" CA LEU C 170 " pdb=" N LEU C 170 " pdb=" C LEU C 170 " pdb=" CB LEU C 170 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" CA LEU E 133 " pdb=" N LEU E 133 " pdb=" C LEU E 133 " pdb=" CB LEU E 133 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.73e-01 ... (remaining 2919 not shown) Planarity restraints: 3186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 134 " -0.046 5.00e-02 4.00e+02 6.86e-02 7.53e+00 pdb=" N PRO C 135 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 135 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 135 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 134 " 0.046 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO E 135 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 135 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 135 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 134 " -0.046 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO A 135 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 135 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 135 " -0.038 5.00e-02 4.00e+02 ... (remaining 3183 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 4322 2.79 - 3.32: 15949 3.32 - 3.85: 29623 3.85 - 4.37: 33278 4.37 - 4.90: 60477 Nonbonded interactions: 143649 Sorted by model distance: nonbonded pdb=" OG1 THR E 147 " pdb=" OD2 ASP F 213 " model vdw 2.269 3.040 nonbonded pdb=" OG1 THR B 147 " pdb=" OD2 ASP C 213 " model vdw 2.290 3.040 nonbonded pdb=" OG1 THR D 147 " pdb=" OD2 ASP E 213 " model vdw 2.352 3.040 nonbonded pdb=" O ARG D 207 " pdb=" OG SER D 211 " model vdw 2.381 3.040 nonbonded pdb=" O ARG B 207 " pdb=" OG SER B 211 " model vdw 2.381 3.040 ... (remaining 143644 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } 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: 3.250 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: 0.030 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.210 Process input model: 36.800 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 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:12.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 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 : 0.005 0.065 18930 Z= 0.228 Angle : 0.868 12.071 25614 Z= 0.482 Chirality : 0.050 0.166 2922 Planarity : 0.007 0.069 3186 Dihedral : 8.376 45.907 6978 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.15), residues: 2220 helix: -1.51 (0.11), residues: 1254 sheet: 0.50 (0.36), residues: 180 loop : -2.08 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP C 138 HIS 0.005 0.001 HIS D 340 PHE 0.039 0.003 PHE D 153 TYR 0.023 0.002 TYR D 200 ARG 0.015 0.001 ARG F 301 Details of bonding type rmsd hydrogen bonds : bond 0.13449 ( 1057) hydrogen bonds : angle 5.90207 ( 3084) SS BOND : bond 0.00034 ( 6) SS BOND : angle 0.90721 ( 12) covalent geometry : bond 0.00472 (18924) covalent geometry : angle 0.86775 (25602) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 511 time to evaluate : 2.037 Fit side-chains REVERT: A 304 LYS cc_start: 0.8125 (ttmt) cc_final: 0.7698 (mtmt) REVERT: B 132 LEU cc_start: 0.7485 (mt) cc_final: 0.7250 (mt) REVERT: B 156 MET cc_start: 0.7928 (ttt) cc_final: 0.7689 (ttt) REVERT: B 221 GLN cc_start: 0.7462 (mt0) cc_final: 0.7259 (mm110) REVERT: B 304 LYS cc_start: 0.8080 (ttmt) cc_final: 0.7503 (mttt) REVERT: B 425 GLN cc_start: 0.7813 (mt0) cc_final: 0.7608 (mt0) REVERT: C 132 LEU cc_start: 0.7633 (mt) cc_final: 0.7405 (mt) REVERT: C 209 LEU cc_start: 0.7571 (tp) cc_final: 0.7335 (tp) REVERT: C 304 LYS cc_start: 0.8024 (ttmt) cc_final: 0.7625 (mttt) REVERT: C 306 MET cc_start: 0.6996 (mmm) cc_final: 0.6628 (mtm) REVERT: C 388 MET cc_start: 0.6882 (ptt) cc_final: 0.6571 (ptt) REVERT: C 401 MET cc_start: 0.8700 (ptp) cc_final: 0.8390 (ptp) REVERT: D 128 ILE cc_start: 0.8001 (mt) cc_final: 0.7717 (pp) REVERT: D 300 PHE cc_start: 0.7225 (m-10) cc_final: 0.6707 (t80) REVERT: D 425 GLN cc_start: 0.7725 (mt0) cc_final: 0.7493 (mt0) REVERT: E 128 ILE cc_start: 0.8194 (mt) cc_final: 0.7811 (mm) REVERT: E 132 LEU cc_start: 0.7633 (mt) cc_final: 0.7296 (mt) REVERT: E 194 PHE cc_start: 0.8072 (t80) cc_final: 0.7424 (t80) REVERT: E 215 ASN cc_start: 0.7643 (p0) cc_final: 0.7085 (t0) REVERT: E 304 LYS cc_start: 0.7959 (ttmt) cc_final: 0.7528 (mttt) REVERT: E 373 GLN cc_start: 0.7229 (tt0) cc_final: 0.7003 (pt0) REVERT: E 388 MET cc_start: 0.6889 (ptt) cc_final: 0.6666 (ptt) REVERT: F 172 PHE cc_start: 0.7559 (t80) cc_final: 0.6097 (m-10) REVERT: F 304 LYS cc_start: 0.8323 (ttmt) cc_final: 0.7733 (mttt) REVERT: F 306 MET cc_start: 0.6989 (mmm) cc_final: 0.6564 (mtp) outliers start: 0 outliers final: 2 residues processed: 511 average time/residue: 1.4184 time to fit residues: 802.2802 Evaluate side-chains 281 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 279 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain D residue 459 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 0.0770 chunk 129 optimal weight: 0.9980 chunk 201 optimal weight: 0.6980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 273 GLN A 305 HIS A 373 GLN B 234 HIS B 245 GLN B 273 GLN B 305 HIS B 414 GLN C 215 ASN C 273 GLN C 305 HIS ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 GLN D 234 HIS D 273 GLN D 305 HIS D 414 GLN D 426 HIS E 247 GLN E 273 GLN E 305 HIS F 273 GLN F 305 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.138455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.109969 restraints weight = 24414.680| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.19 r_work: 0.3211 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18930 Z= 0.146 Angle : 0.606 11.284 25614 Z= 0.312 Chirality : 0.041 0.141 2922 Planarity : 0.005 0.058 3186 Dihedral : 4.651 28.228 2518 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.53 % Allowed : 11.13 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.17), residues: 2220 helix: 0.64 (0.14), residues: 1308 sheet: 0.84 (0.35), residues: 180 loop : -1.59 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 168 HIS 0.004 0.001 HIS A 269 PHE 0.019 0.002 PHE B 264 TYR 0.019 0.002 TYR D 216 ARG 0.007 0.001 ARG E 176 Details of bonding type rmsd hydrogen bonds : bond 0.04306 ( 1057) hydrogen bonds : angle 4.22363 ( 3084) SS BOND : bond 0.00665 ( 6) SS BOND : angle 2.96451 ( 12) covalent geometry : bond 0.00346 (18924) covalent geometry : angle 0.60224 (25602) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 313 time to evaluate : 2.252 Fit side-chains revert: symmetry clash REVERT: A 300 PHE cc_start: 0.7655 (m-10) cc_final: 0.6827 (t80) REVERT: A 337 ASP cc_start: 0.7426 (m-30) cc_final: 0.6937 (t0) REVERT: B 132 LEU cc_start: 0.7521 (mt) cc_final: 0.7303 (mt) REVERT: B 196 PHE cc_start: 0.7771 (t80) cc_final: 0.7468 (t80) REVERT: B 221 GLN cc_start: 0.7789 (mt0) cc_final: 0.7527 (mm110) REVERT: B 300 PHE cc_start: 0.7341 (m-10) cc_final: 0.6532 (t80) REVERT: B 442 GLU cc_start: 0.8173 (pp20) cc_final: 0.7798 (pp20) REVERT: C 132 LEU cc_start: 0.7543 (mt) cc_final: 0.7297 (mt) REVERT: C 198 VAL cc_start: 0.8474 (t) cc_final: 0.8204 (m) REVERT: C 251 THR cc_start: 0.8790 (t) cc_final: 0.8422 (m) REVERT: C 304 LYS cc_start: 0.8218 (ttmt) cc_final: 0.7551 (mttt) REVERT: C 306 MET cc_start: 0.7827 (mmm) cc_final: 0.7216 (mtm) REVERT: D 128 ILE cc_start: 0.7968 (mt) cc_final: 0.7710 (pp) REVERT: D 304 LYS cc_start: 0.8335 (ttmm) cc_final: 0.7373 (mtmt) REVERT: D 306 MET cc_start: 0.7969 (mmm) cc_final: 0.6853 (mtm) REVERT: D 334 ARG cc_start: 0.7942 (mmm-85) cc_final: 0.7656 (tpt90) REVERT: D 373 GLN cc_start: 0.7618 (pt0) cc_final: 0.7376 (pt0) REVERT: D 442 GLU cc_start: 0.8179 (pp20) cc_final: 0.7772 (pp20) REVERT: E 128 ILE cc_start: 0.8200 (mt) cc_final: 0.7785 (mm) REVERT: E 132 LEU cc_start: 0.7475 (mt) cc_final: 0.7133 (mt) REVERT: E 251 THR cc_start: 0.8800 (t) cc_final: 0.8428 (m) REVERT: E 300 PHE cc_start: 0.7683 (m-10) cc_final: 0.7295 (t80) REVERT: E 353 ARG cc_start: 0.8202 (mtt90) cc_final: 0.7875 (mtt90) REVERT: E 373 GLN cc_start: 0.7254 (tt0) cc_final: 0.7005 (mt0) REVERT: F 304 LYS cc_start: 0.8399 (ttmt) cc_final: 0.7521 (mttt) REVERT: F 306 MET cc_start: 0.7348 (mmm) cc_final: 0.6779 (mtp) REVERT: F 329 ILE cc_start: 0.6665 (OUTLIER) cc_final: 0.6227 (tt) REVERT: F 455 LYS cc_start: 0.8846 (mtpp) cc_final: 0.8613 (mptm) outliers start: 90 outliers final: 43 residues processed: 354 average time/residue: 1.2148 time to fit residues: 484.3954 Evaluate side-chains 306 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 262 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 138 TRP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain E residue 138 TRP Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain F residue 459 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 64 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 133 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 207 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 208 optimal weight: 0.6980 chunk 191 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 HIS B 305 HIS ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS C 215 ASN C 305 HIS ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN D 247 GLN D 305 HIS E 269 HIS E 305 HIS F 217 GLN F 269 HIS F 305 HIS F 462 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.137838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.109226 restraints weight = 24386.402| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.18 r_work: 0.3199 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18930 Z= 0.135 Angle : 0.582 14.222 25614 Z= 0.293 Chirality : 0.041 0.130 2922 Planarity : 0.005 0.053 3186 Dihedral : 4.333 29.104 2516 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.73 % Allowed : 13.65 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.18), residues: 2220 helix: 1.65 (0.15), residues: 1266 sheet: 1.16 (0.37), residues: 180 loop : -1.48 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 138 HIS 0.004 0.001 HIS A 269 PHE 0.013 0.001 PHE F 429 TYR 0.020 0.002 TYR D 222 ARG 0.008 0.000 ARG C 176 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 1057) hydrogen bonds : angle 4.00217 ( 3084) SS BOND : bond 0.00406 ( 6) SS BOND : angle 1.47635 ( 12) covalent geometry : bond 0.00317 (18924) covalent geometry : angle 0.58110 (25602) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 299 time to evaluate : 2.070 Fit side-chains revert: symmetry clash REVERT: A 304 LYS cc_start: 0.8390 (ttmm) cc_final: 0.7345 (mttt) REVERT: A 337 ASP cc_start: 0.7240 (m-30) cc_final: 0.6828 (t0) REVERT: B 132 LEU cc_start: 0.7579 (mt) cc_final: 0.7170 (mt) REVERT: B 221 GLN cc_start: 0.7859 (mt0) cc_final: 0.7587 (mm110) REVERT: B 300 PHE cc_start: 0.7425 (m-10) cc_final: 0.6696 (t80) REVERT: C 132 LEU cc_start: 0.7357 (mt) cc_final: 0.7123 (mt) REVERT: C 194 PHE cc_start: 0.7822 (t80) cc_final: 0.7509 (t80) REVERT: C 251 THR cc_start: 0.8743 (t) cc_final: 0.8380 (m) REVERT: C 353 ARG cc_start: 0.8200 (mtt90) cc_final: 0.7901 (mtt90) REVERT: D 194 PHE cc_start: 0.8189 (t80) cc_final: 0.7842 (t80) REVERT: D 300 PHE cc_start: 0.7424 (m-10) cc_final: 0.6712 (t80) REVERT: D 334 ARG cc_start: 0.7995 (mmm-85) cc_final: 0.7597 (tpt90) REVERT: D 373 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7409 (pt0) REVERT: E 132 LEU cc_start: 0.7581 (mt) cc_final: 0.7262 (mt) REVERT: E 179 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8408 (mtm) REVERT: E 194 PHE cc_start: 0.8023 (t80) cc_final: 0.7559 (t80) REVERT: E 222 TYR cc_start: 0.7384 (t80) cc_final: 0.7062 (t80) REVERT: E 251 THR cc_start: 0.8738 (t) cc_final: 0.8360 (m) REVERT: E 304 LYS cc_start: 0.8298 (ttmm) cc_final: 0.7394 (mttt) REVERT: E 353 ARG cc_start: 0.8210 (mtt90) cc_final: 0.7881 (mtt90) REVERT: E 373 GLN cc_start: 0.7197 (tt0) cc_final: 0.6691 (mt0) REVERT: F 300 PHE cc_start: 0.7364 (m-10) cc_final: 0.6729 (t80) REVERT: F 304 LYS cc_start: 0.8418 (ttmt) cc_final: 0.7986 (tmtt) REVERT: F 306 MET cc_start: 0.7493 (mmm) cc_final: 0.6933 (mtp) REVERT: F 455 LYS cc_start: 0.8815 (mtpp) cc_final: 0.8599 (mptm) outliers start: 94 outliers final: 42 residues processed: 340 average time/residue: 1.1579 time to fit residues: 446.4305 Evaluate side-chains 299 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 255 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 355 LYS Chi-restraints excluded: chain C residue 416 ASN Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 373 GLN Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain E residue 442 GLU Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain F residue 459 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 34 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 93 optimal weight: 0.0050 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 199 optimal weight: 2.9990 chunk 213 optimal weight: 0.5980 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 HIS B 305 HIS ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN C 269 HIS C 305 HIS D 305 HIS E 217 GLN F 305 HIS F 462 GLN F 512 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.136108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.107366 restraints weight = 24335.550| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.17 r_work: 0.3175 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18930 Z= 0.154 Angle : 0.593 15.341 25614 Z= 0.298 Chirality : 0.042 0.211 2922 Planarity : 0.005 0.050 3186 Dihedral : 4.313 32.446 2516 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.98 % Allowed : 15.46 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.18), residues: 2220 helix: 1.94 (0.15), residues: 1266 sheet: 1.62 (0.37), residues: 174 loop : -1.31 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 138 HIS 0.005 0.001 HIS E 305 PHE 0.014 0.002 PHE B 514 TYR 0.017 0.002 TYR D 222 ARG 0.008 0.000 ARG B 176 Details of bonding type rmsd hydrogen bonds : bond 0.04313 ( 1057) hydrogen bonds : angle 4.00595 ( 3084) SS BOND : bond 0.00342 ( 6) SS BOND : angle 1.06592 ( 12) covalent geometry : bond 0.00373 (18924) covalent geometry : angle 0.59290 (25602) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 283 time to evaluate : 2.180 Fit side-chains REVERT: A 300 PHE cc_start: 0.7474 (m-10) cc_final: 0.6860 (t80) REVERT: A 304 LYS cc_start: 0.8408 (ttmm) cc_final: 0.7918 (tmtt) REVERT: A 306 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.6344 (mtp) REVERT: B 132 LEU cc_start: 0.7415 (mt) cc_final: 0.7192 (mt) REVERT: B 221 GLN cc_start: 0.7841 (mt0) cc_final: 0.7626 (mm110) REVERT: B 300 PHE cc_start: 0.7464 (m-10) cc_final: 0.6844 (t80) REVERT: B 304 LYS cc_start: 0.8378 (ttmm) cc_final: 0.7879 (tmtt) REVERT: B 306 MET cc_start: 0.7943 (tpt) cc_final: 0.7600 (mmm) REVERT: B 403 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7363 (tpp-160) REVERT: C 132 LEU cc_start: 0.7417 (mt) cc_final: 0.7175 (mt) REVERT: C 194 PHE cc_start: 0.7887 (t80) cc_final: 0.7590 (t80) REVERT: C 251 THR cc_start: 0.8751 (t) cc_final: 0.8398 (m) REVERT: C 304 LYS cc_start: 0.8431 (ttmm) cc_final: 0.7405 (mttt) REVERT: C 353 ARG cc_start: 0.8243 (mtt90) cc_final: 0.7948 (mtt90) REVERT: D 194 PHE cc_start: 0.8320 (t80) cc_final: 0.8084 (t80) REVERT: D 242 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7741 (mp0) REVERT: D 300 PHE cc_start: 0.7455 (m-10) cc_final: 0.6915 (t80) REVERT: D 304 LYS cc_start: 0.8346 (ttmm) cc_final: 0.7847 (tmtt) REVERT: D 306 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7617 (mmm) REVERT: D 334 ARG cc_start: 0.7930 (mmm-85) cc_final: 0.7560 (tpt90) REVERT: E 132 LEU cc_start: 0.7614 (mt) cc_final: 0.7269 (mt) REVERT: E 194 PHE cc_start: 0.7863 (t80) cc_final: 0.7490 (t80) REVERT: E 215 ASN cc_start: 0.7402 (OUTLIER) cc_final: 0.6455 (p0) REVERT: E 249 MET cc_start: 0.8638 (mmp) cc_final: 0.8421 (mmp) REVERT: E 251 THR cc_start: 0.8747 (t) cc_final: 0.8380 (m) REVERT: E 304 LYS cc_start: 0.8355 (ttmm) cc_final: 0.7419 (mttt) REVERT: E 353 ARG cc_start: 0.8235 (mtt90) cc_final: 0.7918 (mtt90) REVERT: E 373 GLN cc_start: 0.7243 (tt0) cc_final: 0.6643 (mt0) REVERT: F 300 PHE cc_start: 0.7467 (m-10) cc_final: 0.6829 (OUTLIER) REVERT: F 304 LYS cc_start: 0.8438 (ttmt) cc_final: 0.8011 (tmtt) REVERT: F 306 MET cc_start: 0.7826 (mmm) cc_final: 0.7051 (mtp) outliers start: 99 outliers final: 58 residues processed: 327 average time/residue: 1.1903 time to fit residues: 440.1248 Evaluate side-chains 316 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 254 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 416 ASN Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 138 TRP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 306 MET Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 416 ASN Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 215 ASN Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain F residue 487 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 208 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 chunk 193 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 117 optimal weight: 0.7980 chunk 159 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS A 305 HIS ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN C 340 HIS ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 GLN E 340 HIS F 305 HIS ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.138926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.110254 restraints weight = 24410.804| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.15 r_work: 0.3228 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18930 Z= 0.136 Angle : 0.568 16.746 25614 Z= 0.287 Chirality : 0.041 0.212 2922 Planarity : 0.004 0.047 3186 Dihedral : 4.189 36.217 2516 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 5.19 % Allowed : 15.81 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.18), residues: 2220 helix: 2.11 (0.15), residues: 1266 sheet: 1.58 (0.36), residues: 174 loop : -1.23 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 138 HIS 0.005 0.001 HIS C 305 PHE 0.013 0.001 PHE F 429 TYR 0.015 0.001 TYR D 222 ARG 0.007 0.000 ARG C 176 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 1057) hydrogen bonds : angle 3.92140 ( 3084) SS BOND : bond 0.00293 ( 6) SS BOND : angle 0.86984 ( 12) covalent geometry : bond 0.00325 (18924) covalent geometry : angle 0.56773 (25602) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 283 time to evaluate : 1.979 Fit side-chains REVERT: A 131 ILE cc_start: 0.6878 (OUTLIER) cc_final: 0.6601 (tt) REVERT: A 300 PHE cc_start: 0.7518 (m-10) cc_final: 0.7200 (t80) REVERT: A 306 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.6486 (ttp) REVERT: B 132 LEU cc_start: 0.7627 (mt) cc_final: 0.7264 (mt) REVERT: B 221 GLN cc_start: 0.7829 (mt0) cc_final: 0.7599 (mm110) REVERT: B 300 PHE cc_start: 0.7507 (m-10) cc_final: 0.6866 (t80) REVERT: B 304 LYS cc_start: 0.8348 (ttmm) cc_final: 0.7895 (tmtt) REVERT: B 403 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7352 (tpp-160) REVERT: C 132 LEU cc_start: 0.7506 (mt) cc_final: 0.7220 (mt) REVERT: C 194 PHE cc_start: 0.7880 (t80) cc_final: 0.7669 (t80) REVERT: C 251 THR cc_start: 0.8726 (t) cc_final: 0.8411 (m) REVERT: C 304 LYS cc_start: 0.8362 (ttmm) cc_final: 0.7387 (mttt) REVERT: C 353 ARG cc_start: 0.8266 (mtt90) cc_final: 0.7975 (mtt90) REVERT: D 194 PHE cc_start: 0.8258 (t80) cc_final: 0.7997 (t80) REVERT: D 242 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7611 (mp0) REVERT: D 300 PHE cc_start: 0.7510 (m-10) cc_final: 0.6902 (t80) REVERT: D 304 LYS cc_start: 0.8358 (ttmm) cc_final: 0.7898 (tmtt) REVERT: D 334 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7469 (tpt90) REVERT: E 132 LEU cc_start: 0.7656 (mt) cc_final: 0.7146 (mt) REVERT: E 194 PHE cc_start: 0.7849 (t80) cc_final: 0.7565 (t80) REVERT: E 215 ASN cc_start: 0.7402 (OUTLIER) cc_final: 0.6472 (p0) REVERT: E 251 THR cc_start: 0.8748 (t) cc_final: 0.8415 (m) REVERT: E 304 LYS cc_start: 0.8384 (ttmm) cc_final: 0.7480 (mttt) REVERT: E 353 ARG cc_start: 0.8237 (mtt90) cc_final: 0.7929 (mtt90) REVERT: E 373 GLN cc_start: 0.7233 (tt0) cc_final: 0.6676 (mt0) REVERT: F 300 PHE cc_start: 0.7558 (m-10) cc_final: 0.6879 (OUTLIER) REVERT: F 304 LYS cc_start: 0.8435 (ttmt) cc_final: 0.8031 (tmtt) REVERT: F 306 MET cc_start: 0.7807 (mmm) cc_final: 0.7056 (mtp) REVERT: F 487 ASP cc_start: 0.6980 (OUTLIER) cc_final: 0.6755 (t70) outliers start: 103 outliers final: 58 residues processed: 330 average time/residue: 1.1076 time to fit residues: 415.5070 Evaluate side-chains 325 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 261 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 416 ASN Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 138 TRP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 416 ASN Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 215 ASN Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 516 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 487 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 43 optimal weight: 0.4980 chunk 145 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 95 optimal weight: 0.5980 chunk 1 optimal weight: 0.4980 chunk 60 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 HIS ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS D 221 GLN D 247 GLN ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 HIS F 340 HIS F 512 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.139493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.110890 restraints weight = 24558.456| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.15 r_work: 0.3236 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18930 Z= 0.126 Angle : 0.554 13.215 25614 Z= 0.280 Chirality : 0.041 0.192 2922 Planarity : 0.004 0.046 3186 Dihedral : 4.084 40.713 2516 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.98 % Allowed : 16.62 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.18), residues: 2220 helix: 2.41 (0.15), residues: 1236 sheet: 1.57 (0.35), residues: 174 loop : -1.20 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 458 HIS 0.004 0.001 HIS B 305 PHE 0.013 0.001 PHE A 429 TYR 0.013 0.001 TYR B 222 ARG 0.006 0.000 ARG F 176 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 1057) hydrogen bonds : angle 3.84227 ( 3084) SS BOND : bond 0.00260 ( 6) SS BOND : angle 0.74965 ( 12) covalent geometry : bond 0.00300 (18924) covalent geometry : angle 0.55377 (25602) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 270 time to evaluate : 2.167 Fit side-chains REVERT: A 131 ILE cc_start: 0.6986 (OUTLIER) cc_final: 0.6782 (tt) REVERT: A 221 GLN cc_start: 0.7454 (mm110) cc_final: 0.7197 (mm110) REVERT: A 304 LYS cc_start: 0.8426 (ttmm) cc_final: 0.7446 (mtmt) REVERT: B 132 LEU cc_start: 0.7695 (mt) cc_final: 0.7343 (mt) REVERT: B 221 GLN cc_start: 0.7755 (mt0) cc_final: 0.7460 (mm110) REVERT: B 242 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7717 (mp0) REVERT: B 300 PHE cc_start: 0.7436 (m-10) cc_final: 0.6837 (t80) REVERT: B 304 LYS cc_start: 0.8315 (ttmm) cc_final: 0.7903 (tmtt) REVERT: B 403 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7350 (tpp-160) REVERT: C 132 LEU cc_start: 0.7505 (mt) cc_final: 0.7212 (mt) REVERT: C 194 PHE cc_start: 0.7867 (t80) cc_final: 0.7662 (t80) REVERT: C 249 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8338 (mmm) REVERT: C 251 THR cc_start: 0.8694 (t) cc_final: 0.8399 (m) REVERT: C 304 LYS cc_start: 0.8374 (ttmm) cc_final: 0.7447 (mttt) REVERT: C 353 ARG cc_start: 0.8280 (mtt90) cc_final: 0.7984 (mtt90) REVERT: D 194 PHE cc_start: 0.8356 (t80) cc_final: 0.8138 (t80) REVERT: D 242 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: D 300 PHE cc_start: 0.7476 (m-10) cc_final: 0.6901 (t80) REVERT: D 304 LYS cc_start: 0.8315 (ttmm) cc_final: 0.7893 (tmtt) REVERT: D 334 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7589 (ttp80) REVERT: E 132 LEU cc_start: 0.7597 (mt) cc_final: 0.7228 (mt) REVERT: E 194 PHE cc_start: 0.7893 (t80) cc_final: 0.7585 (t80) REVERT: E 214 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6603 (mpt90) REVERT: E 215 ASN cc_start: 0.7557 (t0) cc_final: 0.6664 (p0) REVERT: E 221 GLN cc_start: 0.7461 (mm110) cc_final: 0.7045 (mm-40) REVERT: E 251 THR cc_start: 0.8715 (t) cc_final: 0.8409 (m) REVERT: E 304 LYS cc_start: 0.8467 (ttmm) cc_final: 0.7458 (mttt) REVERT: E 353 ARG cc_start: 0.8261 (mtt90) cc_final: 0.7938 (mtt90) REVERT: E 373 GLN cc_start: 0.7202 (tt0) cc_final: 0.6616 (mt0) REVERT: F 300 PHE cc_start: 0.7560 (m-10) cc_final: 0.6885 (OUTLIER) REVERT: F 304 LYS cc_start: 0.8449 (ttmt) cc_final: 0.8063 (tmtt) REVERT: F 306 MET cc_start: 0.7819 (mmm) cc_final: 0.7140 (mtp) REVERT: F 487 ASP cc_start: 0.6979 (OUTLIER) cc_final: 0.6743 (t70) outliers start: 99 outliers final: 50 residues processed: 316 average time/residue: 1.1027 time to fit residues: 396.7429 Evaluate side-chains 312 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 255 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 416 ASN Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 138 TRP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 487 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 135 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 HIS B 247 GLN ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 GLN E 247 GLN F 305 HIS ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.136116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107492 restraints weight = 24446.513| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.13 r_work: 0.3176 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18930 Z= 0.187 Angle : 0.604 9.378 25614 Z= 0.309 Chirality : 0.043 0.158 2922 Planarity : 0.005 0.046 3186 Dihedral : 4.389 47.482 2516 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.78 % Allowed : 16.67 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.18), residues: 2220 helix: 2.03 (0.15), residues: 1266 sheet: 1.65 (0.35), residues: 174 loop : -1.17 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 458 HIS 0.006 0.001 HIS F 512 PHE 0.019 0.002 PHE B 514 TYR 0.013 0.002 TYR C 222 ARG 0.008 0.000 ARG F 176 Details of bonding type rmsd hydrogen bonds : bond 0.04704 ( 1057) hydrogen bonds : angle 4.07231 ( 3084) SS BOND : bond 0.00276 ( 6) SS BOND : angle 0.85865 ( 12) covalent geometry : bond 0.00463 (18924) covalent geometry : angle 0.60384 (25602) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 271 time to evaluate : 2.191 Fit side-chains REVERT: A 121 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6614 (pt) REVERT: A 131 ILE cc_start: 0.7029 (OUTLIER) cc_final: 0.6827 (tt) REVERT: A 304 LYS cc_start: 0.8464 (ttmm) cc_final: 0.7552 (mtmt) REVERT: B 132 LEU cc_start: 0.7757 (mt) cc_final: 0.7300 (mt) REVERT: B 174 LYS cc_start: 0.7514 (mmtm) cc_final: 0.7295 (mmtt) REVERT: B 221 GLN cc_start: 0.7837 (mt0) cc_final: 0.7595 (mm110) REVERT: B 251 THR cc_start: 0.8693 (t) cc_final: 0.8409 (m) REVERT: B 300 PHE cc_start: 0.7506 (m-10) cc_final: 0.6864 (t80) REVERT: B 403 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7457 (tpp-160) REVERT: C 132 LEU cc_start: 0.7732 (mt) cc_final: 0.7389 (mt) REVERT: C 194 PHE cc_start: 0.7860 (t80) cc_final: 0.7586 (t80) REVERT: C 238 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8192 (pt) REVERT: C 251 THR cc_start: 0.8776 (t) cc_final: 0.8450 (m) REVERT: C 304 LYS cc_start: 0.8420 (ttmm) cc_final: 0.7453 (mttt) REVERT: C 353 ARG cc_start: 0.8283 (mtt90) cc_final: 0.7990 (mtt90) REVERT: D 242 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: D 251 THR cc_start: 0.8681 (t) cc_final: 0.8379 (m) REVERT: D 304 LYS cc_start: 0.8364 (ttmm) cc_final: 0.7447 (mtmt) REVERT: D 334 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7538 (ttp80) REVERT: D 513 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8468 (pptt) REVERT: E 132 LEU cc_start: 0.7649 (mt) cc_final: 0.7212 (mt) REVERT: E 214 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6700 (mpt90) REVERT: E 215 ASN cc_start: 0.7577 (t0) cc_final: 0.6696 (p0) REVERT: E 238 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8179 (pt) REVERT: E 245 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7782 (pm20) REVERT: E 251 THR cc_start: 0.8775 (t) cc_final: 0.8446 (m) REVERT: E 353 ARG cc_start: 0.8293 (mtt90) cc_final: 0.7998 (mtt90) REVERT: E 373 GLN cc_start: 0.7261 (tt0) cc_final: 0.6630 (mt0) REVERT: F 304 LYS cc_start: 0.8513 (ttmt) cc_final: 0.8289 (ttmm) REVERT: F 403 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7511 (ttp80) REVERT: F 487 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.6813 (t70) outliers start: 95 outliers final: 54 residues processed: 319 average time/residue: 1.0795 time to fit residues: 393.0968 Evaluate side-chains 326 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 260 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 416 ASN Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 138 TRP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 513 LYS Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 487 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 195 optimal weight: 0.8980 chunk 136 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 204 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 216 optimal weight: 2.9990 chunk 18 optimal weight: 0.0070 chunk 142 optimal weight: 1.9990 chunk 201 optimal weight: 0.6980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN D 221 GLN ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 GLN E 245 GLN F 305 HIS F 462 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.139086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.110664 restraints weight = 24293.977| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.13 r_work: 0.3225 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18930 Z= 0.121 Angle : 0.554 8.744 25614 Z= 0.279 Chirality : 0.040 0.152 2922 Planarity : 0.004 0.045 3186 Dihedral : 4.115 46.720 2516 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.33 % Allowed : 17.42 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.18), residues: 2220 helix: 2.46 (0.15), residues: 1236 sheet: 1.59 (0.35), residues: 174 loop : -1.22 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 458 HIS 0.004 0.001 HIS D 305 PHE 0.013 0.001 PHE B 196 TYR 0.013 0.001 TYR B 222 ARG 0.007 0.000 ARG F 176 Details of bonding type rmsd hydrogen bonds : bond 0.03815 ( 1057) hydrogen bonds : angle 3.85890 ( 3084) SS BOND : bond 0.00302 ( 6) SS BOND : angle 0.86578 ( 12) covalent geometry : bond 0.00285 (18924) covalent geometry : angle 0.55332 (25602) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 273 time to evaluate : 2.026 Fit side-chains REVERT: A 121 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6517 (pt) REVERT: A 131 ILE cc_start: 0.6998 (OUTLIER) cc_final: 0.6777 (tt) REVERT: A 221 GLN cc_start: 0.7442 (mm110) cc_final: 0.7182 (mm110) REVERT: A 304 LYS cc_start: 0.8429 (ttmm) cc_final: 0.7506 (mtmt) REVERT: A 487 ASP cc_start: 0.7023 (t70) cc_final: 0.6811 (t70) REVERT: B 132 LEU cc_start: 0.7745 (mt) cc_final: 0.7316 (mt) REVERT: B 221 GLN cc_start: 0.7697 (mt0) cc_final: 0.7432 (mm110) REVERT: B 304 LYS cc_start: 0.8234 (ttmm) cc_final: 0.7271 (mtmt) REVERT: B 403 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7348 (tpp-160) REVERT: B 442 GLU cc_start: 0.8226 (pp20) cc_final: 0.7931 (pp20) REVERT: C 121 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.7059 (pt) REVERT: C 132 LEU cc_start: 0.7523 (mt) cc_final: 0.7069 (mt) REVERT: C 251 THR cc_start: 0.8658 (t) cc_final: 0.8394 (m) REVERT: C 304 LYS cc_start: 0.8362 (ttmm) cc_final: 0.7408 (mttt) REVERT: C 353 ARG cc_start: 0.8253 (mtt90) cc_final: 0.7962 (mtt90) REVERT: D 221 GLN cc_start: 0.7656 (mm-40) cc_final: 0.7326 (mm110) REVERT: D 242 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: D 300 PHE cc_start: 0.7493 (m-10) cc_final: 0.6972 (t80) REVERT: D 304 LYS cc_start: 0.8291 (ttmm) cc_final: 0.7847 (tmtt) REVERT: D 334 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7590 (ttp80) REVERT: D 442 GLU cc_start: 0.8246 (pp20) cc_final: 0.7936 (pp20) REVERT: E 132 LEU cc_start: 0.7725 (mt) cc_final: 0.7301 (mt) REVERT: E 214 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6621 (mpt90) REVERT: E 215 ASN cc_start: 0.7567 (t0) cc_final: 0.6642 (p0) REVERT: E 221 GLN cc_start: 0.7487 (mm-40) cc_final: 0.7207 (mm110) REVERT: E 251 THR cc_start: 0.8719 (t) cc_final: 0.8424 (m) REVERT: E 304 LYS cc_start: 0.8297 (ttmm) cc_final: 0.7362 (mttt) REVERT: E 373 GLN cc_start: 0.7114 (tt0) cc_final: 0.6802 (tt0) REVERT: F 304 LYS cc_start: 0.8419 (ttmt) cc_final: 0.7644 (mtmt) REVERT: F 403 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7341 (ttp80) REVERT: F 487 ASP cc_start: 0.6941 (OUTLIER) cc_final: 0.6683 (t70) outliers start: 86 outliers final: 52 residues processed: 315 average time/residue: 1.1096 time to fit residues: 399.4436 Evaluate side-chains 320 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 259 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 416 ASN Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 138 TRP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain F residue 487 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 210 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 186 optimal weight: 0.8980 chunk 218 optimal weight: 0.4980 chunk 95 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 17 optimal weight: 0.1980 chunk 21 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 GLN B 425 GLN C 221 GLN ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 462 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.139032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110590 restraints weight = 24374.336| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.13 r_work: 0.3224 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18930 Z= 0.126 Angle : 0.563 12.743 25614 Z= 0.282 Chirality : 0.041 0.150 2922 Planarity : 0.004 0.046 3186 Dihedral : 4.077 46.890 2516 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.88 % Allowed : 18.23 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.18), residues: 2220 helix: 2.48 (0.15), residues: 1236 sheet: 1.56 (0.34), residues: 174 loop : -1.15 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 458 HIS 0.005 0.001 HIS C 305 PHE 0.013 0.001 PHE C 153 TYR 0.012 0.001 TYR B 222 ARG 0.007 0.000 ARG D 176 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 1057) hydrogen bonds : angle 3.83683 ( 3084) SS BOND : bond 0.00235 ( 6) SS BOND : angle 0.66203 ( 12) covalent geometry : bond 0.00300 (18924) covalent geometry : angle 0.56279 (25602) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 269 time to evaluate : 2.381 Fit side-chains REVERT: A 121 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6545 (pt) REVERT: A 131 ILE cc_start: 0.6917 (OUTLIER) cc_final: 0.6708 (tt) REVERT: A 221 GLN cc_start: 0.7475 (mm110) cc_final: 0.7213 (mm110) REVERT: A 304 LYS cc_start: 0.8405 (ttmm) cc_final: 0.7443 (mttt) REVERT: B 132 LEU cc_start: 0.7768 (mt) cc_final: 0.7318 (mt) REVERT: B 221 GLN cc_start: 0.7694 (mt0) cc_final: 0.7423 (mm110) REVERT: B 304 LYS cc_start: 0.8201 (ttmm) cc_final: 0.7196 (mtmt) REVERT: B 403 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7347 (tpp-160) REVERT: C 121 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7122 (pt) REVERT: C 132 LEU cc_start: 0.7426 (mt) cc_final: 0.7076 (mt) REVERT: C 251 THR cc_start: 0.8676 (t) cc_final: 0.8425 (m) REVERT: C 304 LYS cc_start: 0.8379 (ttmm) cc_final: 0.7419 (mttt) REVERT: C 353 ARG cc_start: 0.8240 (mtt90) cc_final: 0.7936 (mtt90) REVERT: D 221 GLN cc_start: 0.7628 (mm-40) cc_final: 0.7369 (mm110) REVERT: D 242 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7578 (mt-10) REVERT: D 300 PHE cc_start: 0.7518 (m-10) cc_final: 0.6986 (t80) REVERT: D 304 LYS cc_start: 0.8287 (ttmm) cc_final: 0.7851 (tmtt) REVERT: D 334 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7550 (ttp80) REVERT: E 121 LEU cc_start: 0.7521 (pp) cc_final: 0.7281 (pt) REVERT: E 132 LEU cc_start: 0.7710 (mt) cc_final: 0.7275 (mt) REVERT: E 214 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6597 (mpt90) REVERT: E 215 ASN cc_start: 0.7587 (t0) cc_final: 0.6665 (p0) REVERT: E 221 GLN cc_start: 0.7478 (mm-40) cc_final: 0.7182 (mm110) REVERT: E 251 THR cc_start: 0.8643 (t) cc_final: 0.8368 (m) REVERT: E 304 LYS cc_start: 0.8252 (ttmm) cc_final: 0.7352 (mttt) REVERT: E 373 GLN cc_start: 0.7127 (tt0) cc_final: 0.6836 (tt0) REVERT: F 221 GLN cc_start: 0.7371 (mm110) cc_final: 0.7085 (mm110) REVERT: F 304 LYS cc_start: 0.8369 (ttmt) cc_final: 0.7576 (mtmt) REVERT: F 403 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7351 (ttp80) REVERT: F 487 ASP cc_start: 0.7017 (OUTLIER) cc_final: 0.6761 (t70) outliers start: 77 outliers final: 53 residues processed: 309 average time/residue: 1.0825 time to fit residues: 381.7954 Evaluate side-chains 317 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 255 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 416 ASN Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 138 TRP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain F residue 487 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 159 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 188 optimal weight: 6.9990 chunk 57 optimal weight: 0.0670 chunk 152 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 chunk 128 optimal weight: 0.0870 chunk 32 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 HIS B 425 GLN D 340 HIS D 425 GLN F 462 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.140304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.112307 restraints weight = 24364.492| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.11 r_work: 0.3252 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18930 Z= 0.111 Angle : 0.552 12.251 25614 Z= 0.276 Chirality : 0.040 0.143 2922 Planarity : 0.004 0.045 3186 Dihedral : 3.930 46.200 2516 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.37 % Allowed : 18.73 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.18), residues: 2220 helix: 2.55 (0.15), residues: 1236 sheet: 1.51 (0.34), residues: 174 loop : -1.14 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 458 HIS 0.005 0.001 HIS C 305 PHE 0.015 0.001 PHE C 153 TYR 0.013 0.001 TYR B 222 ARG 0.007 0.000 ARG D 176 Details of bonding type rmsd hydrogen bonds : bond 0.03534 ( 1057) hydrogen bonds : angle 3.74210 ( 3084) SS BOND : bond 0.00244 ( 6) SS BOND : angle 0.63837 ( 12) covalent geometry : bond 0.00256 (18924) covalent geometry : angle 0.55155 (25602) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 263 time to evaluate : 2.033 Fit side-chains REVERT: A 121 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6566 (pt) REVERT: A 221 GLN cc_start: 0.7454 (mm110) cc_final: 0.7226 (mm110) REVERT: A 304 LYS cc_start: 0.8348 (ttmm) cc_final: 0.7394 (mttt) REVERT: A 329 ILE cc_start: 0.6571 (mp) cc_final: 0.6266 (OUTLIER) REVERT: B 221 GLN cc_start: 0.7609 (mt0) cc_final: 0.7361 (mm110) REVERT: B 304 LYS cc_start: 0.8284 (ttmm) cc_final: 0.7277 (mtmt) REVERT: B 403 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7349 (tpp-160) REVERT: B 442 GLU cc_start: 0.8170 (pp20) cc_final: 0.7889 (pp20) REVERT: C 121 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7109 (pt) REVERT: C 132 LEU cc_start: 0.7643 (mt) cc_final: 0.7269 (mt) REVERT: C 221 GLN cc_start: 0.7467 (mm-40) cc_final: 0.7219 (mm110) REVERT: C 249 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8214 (mmm) REVERT: C 304 LYS cc_start: 0.8352 (ttmm) cc_final: 0.7437 (mttt) REVERT: D 221 GLN cc_start: 0.7482 (mm-40) cc_final: 0.7231 (mm110) REVERT: D 242 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: D 300 PHE cc_start: 0.7524 (m-10) cc_final: 0.6990 (t80) REVERT: D 304 LYS cc_start: 0.8275 (ttmm) cc_final: 0.7884 (tmtt) REVERT: D 334 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7557 (ttp80) REVERT: D 442 GLU cc_start: 0.8156 (pp20) cc_final: 0.7859 (pp20) REVERT: E 121 LEU cc_start: 0.7517 (pp) cc_final: 0.7292 (pt) REVERT: E 132 LEU cc_start: 0.7582 (mt) cc_final: 0.7196 (mt) REVERT: E 214 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6663 (mpt90) REVERT: E 215 ASN cc_start: 0.7693 (t0) cc_final: 0.6810 (p0) REVERT: E 221 GLN cc_start: 0.7334 (mm-40) cc_final: 0.7026 (mm-40) REVERT: E 304 LYS cc_start: 0.8207 (ttmm) cc_final: 0.7425 (mttt) REVERT: E 373 GLN cc_start: 0.7018 (tt0) cc_final: 0.6727 (tt0) REVERT: F 221 GLN cc_start: 0.7275 (mm110) cc_final: 0.7005 (mm110) REVERT: F 304 LYS cc_start: 0.8308 (ttmt) cc_final: 0.7549 (mtmt) REVERT: F 403 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7324 (ttp80) REVERT: F 487 ASP cc_start: 0.6952 (OUTLIER) cc_final: 0.6710 (t70) outliers start: 67 outliers final: 38 residues processed: 304 average time/residue: 1.1791 time to fit residues: 407.8685 Evaluate side-chains 298 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 252 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 416 ASN Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 138 TRP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain F residue 487 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 44 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 175 optimal weight: 2.9990 chunk 204 optimal weight: 0.0770 chunk 60 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 GLN F 462 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.140045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111559 restraints weight = 24279.192| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.14 r_work: 0.3248 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18930 Z= 0.123 Angle : 0.572 14.468 25614 Z= 0.284 Chirality : 0.041 0.173 2922 Planarity : 0.004 0.046 3186 Dihedral : 3.966 47.015 2516 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.02 % Allowed : 19.79 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.18), residues: 2220 helix: 2.55 (0.15), residues: 1236 sheet: 1.52 (0.33), residues: 174 loop : -1.12 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 458 HIS 0.005 0.001 HIS C 305 PHE 0.013 0.001 PHE F 429 TYR 0.013 0.001 TYR B 222 ARG 0.007 0.000 ARG D 176 Details of bonding type rmsd hydrogen bonds : bond 0.03738 ( 1057) hydrogen bonds : angle 3.77912 ( 3084) SS BOND : bond 0.00197 ( 6) SS BOND : angle 0.55342 ( 12) covalent geometry : bond 0.00292 (18924) covalent geometry : angle 0.57173 (25602) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12319.66 seconds wall clock time: 213 minutes 0.65 seconds (12780.65 seconds total)