Starting phenix.real_space_refine on Wed Jan 22 11:36:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jk6_61545/01_2025/9jk6_61545.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jk6_61545/01_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_61545/01_2025/9jk6_61545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jk6_61545/01_2025/9jk6_61545.map" model { file = "/net/cci-nas-00/data/ceres_data/9jk6_61545/01_2025/9jk6_61545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jk6_61545/01_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 7.50, 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 145 " - pdb=" SG CYS A 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: 4.85 Conformation dependent library (CDL) restraints added in 2.4 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: 1.99 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: 6.22 Time building geometry restraints manager: 5.13 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: 10279 10.86 - 21.71: 887 21.71 - 32.57: 138 32.57 - 43.43: 26 43.43 - 54.28: 7 Dihedral angle restraints: 11337 sinusoidal: 4653 harmonic: 6684 Sorted by residual: dihedral pdb=" CB CYS A 145 " pdb=" SG CYS A 145 " pdb=" SG CYS A 149 " pdb=" CB CYS A 149 " ideal model delta sinusoidal sigma weight residual 93.00 38.72 54.28 1 1.00e+01 1.00e-02 4.00e+01 dihedral pdb=" CA ILE B 131 " pdb=" C ILE B 131 " pdb=" N LEU B 132 " pdb=" CA LEU B 132 " ideal model delta harmonic sigma weight residual -180.00 -160.96 -19.04 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ILE F 131 " pdb=" C ILE F 131 " pdb=" N LEU F 132 " pdb=" CA LEU F 132 " ideal model delta harmonic sigma weight residual -180.00 -160.97 -19.03 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 11334 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: 2.03 - 2.60: 103 2.60 - 3.18: 14465 3.18 - 3.75: 27210 3.75 - 4.33: 37566 4.33 - 4.90: 64320 Nonbonded interactions: 143664 Sorted by model distance: nonbonded pdb=" SG CYS C 145 " pdb=" SG CYS C 149 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS D 145 " pdb=" SG CYS D 149 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS B 145 " pdb=" SG CYS B 149 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS E 145 " pdb=" SG CYS E 149 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS F 145 " pdb=" SG CYS F 149 " model vdw 2.032 3.760 ... (remaining 143659 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: 0.14 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: 3.850 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: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 36.610 Find NCS groups from input model: 0.340 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:13.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.960 ------------------------------------------------------------------------------- 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 18924 Z= 0.300 Angle : 0.868 12.071 25602 Z= 0.482 Chirality : 0.050 0.166 2922 Planarity : 0.007 0.069 3186 Dihedral : 8.376 45.907 6978 Min Nonbonded Distance : 2.031 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 *********************** 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 : 2.107 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: 1.5910 time to fit residues: 895.2795 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 : 2.218 ------------------------------------------------------------------------------- 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 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 = 0.3708 r_free = 0.3708 target = 0.138077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.109754 restraints weight = 24460.005| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.19 r_work: 0.3199 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18924 Z= 0.224 Angle : 0.599 11.037 25602 Z= 0.309 Chirality : 0.041 0.137 2922 Planarity : 0.005 0.059 3186 Dihedral : 4.623 28.817 2518 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.53 % Allowed : 11.08 % Favored : 84.39 % 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: -0.15 (0.17), residues: 2220 helix: 0.62 (0.14), residues: 1308 sheet: 0.83 (0.35), residues: 180 loop : -1.60 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 168 HIS 0.004 0.001 HIS A 269 PHE 0.018 0.002 PHE B 264 TYR 0.019 0.002 TYR D 216 ARG 0.008 0.001 ARG E 176 *********************** 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 406 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 316 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 PHE cc_start: 0.7672 (m-10) cc_final: 0.6847 (t80) REVERT: A 337 ASP cc_start: 0.7431 (m-30) cc_final: 0.6967 (t0) REVERT: B 132 LEU cc_start: 0.7407 (mt) cc_final: 0.7190 (mt) REVERT: B 221 GLN cc_start: 0.7825 (mt0) cc_final: 0.7584 (mm110) REVERT: B 300 PHE cc_start: 0.7358 (m-10) cc_final: 0.6566 (t80) REVERT: B 373 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7814 (pt0) REVERT: B 442 GLU cc_start: 0.8196 (pp20) cc_final: 0.7790 (pp20) REVERT: C 132 LEU cc_start: 0.7574 (mt) cc_final: 0.7321 (mt) REVERT: C 198 VAL cc_start: 0.8520 (t) cc_final: 0.8260 (m) REVERT: C 251 THR cc_start: 0.8775 (t) cc_final: 0.8414 (m) REVERT: C 304 LYS cc_start: 0.8229 (ttmt) cc_final: 0.7559 (mttt) REVERT: C 306 MET cc_start: 0.7891 (mmm) cc_final: 0.7258 (mtm) REVERT: D 128 ILE cc_start: 0.7966 (mt) cc_final: 0.7698 (pp) REVERT: D 304 LYS cc_start: 0.8363 (ttmm) cc_final: 0.7392 (mtmt) REVERT: D 306 MET cc_start: 0.8009 (mmm) cc_final: 0.6849 (mtm) REVERT: D 334 ARG cc_start: 0.7926 (mmm-85) cc_final: 0.7658 (tpt90) REVERT: D 373 GLN cc_start: 0.7678 (pt0) cc_final: 0.7376 (pt0) REVERT: E 128 ILE cc_start: 0.8206 (mt) cc_final: 0.7816 (mm) REVERT: E 132 LEU cc_start: 0.7511 (mt) cc_final: 0.7181 (mt) REVERT: E 251 THR cc_start: 0.8783 (t) cc_final: 0.8420 (m) REVERT: E 300 PHE cc_start: 0.7682 (m-10) cc_final: 0.7307 (t80) REVERT: E 353 ARG cc_start: 0.8219 (mtt90) cc_final: 0.7893 (mtt90) REVERT: E 373 GLN cc_start: 0.7254 (tt0) cc_final: 0.7014 (mt0) REVERT: E 516 LEU cc_start: 0.7953 (tp) cc_final: 0.7746 (tm) REVERT: F 300 PHE cc_start: 0.7307 (m-10) cc_final: 0.6636 (t80) REVERT: F 306 MET cc_start: 0.7359 (mmm) cc_final: 0.6805 (mtp) REVERT: F 329 ILE cc_start: 0.6726 (OUTLIER) cc_final: 0.6301 (tt) REVERT: F 455 LYS cc_start: 0.8918 (mtpp) cc_final: 0.8656 (mptm) outliers start: 90 outliers final: 43 residues processed: 356 average time/residue: 1.3755 time to fit residues: 549.4839 Evaluate side-chains 301 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 256 time to evaluate : 2.203 ------------------------------------------------------------------------------- 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 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 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 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 373 GLN 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 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 206 VAL Chi-restraints excluded: chain F residue 209 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=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: 0.7980 chunk 133 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 208 optimal weight: 0.5980 chunk 191 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 426 HIS C 269 HIS C 305 HIS ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.136512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.108363 restraints weight = 24535.729| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.18 r_work: 0.3190 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18924 Z= 0.219 Angle : 0.579 13.253 25602 Z= 0.295 Chirality : 0.041 0.132 2922 Planarity : 0.005 0.054 3186 Dihedral : 4.374 29.913 2516 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.98 % Allowed : 13.54 % Favored : 81.47 % 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: 0.80 (0.18), residues: 2220 helix: 1.62 (0.15), residues: 1266 sheet: 1.17 (0.37), residues: 180 loop : -1.53 (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 *********************** 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 389 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 290 time to evaluate : 1.965 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7696 (mt) cc_final: 0.7388 (mt) REVERT: A 304 LYS cc_start: 0.8393 (ttmm) cc_final: 0.7484 (mtmt) REVERT: A 306 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.6137 (mtp) REVERT: A 337 ASP cc_start: 0.7239 (m-30) cc_final: 0.6830 (t0) REVERT: B 132 LEU cc_start: 0.7511 (mt) cc_final: 0.7111 (mt) REVERT: B 221 GLN cc_start: 0.7842 (mt0) cc_final: 0.7591 (mm110) REVERT: B 300 PHE cc_start: 0.7436 (m-10) cc_final: 0.6719 (t80) REVERT: C 132 LEU cc_start: 0.7423 (mt) cc_final: 0.7174 (mt) REVERT: C 194 PHE cc_start: 0.7848 (t80) cc_final: 0.7520 (t80) REVERT: C 251 THR cc_start: 0.8727 (t) cc_final: 0.8373 (m) REVERT: C 300 PHE cc_start: 0.7699 (m-10) cc_final: 0.7284 (t80) REVERT: C 353 ARG cc_start: 0.8212 (mtt90) cc_final: 0.7904 (mtt90) REVERT: D 194 PHE cc_start: 0.8196 (t80) cc_final: 0.7882 (t80) REVERT: D 300 PHE cc_start: 0.7428 (m-10) cc_final: 0.6730 (t80) REVERT: D 334 ARG cc_start: 0.7978 (mmm-85) cc_final: 0.7595 (tpt90) REVERT: E 132 LEU cc_start: 0.7590 (mt) cc_final: 0.7260 (mt) REVERT: E 222 TYR cc_start: 0.7388 (t80) cc_final: 0.7078 (t80) REVERT: E 251 THR cc_start: 0.8744 (t) cc_final: 0.8375 (m) REVERT: E 304 LYS cc_start: 0.8250 (ttmm) cc_final: 0.7339 (mttt) REVERT: E 353 ARG cc_start: 0.8208 (mtt90) cc_final: 0.7881 (mtt90) REVERT: E 373 GLN cc_start: 0.7211 (tt0) cc_final: 0.6618 (mt0) REVERT: F 132 LEU cc_start: 0.7663 (mt) cc_final: 0.7299 (mt) REVERT: F 304 LYS cc_start: 0.8435 (ttmm) cc_final: 0.7394 (mttt) REVERT: F 306 MET cc_start: 0.7600 (mmm) cc_final: 0.7046 (mtp) outliers start: 99 outliers final: 44 residues processed: 334 average time/residue: 1.2950 time to fit residues: 490.1315 Evaluate side-chains 297 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 252 time to evaluate : 2.042 ------------------------------------------------------------------------------- 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 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 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 198 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 238 ILE 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 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 459 LEU Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 249 MET 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 Chi-restraints excluded: chain F residue 487 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 34 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 chunk 213 optimal weight: 0.5980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS ** 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 452 GLN C 305 HIS ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN D 305 HIS D 452 GLN ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 HIS F 512 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.134718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.106425 restraints weight = 24586.221| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.17 r_work: 0.3168 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18924 Z= 0.244 Angle : 0.590 15.913 25602 Z= 0.298 Chirality : 0.042 0.184 2922 Planarity : 0.005 0.050 3186 Dihedral : 4.351 33.804 2516 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.19 % Allowed : 15.26 % 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: 1.19 (0.18), residues: 2220 helix: 1.90 (0.15), residues: 1266 sheet: 1.62 (0.36), residues: 174 loop : -1.35 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 138 HIS 0.005 0.001 HIS E 305 PHE 0.015 0.002 PHE B 514 TYR 0.017 0.002 TYR D 222 ARG 0.008 0.000 ARG C 176 *********************** 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 387 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 284 time to evaluate : 2.157 Fit side-chains REVERT: A 300 PHE cc_start: 0.7609 (m-10) cc_final: 0.6837 (t80) REVERT: A 304 LYS cc_start: 0.8415 (ttmm) cc_final: 0.7907 (tmtt) REVERT: B 132 LEU cc_start: 0.7366 (mt) cc_final: 0.7147 (mt) REVERT: B 221 GLN cc_start: 0.7865 (mt0) cc_final: 0.7654 (mm110) REVERT: B 242 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: B 300 PHE cc_start: 0.7468 (m-10) cc_final: 0.6795 (t80) REVERT: B 306 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7637 (mmm) REVERT: B 403 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7355 (tpp-160) REVERT: C 132 LEU cc_start: 0.7582 (mt) cc_final: 0.7255 (mt) REVERT: C 194 PHE cc_start: 0.7884 (t80) cc_final: 0.7579 (t80) REVERT: C 247 GLN cc_start: 0.8335 (tp40) cc_final: 0.8130 (tp40) REVERT: C 251 THR cc_start: 0.8747 (t) cc_final: 0.8380 (m) REVERT: C 304 LYS cc_start: 0.8312 (ttmm) cc_final: 0.7389 (mttt) REVERT: C 353 ARG cc_start: 0.8220 (mtt90) cc_final: 0.7923 (mtt90) REVERT: D 194 PHE cc_start: 0.8338 (t80) cc_final: 0.8094 (t80) REVERT: D 242 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: D 300 PHE cc_start: 0.7450 (m-10) cc_final: 0.6907 (t80) REVERT: D 306 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7645 (mmm) REVERT: D 334 ARG cc_start: 0.7923 (mmm-85) cc_final: 0.7555 (tpt90) REVERT: E 132 LEU cc_start: 0.7611 (mt) cc_final: 0.7281 (mt) REVERT: E 194 PHE cc_start: 0.7848 (t80) cc_final: 0.7478 (t80) REVERT: E 215 ASN cc_start: 0.7551 (OUTLIER) cc_final: 0.6698 (p0) REVERT: E 222 TYR cc_start: 0.7469 (t80) cc_final: 0.7187 (t80) REVERT: E 249 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8448 (mmm) REVERT: E 251 THR cc_start: 0.8756 (t) cc_final: 0.8395 (m) REVERT: E 304 LYS cc_start: 0.8383 (ttmm) cc_final: 0.7452 (mttt) REVERT: E 353 ARG cc_start: 0.8223 (mtt90) cc_final: 0.7912 (mtt90) REVERT: E 373 GLN cc_start: 0.7254 (tt0) cc_final: 0.6649 (mt0) REVERT: F 300 PHE cc_start: 0.7507 (m-10) cc_final: 0.6814 (t80) REVERT: F 306 MET cc_start: 0.7815 (mmm) cc_final: 0.7055 (mtp) REVERT: F 420 MET cc_start: 0.8095 (tmm) cc_final: 0.7835 (mmt) REVERT: F 462 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8686 (mp10) outliers start: 103 outliers final: 55 residues processed: 332 average time/residue: 1.2431 time to fit residues: 467.9581 Evaluate side-chains 315 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 252 time to evaluate : 1.981 ------------------------------------------------------------------------------- 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 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 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 242 GLU Chi-restraints excluded: chain B residue 306 MET 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 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 148 ILE 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 306 MET 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 195 LEU 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 249 MET 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 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: 0.5980 chunk 42 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 28 optimal weight: 0.2980 chunk 117 optimal weight: 0.5980 chunk 159 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 77 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 C 340 HIS C 462 GLN ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 HIS E 462 GLN F 305 HIS F 340 HIS F 462 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.137382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.109251 restraints weight = 24626.869| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.16 r_work: 0.3208 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18924 Z= 0.166 Angle : 0.556 16.870 25602 Z= 0.277 Chirality : 0.040 0.201 2922 Planarity : 0.004 0.047 3186 Dihedral : 4.071 36.114 2516 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.58 % Allowed : 15.96 % Favored : 79.46 % 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: 1.49 (0.18), residues: 2220 helix: 2.16 (0.15), residues: 1266 sheet: 1.55 (0.35), residues: 174 loop : -1.21 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 138 HIS 0.004 0.001 HIS C 305 PHE 0.012 0.001 PHE F 429 TYR 0.014 0.001 TYR D 222 ARG 0.006 0.000 ARG A 176 *********************** 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 374 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 283 time to evaluate : 2.088 Fit side-chains REVERT: A 131 ILE cc_start: 0.6660 (OUTLIER) cc_final: 0.6319 (tt) REVERT: A 300 PHE cc_start: 0.7639 (m-10) cc_final: 0.7184 (t80) REVERT: B 132 LEU cc_start: 0.7458 (mt) cc_final: 0.7164 (mt) REVERT: B 174 LYS cc_start: 0.7479 (mmtm) cc_final: 0.7245 (mmtt) REVERT: B 221 GLN cc_start: 0.7726 (mt0) cc_final: 0.7496 (mm110) REVERT: B 242 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: B 304 LYS cc_start: 0.8257 (ttmm) cc_final: 0.7375 (mtmt) REVERT: B 403 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7292 (tpp-160) REVERT: C 132 LEU cc_start: 0.7443 (mt) cc_final: 0.7147 (mt) REVERT: C 194 PHE cc_start: 0.7793 (t80) cc_final: 0.7553 (t80) REVERT: C 304 LYS cc_start: 0.8275 (ttmm) cc_final: 0.7419 (mttt) REVERT: C 353 ARG cc_start: 0.8208 (mtt90) cc_final: 0.7906 (mtt90) REVERT: D 194 PHE cc_start: 0.8296 (t80) cc_final: 0.8067 (t80) REVERT: D 221 GLN cc_start: 0.7653 (mm110) cc_final: 0.7311 (mm110) REVERT: D 304 LYS cc_start: 0.8222 (ttmm) cc_final: 0.7354 (mtmt) REVERT: D 334 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7685 (ttp80) REVERT: E 132 LEU cc_start: 0.7574 (mt) cc_final: 0.7172 (mt) REVERT: E 194 PHE cc_start: 0.7871 (t80) cc_final: 0.7570 (t80) REVERT: E 215 ASN cc_start: 0.7521 (OUTLIER) cc_final: 0.6601 (p0) REVERT: E 245 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7778 (pm20) REVERT: E 249 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8441 (mmp) REVERT: E 251 THR cc_start: 0.8679 (t) cc_final: 0.8342 (m) REVERT: E 304 LYS cc_start: 0.8375 (ttmm) cc_final: 0.7423 (mttt) REVERT: E 353 ARG cc_start: 0.8205 (mtt90) cc_final: 0.7887 (mtt90) REVERT: E 373 GLN cc_start: 0.7106 (tt0) cc_final: 0.6645 (mt0) REVERT: F 300 PHE cc_start: 0.7466 (m-10) cc_final: 0.7084 (t80) REVERT: F 306 MET cc_start: 0.7821 (mmm) cc_final: 0.6977 (mtp) outliers start: 91 outliers final: 40 residues processed: 329 average time/residue: 1.3067 time to fit residues: 484.0973 Evaluate side-chains 307 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 260 time to evaluate : 2.236 ------------------------------------------------------------------------------- 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 188 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 206 VAL 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 242 GLU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 246 LEU 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 209 LEU 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 215 ASN Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain E residue 249 MET 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 F residue 142 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: 4.9990 chunk 145 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 185 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 GLN F 305 HIS ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.134111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105404 restraints weight = 24820.824| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.17 r_work: 0.3146 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18924 Z= 0.292 Angle : 0.615 15.813 25602 Z= 0.311 Chirality : 0.043 0.196 2922 Planarity : 0.005 0.047 3186 Dihedral : 4.368 43.846 2516 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.93 % Allowed : 16.36 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.18), residues: 2220 helix: 2.17 (0.15), residues: 1236 sheet: 1.68 (0.35), residues: 174 loop : -1.27 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 458 HIS 0.005 0.001 HIS B 305 PHE 0.018 0.002 PHE B 514 TYR 0.014 0.002 TYR C 222 ARG 0.006 0.000 ARG C 176 *********************** 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 371 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 273 time to evaluate : 2.038 Fit side-chains REVERT: A 131 ILE cc_start: 0.6923 (OUTLIER) cc_final: 0.6697 (tt) REVERT: A 233 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8094 (OUTLIER) REVERT: A 304 LYS cc_start: 0.8398 (ttmm) cc_final: 0.7394 (mttt) REVERT: B 132 LEU cc_start: 0.7505 (mt) cc_final: 0.7071 (mt) REVERT: B 221 GLN cc_start: 0.7800 (mt0) cc_final: 0.7572 (mm110) REVERT: B 242 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: B 251 THR cc_start: 0.8679 (t) cc_final: 0.8385 (m) REVERT: B 304 LYS cc_start: 0.8280 (ttmm) cc_final: 0.7255 (mtmt) REVERT: B 403 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7455 (tpp-160) REVERT: C 132 LEU cc_start: 0.7575 (mt) cc_final: 0.7232 (mt) REVERT: C 194 PHE cc_start: 0.7864 (t80) cc_final: 0.7616 (t80) REVERT: C 233 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8225 (mt) REVERT: C 238 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8152 (pt) REVERT: C 251 THR cc_start: 0.8751 (t) cc_final: 0.8408 (m) REVERT: C 304 LYS cc_start: 0.8377 (ttmm) cc_final: 0.7399 (mttt) REVERT: C 353 ARG cc_start: 0.8255 (mtt90) cc_final: 0.7954 (mtt90) REVERT: D 242 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7805 (mp0) REVERT: D 251 THR cc_start: 0.8685 (t) cc_final: 0.8417 (m) REVERT: D 304 LYS cc_start: 0.8270 (ttmm) cc_final: 0.7438 (mtmt) REVERT: D 334 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7628 (ttp80) REVERT: E 132 LEU cc_start: 0.7559 (mt) cc_final: 0.7169 (mt) REVERT: E 214 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6920 (mpt90) REVERT: E 215 ASN cc_start: 0.7613 (t0) cc_final: 0.6726 (p0) REVERT: E 251 THR cc_start: 0.8800 (t) cc_final: 0.8442 (m) REVERT: E 353 ARG cc_start: 0.8260 (mtt90) cc_final: 0.7952 (mtt90) REVERT: E 373 GLN cc_start: 0.7275 (tt0) cc_final: 0.6628 (mt0) REVERT: F 304 LYS cc_start: 0.8412 (ttmm) cc_final: 0.8131 (ttmm) REVERT: F 403 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7326 (ttp80) outliers start: 98 outliers final: 54 residues processed: 325 average time/residue: 1.2039 time to fit residues: 442.6407 Evaluate side-chains 317 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 254 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 206 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 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 242 GLU Chi-restraints excluded: chain B residue 329 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 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 246 LEU 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 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 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 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 F residue 142 LEU Chi-restraints excluded: chain F residue 195 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 80 optimal weight: 0.2980 chunk 135 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 178 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 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 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 GLN D 247 GLN ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 GLN F 305 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.136382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107790 restraints weight = 24562.456| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.17 r_work: 0.3180 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18924 Z= 0.206 Angle : 0.569 13.234 25602 Z= 0.287 Chirality : 0.041 0.159 2922 Planarity : 0.004 0.046 3186 Dihedral : 4.169 45.845 2516 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.58 % Allowed : 17.12 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.57 (0.18), residues: 2220 helix: 2.34 (0.15), residues: 1236 sheet: 1.61 (0.35), residues: 174 loop : -1.24 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 458 HIS 0.004 0.001 HIS D 305 PHE 0.013 0.001 PHE F 429 TYR 0.013 0.001 TYR D 222 ARG 0.006 0.000 ARG F 176 *********************** 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 364 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 273 time to evaluate : 2.094 Fit side-chains REVERT: A 121 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6653 (pt) REVERT: A 131 ILE cc_start: 0.6895 (OUTLIER) cc_final: 0.6650 (tt) REVERT: A 221 GLN cc_start: 0.7442 (mm110) cc_final: 0.7187 (mm110) REVERT: A 233 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8041 (OUTLIER) REVERT: A 304 LYS cc_start: 0.8373 (ttmm) cc_final: 0.7421 (mttt) REVERT: B 132 LEU cc_start: 0.7587 (mt) cc_final: 0.7159 (mt) REVERT: B 221 GLN cc_start: 0.7737 (mt0) cc_final: 0.7462 (mm110) REVERT: B 242 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: B 304 LYS cc_start: 0.8263 (ttmm) cc_final: 0.7266 (mtmt) REVERT: B 403 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7357 (tpp-160) REVERT: C 132 LEU cc_start: 0.7539 (mt) cc_final: 0.7061 (mt) REVERT: C 251 THR cc_start: 0.8680 (t) cc_final: 0.8370 (m) REVERT: C 304 LYS cc_start: 0.8384 (ttmm) cc_final: 0.7421 (mttt) REVERT: C 353 ARG cc_start: 0.8233 (mtt90) cc_final: 0.7937 (mtt90) REVERT: D 242 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: D 304 LYS cc_start: 0.8249 (ttmm) cc_final: 0.7406 (mtmt) REVERT: D 334 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7640 (ttp80) REVERT: D 442 GLU cc_start: 0.8279 (pp20) cc_final: 0.7859 (pp20) REVERT: E 132 LEU cc_start: 0.7710 (mt) cc_final: 0.7327 (mt) REVERT: E 214 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6862 (mpt90) REVERT: E 215 ASN cc_start: 0.7644 (t0) cc_final: 0.6718 (p0) REVERT: E 251 THR cc_start: 0.8715 (t) cc_final: 0.8389 (m) REVERT: E 304 LYS cc_start: 0.8382 (ttmm) cc_final: 0.7462 (mttt) REVERT: E 353 ARG cc_start: 0.8230 (mtt90) cc_final: 0.7913 (mtt90) REVERT: E 373 GLN cc_start: 0.7160 (tt0) cc_final: 0.6828 (tt0) REVERT: F 304 LYS cc_start: 0.8319 (ttmm) cc_final: 0.7418 (mtmt) REVERT: F 403 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7275 (ttp80) outliers start: 91 outliers final: 58 residues processed: 320 average time/residue: 1.2251 time to fit residues: 443.2684 Evaluate side-chains 319 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 253 time to evaluate : 2.050 ------------------------------------------------------------------------------- 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 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 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 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 206 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 416 ASN Chi-restraints excluded: chain B residue 459 LEU 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 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 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: 1.9990 chunk 136 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 204 optimal weight: 0.0970 chunk 60 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 216 optimal weight: 0.0270 chunk 18 optimal weight: 0.0070 chunk 142 optimal weight: 3.9990 chunk 201 optimal weight: 0.6980 overall best weight: 0.3454 ------------------------------------------------------------------------------- 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 221 GLN D 340 HIS E 221 GLN E 245 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 = 0.3725 r_free = 0.3725 target = 0.139313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.111025 restraints weight = 24393.056| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.16 r_work: 0.3226 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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 : 0.002 0.033 18924 Z= 0.155 Angle : 0.546 12.603 25602 Z= 0.273 Chirality : 0.040 0.156 2922 Planarity : 0.004 0.046 3186 Dihedral : 3.922 45.134 2516 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.73 % Allowed : 18.38 % 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: 1.71 (0.18), residues: 2220 helix: 2.34 (0.15), residues: 1266 sheet: 1.54 (0.34), residues: 174 loop : -1.08 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 458 HIS 0.004 0.001 HIS C 305 PHE 0.014 0.001 PHE C 153 TYR 0.013 0.001 TYR D 200 ARG 0.007 0.000 ARG B 176 *********************** 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 334 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 260 time to evaluate : 2.303 Fit side-chains REVERT: A 121 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6599 (pt) REVERT: A 131 ILE cc_start: 0.6771 (OUTLIER) cc_final: 0.6497 (tt) REVERT: A 233 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.8013 (OUTLIER) REVERT: A 304 LYS cc_start: 0.8320 (ttmm) cc_final: 0.7388 (mttt) REVERT: A 351 GLU cc_start: 0.8238 (mp0) cc_final: 0.7997 (mp0) REVERT: B 132 LEU cc_start: 0.7617 (mt) cc_final: 0.7199 (mt) REVERT: B 174 LYS cc_start: 0.7351 (mmtm) cc_final: 0.7149 (mmtt) REVERT: B 221 GLN cc_start: 0.7645 (mt0) cc_final: 0.7393 (mm110) REVERT: B 247 GLN cc_start: 0.8382 (tp40) cc_final: 0.8179 (tp40) REVERT: B 304 LYS cc_start: 0.8234 (ttmm) cc_final: 0.7231 (mtmt) REVERT: B 403 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7310 (tpp-160) REVERT: B 442 GLU cc_start: 0.8155 (pp20) cc_final: 0.7846 (pp20) REVERT: C 132 LEU cc_start: 0.7399 (mt) cc_final: 0.7049 (mt) REVERT: C 221 GLN cc_start: 0.7188 (mm110) cc_final: 0.6940 (mm110) REVERT: C 304 LYS cc_start: 0.8315 (ttmm) cc_final: 0.7417 (mttt) REVERT: C 353 ARG cc_start: 0.8207 (mtt90) cc_final: 0.7898 (mtt90) REVERT: D 221 GLN cc_start: 0.7577 (mm-40) cc_final: 0.7233 (mm110) REVERT: D 304 LYS cc_start: 0.8202 (ttmm) cc_final: 0.7415 (mttt) REVERT: D 334 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7596 (ttp80) REVERT: D 442 GLU cc_start: 0.8146 (pp20) cc_final: 0.7687 (pp20) REVERT: E 132 LEU cc_start: 0.7674 (mt) cc_final: 0.7321 (mt) REVERT: E 214 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.6743 (mpt90) REVERT: E 215 ASN cc_start: 0.7630 (t0) cc_final: 0.6713 (p0) REVERT: E 221 GLN cc_start: 0.7332 (mm-40) cc_final: 0.6985 (mm-40) REVERT: E 304 LYS cc_start: 0.8350 (ttmm) cc_final: 0.7379 (mttt) REVERT: E 353 ARG cc_start: 0.8201 (mtt90) cc_final: 0.7908 (mtt90) REVERT: E 373 GLN cc_start: 0.6934 (tt0) cc_final: 0.6624 (tt0) REVERT: F 221 GLN cc_start: 0.7314 (mm110) cc_final: 0.7055 (mm110) REVERT: F 304 LYS cc_start: 0.8301 (ttmm) cc_final: 0.7434 (mtmt) REVERT: F 351 GLU cc_start: 0.8234 (mp0) cc_final: 0.7925 (mp0) outliers start: 74 outliers final: 37 residues processed: 303 average time/residue: 1.2225 time to fit residues: 419.4660 Evaluate side-chains 289 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 247 time to evaluate : 2.122 ------------------------------------------------------------------------------- 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 214 ARG 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 198 VAL Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 459 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 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 206 VAL Chi-restraints excluded: chain D residue 233 ILE 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 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 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 459 LEU Chi-restraints excluded: chain F residue 462 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 210 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 186 optimal weight: 0.6980 chunk 218 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 247 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 = 0.3699 r_free = 0.3699 target = 0.137294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.108800 restraints weight = 24548.788| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.16 r_work: 0.3191 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18924 Z= 0.216 Angle : 0.580 13.894 25602 Z= 0.290 Chirality : 0.041 0.167 2922 Planarity : 0.004 0.046 3186 Dihedral : 4.028 46.160 2516 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.73 % Allowed : 18.73 % Favored : 77.54 % 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: 1.72 (0.18), residues: 2220 helix: 2.42 (0.15), residues: 1242 sheet: 1.57 (0.34), residues: 174 loop : -1.11 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 458 HIS 0.005 0.001 HIS F 305 PHE 0.013 0.001 PHE B 514 TYR 0.012 0.001 TYR B 222 ARG 0.008 0.000 ARG F 176 *********************** 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 332 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 258 time to evaluate : 2.357 Fit side-chains REVERT: A 121 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6562 (pt) REVERT: A 131 ILE cc_start: 0.6788 (OUTLIER) cc_final: 0.6583 (tt) REVERT: A 233 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7826 (mt) REVERT: A 304 LYS cc_start: 0.8319 (ttmm) cc_final: 0.7392 (mtmt) REVERT: A 306 MET cc_start: 0.7864 (tpt) cc_final: 0.7652 (tpt) REVERT: B 132 LEU cc_start: 0.7651 (mt) cc_final: 0.7190 (mt) REVERT: B 221 GLN cc_start: 0.7656 (mt0) cc_final: 0.7413 (mm110) REVERT: B 300 PHE cc_start: 0.7484 (m-10) cc_final: 0.7028 (t80) REVERT: B 304 LYS cc_start: 0.8205 (ttmm) cc_final: 0.7803 (tmtt) REVERT: B 403 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7372 (tpp-160) REVERT: B 420 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7949 (tmm) REVERT: C 132 LEU cc_start: 0.7615 (mt) cc_final: 0.7227 (mt) REVERT: C 221 GLN cc_start: 0.7356 (mm110) cc_final: 0.7048 (mm110) REVERT: C 304 LYS cc_start: 0.8342 (ttmm) cc_final: 0.7440 (mttt) REVERT: C 353 ARG cc_start: 0.8244 (mtt90) cc_final: 0.7948 (mtt90) REVERT: D 221 GLN cc_start: 0.7640 (mm-40) cc_final: 0.7362 (mm110) REVERT: D 242 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7587 (mt-10) REVERT: D 304 LYS cc_start: 0.8164 (ttmm) cc_final: 0.7382 (mtmt) REVERT: D 334 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7595 (ttp80) REVERT: E 132 LEU cc_start: 0.7649 (mt) cc_final: 0.7270 (mt) REVERT: E 214 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6800 (mpt90) REVERT: E 215 ASN cc_start: 0.7631 (t0) cc_final: 0.6701 (p0) REVERT: E 221 GLN cc_start: 0.7500 (mm-40) cc_final: 0.7209 (mm110) REVERT: E 251 THR cc_start: 0.8673 (t) cc_final: 0.8394 (m) REVERT: E 304 LYS cc_start: 0.8321 (ttmm) cc_final: 0.7340 (mttt) REVERT: E 353 ARG cc_start: 0.8245 (mtt90) cc_final: 0.7952 (mtt90) REVERT: E 373 GLN cc_start: 0.7097 (tt0) cc_final: 0.6801 (tt0) REVERT: F 209 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.7050 (mp) REVERT: F 233 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8056 (OUTLIER) REVERT: F 304 LYS cc_start: 0.8302 (ttmm) cc_final: 0.7399 (mtmt) REVERT: F 403 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7293 (ttp80) outliers start: 74 outliers final: 48 residues processed: 298 average time/residue: 1.2151 time to fit residues: 410.5604 Evaluate side-chains 308 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 250 time to evaluate : 2.004 ------------------------------------------------------------------------------- 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 195 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 214 ARG 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 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 206 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 459 LEU 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 148 ILE Chi-restraints excluded: chain D residue 192 LEU 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 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 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 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 209 LEU Chi-restraints excluded: chain F residue 233 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 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: 0.8980 chunk 143 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 152 optimal weight: 0.3980 chunk 108 optimal weight: 0.7980 chunk 128 optimal weight: 0.0270 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 GLN D 425 GLN F 462 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.137765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.109215 restraints weight = 24601.072| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.17 r_work: 0.3196 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18924 Z= 0.197 Angle : 0.570 12.383 25602 Z= 0.286 Chirality : 0.041 0.155 2922 Planarity : 0.004 0.046 3186 Dihedral : 4.020 46.939 2516 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.92 % Allowed : 19.44 % Favored : 77.64 % 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: 1.72 (0.18), residues: 2220 helix: 2.44 (0.15), residues: 1236 sheet: 1.56 (0.34), residues: 174 loop : -1.11 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 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 F 176 ********************** 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 316 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 258 time to evaluate : 2.345 Fit side-chains REVERT: A 121 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6550 (pt) REVERT: A 221 GLN cc_start: 0.7516 (mm110) cc_final: 0.7284 (mm110) REVERT: A 304 LYS cc_start: 0.8278 (ttmm) cc_final: 0.7334 (mtmt) REVERT: B 121 LEU cc_start: 0.7653 (pp) cc_final: 0.7435 (pt) REVERT: B 132 LEU cc_start: 0.7670 (mt) cc_final: 0.7191 (mt) REVERT: B 221 GLN cc_start: 0.7677 (mt0) cc_final: 0.7400 (mm110) REVERT: B 304 LYS cc_start: 0.8185 (ttmm) cc_final: 0.7217 (mtmt) REVERT: B 403 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7387 (tpp-160) REVERT: B 420 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7849 (tmm) REVERT: B 442 GLU cc_start: 0.8218 (pp20) cc_final: 0.7788 (pp20) REVERT: C 132 LEU cc_start: 0.7595 (mt) cc_final: 0.7192 (mt) REVERT: C 221 GLN cc_start: 0.7198 (mm110) cc_final: 0.6916 (mm110) REVERT: C 304 LYS cc_start: 0.8331 (ttmm) cc_final: 0.7388 (mttt) REVERT: C 353 ARG cc_start: 0.8229 (mtt90) cc_final: 0.7931 (mtt90) REVERT: D 221 GLN cc_start: 0.7577 (mm-40) cc_final: 0.7293 (mm110) REVERT: D 242 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: D 304 LYS cc_start: 0.8121 (ttmm) cc_final: 0.7265 (mtmt) REVERT: D 334 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7584 (ttp80) REVERT: E 121 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6899 (pt) REVERT: E 132 LEU cc_start: 0.7642 (mt) cc_final: 0.7233 (mt) REVERT: E 214 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6811 (mpt90) REVERT: E 215 ASN cc_start: 0.7664 (t0) cc_final: 0.6737 (p0) REVERT: E 221 GLN cc_start: 0.7514 (mm-40) cc_final: 0.7246 (mm110) REVERT: E 251 THR cc_start: 0.8654 (t) cc_final: 0.8402 (m) REVERT: E 304 LYS cc_start: 0.8295 (ttmm) cc_final: 0.7434 (mttt) REVERT: E 373 GLN cc_start: 0.7074 (tt0) cc_final: 0.6771 (tt0) REVERT: F 209 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7203 (mp) REVERT: F 221 GLN cc_start: 0.7390 (mm110) cc_final: 0.7105 (mm110) REVERT: F 233 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8006 (OUTLIER) REVERT: F 304 LYS cc_start: 0.8293 (ttmm) cc_final: 0.7380 (mtmt) REVERT: F 403 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7302 (ttp80) REVERT: F 487 ASP cc_start: 0.7069 (t70) cc_final: 0.6811 (t70) outliers start: 58 outliers final: 43 residues processed: 294 average time/residue: 1.1851 time to fit residues: 396.8344 Evaluate side-chains 300 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 248 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 214 ARG 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 209 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 459 LEU 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 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 148 ILE Chi-restraints excluded: chain D residue 192 LEU 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 121 LEU Chi-restraints excluded: chain E residue 195 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 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 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 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 403 ARG Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 462 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 44 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 204 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3702 r_free = 0.3702 target = 0.137628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.109133 restraints weight = 24494.853| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.16 r_work: 0.3198 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 18924 Z= 0.236 Angle : 0.743 59.138 25602 Z= 0.410 Chirality : 0.041 0.188 2922 Planarity : 0.004 0.046 3186 Dihedral : 4.050 46.924 2516 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.22 % Allowed : 18.88 % 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: 1.71 (0.18), residues: 2220 helix: 2.43 (0.15), residues: 1236 sheet: 1.56 (0.34), residues: 174 loop : -1.11 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 458 HIS 0.004 0.001 HIS D 305 PHE 0.013 0.001 PHE F 429 TYR 0.012 0.001 TYR B 222 ARG 0.011 0.000 ARG E 353 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13102.99 seconds wall clock time: 239 minutes 19.73 seconds (14359.73 seconds total)