Starting phenix.real_space_refine on Mon Jun 16 09:41:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jk6_61545/06_2025/9jk6_61545.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jk6_61545/06_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_61545/06_2025/9jk6_61545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jk6_61545/06_2025/9jk6_61545.map" model { file = "/net/cci-nas-00/data/ceres_data/9jk6_61545/06_2025/9jk6_61545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jk6_61545/06_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-5710/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: 8.27, per 1000 atoms: 0.45 Number of scatterers: 18504 At special positions: 0 Unit cell: (105.56, 93.96, 221.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 3120 8.00 N 3192 7.00 C 12120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 145 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 145 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS F 145 " - pdb=" SG CYS F 149 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.07 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: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 115 through 133 Proline residue: A 127 - end of helix removed outlier: 3.653A pdb=" N LEU A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 172 removed outlier: 4.076A pdb=" N GLU A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU A 152 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 207 removed outlier: 3.525A pdb=" N ALA A 187 " --> pdb=" O PHE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 Processing helix chain 'A' and resid 215 through 243 removed outlier: 3.863A pdb=" N ILE A 219 " --> pdb=" O ASN A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 287 removed outlier: 3.888A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 294 Processing helix chain 'A' and resid 295 through 306 removed outlier: 3.555A pdb=" N LYS A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 337 removed outlier: 3.658A pdb=" N ARG A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 370 removed outlier: 4.359A pdb=" N TYR A 345 " --> pdb=" O ASN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 398 Processing helix chain 'A' and resid 401 through 412 Processing helix chain 'A' and resid 419 through 434 Processing helix chain 'A' and resid 436 through 446 removed outlier: 4.859A pdb=" N ARG A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TYR A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 453 removed outlier: 3.600A pdb=" N GLN A 452 " --> pdb=" O PRO A 449 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR A 453 " --> pdb=" O THR A 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 449 through 453' Processing helix chain 'A' and resid 508 through 513 removed outlier: 3.895A pdb=" N HIS A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS A 513 " --> pdb=" O LYS A 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 133 Proline residue: B 127 - end of helix removed outlier: 3.654A pdb=" N LEU B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 172 removed outlier: 4.076A pdb=" N GLU B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU B 152 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE B 172 " --> pdb=" O TRP B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 207 removed outlier: 3.525A pdb=" N ALA B 187 " --> pdb=" O PHE B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 212 Processing helix chain 'B' and resid 215 through 243 removed outlier: 3.863A pdb=" N ILE B 219 " --> pdb=" O ASN B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 287 removed outlier: 3.888A pdb=" N TYR B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 294 Processing helix chain 'B' and resid 295 through 306 removed outlier: 3.555A pdb=" N LYS B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 337 removed outlier: 3.657A pdb=" N ARG B 335 " --> pdb=" O ALA B 331 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 370 removed outlier: 4.359A pdb=" N TYR B 345 " --> pdb=" O ASN B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 398 Processing helix chain 'B' and resid 401 through 412 Processing helix chain 'B' and resid 419 through 434 Processing helix chain 'B' and resid 436 through 446 removed outlier: 4.859A pdb=" N ARG B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TYR B 444 " --> pdb=" O PHE B 440 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 453 removed outlier: 3.600A pdb=" N GLN B 452 " --> pdb=" O PRO B 449 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR B 453 " --> pdb=" O THR B 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 449 through 453' Processing helix chain 'B' and resid 508 through 513 removed outlier: 3.896A pdb=" N HIS B 512 " --> pdb=" O PRO B 509 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS B 513 " --> pdb=" O LYS B 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 133 Proline residue: C 127 - end of helix removed outlier: 3.654A pdb=" N LEU C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 172 removed outlier: 4.076A pdb=" N GLU C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU C 152 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE C 172 " --> pdb=" O TRP C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 207 removed outlier: 3.524A pdb=" N ALA C 187 " --> pdb=" O PHE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 Processing helix chain 'C' and resid 215 through 243 removed outlier: 3.863A pdb=" N ILE C 219 " --> pdb=" O ASN C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 287 removed outlier: 3.889A pdb=" N TYR C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS C 285 " --> pdb=" O GLU C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 294 Processing helix chain 'C' and resid 295 through 306 removed outlier: 3.555A pdb=" N LYS C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 337 removed outlier: 3.658A pdb=" N ARG C 335 " --> pdb=" O ALA C 331 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP C 337 " --> pdb=" O ALA C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 370 removed outlier: 4.359A pdb=" N TYR C 345 " --> pdb=" O ASN C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 398 Processing helix chain 'C' and resid 401 through 412 Processing helix chain 'C' and resid 419 through 434 Processing helix chain 'C' and resid 436 through 446 removed outlier: 4.859A pdb=" N ARG C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TYR C 444 " --> pdb=" O PHE C 440 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER C 446 " --> pdb=" O GLU C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 453 removed outlier: 3.601A pdb=" N GLN C 452 " --> pdb=" O PRO C 449 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR C 453 " --> pdb=" O THR C 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 449 through 453' Processing helix chain 'C' and resid 508 through 513 removed outlier: 3.895A pdb=" N HIS C 512 " --> pdb=" O PRO C 509 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS C 513 " --> pdb=" O LYS C 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 133 Proline residue: D 127 - end of helix removed outlier: 3.653A pdb=" N LEU D 133 " --> pdb=" O ALA D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 172 removed outlier: 4.076A pdb=" N GLU D 150 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY D 151 " --> pdb=" O THR D 147 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE D 172 " --> pdb=" O TRP D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 207 removed outlier: 3.525A pdb=" N ALA D 187 " --> pdb=" O PHE D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 212 Processing helix chain 'D' and resid 215 through 243 removed outlier: 3.864A pdb=" N ILE D 219 " --> pdb=" O ASN D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 287 removed outlier: 3.887A pdb=" N TYR D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS D 285 " --> pdb=" O GLU D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 294 Processing helix chain 'D' and resid 295 through 306 removed outlier: 3.555A pdb=" N LYS D 299 " --> pdb=" O LEU D 295 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 337 removed outlier: 3.658A pdb=" N ARG D 335 " --> pdb=" O ALA D 331 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP D 337 " --> pdb=" O ALA D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 370 removed outlier: 4.359A pdb=" N TYR D 345 " --> pdb=" O ASN D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 398 Processing helix chain 'D' and resid 401 through 412 Processing helix chain 'D' and resid 419 through 434 Processing helix chain 'D' and resid 436 through 446 removed outlier: 4.859A pdb=" N ARG D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TYR D 444 " --> pdb=" O PHE D 440 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER D 446 " --> pdb=" O GLU D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 453 removed outlier: 3.600A pdb=" N GLN D 452 " --> pdb=" O PRO D 449 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR D 453 " --> pdb=" O THR D 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 449 through 453' Processing helix chain 'D' and resid 508 through 513 removed outlier: 3.895A pdb=" N HIS D 512 " --> pdb=" O PRO D 509 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS D 513 " --> pdb=" O LYS D 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 133 Proline residue: E 127 - end of helix removed outlier: 3.653A pdb=" N LEU E 133 " --> pdb=" O ALA E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 172 removed outlier: 4.076A pdb=" N GLU E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY E 151 " --> pdb=" O THR E 147 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU E 152 " --> pdb=" O ILE E 148 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE E 172 " --> pdb=" O TRP E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 207 removed outlier: 3.525A pdb=" N ALA E 187 " --> pdb=" O PHE E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 212 Processing helix chain 'E' and resid 215 through 243 removed outlier: 3.863A pdb=" N ILE E 219 " --> pdb=" O ASN E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 287 removed outlier: 3.888A pdb=" N TYR E 284 " --> pdb=" O LEU E 280 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 294 Processing helix chain 'E' and resid 295 through 306 removed outlier: 3.555A pdb=" N LYS E 299 " --> pdb=" O LEU E 295 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG E 301 " --> pdb=" O ALA E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 337 removed outlier: 3.658A pdb=" N ARG E 335 " --> pdb=" O ALA E 331 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP E 337 " --> pdb=" O ALA E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 370 removed outlier: 4.358A pdb=" N TYR E 345 " --> pdb=" O ASN E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 398 Processing helix chain 'E' and resid 401 through 412 Processing helix chain 'E' and resid 419 through 434 Processing helix chain 'E' and resid 436 through 446 removed outlier: 4.858A pdb=" N ARG E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N TYR E 444 " --> pdb=" O PHE E 440 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER E 446 " --> pdb=" O GLU E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 453 removed outlier: 3.601A pdb=" N GLN E 452 " --> pdb=" O PRO E 449 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR E 453 " --> pdb=" O THR E 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 449 through 453' Processing helix chain 'E' and resid 508 through 513 removed outlier: 3.895A pdb=" N HIS E 512 " --> pdb=" O PRO E 509 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS E 513 " --> pdb=" O LYS E 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 133 Proline residue: F 127 - end of helix removed outlier: 3.654A pdb=" N LEU F 133 " --> pdb=" O ALA F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 172 removed outlier: 4.075A pdb=" N GLU F 150 " --> pdb=" O GLY F 146 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY F 151 " --> pdb=" O THR F 147 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU F 152 " --> pdb=" O ILE F 148 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE F 172 " --> pdb=" O TRP F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 207 removed outlier: 3.525A pdb=" N ALA F 187 " --> pdb=" O PHE F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 212 Processing helix chain 'F' and resid 215 through 243 removed outlier: 3.864A pdb=" N ILE F 219 " --> pdb=" O ASN F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 287 removed outlier: 3.888A pdb=" N TYR F 284 " --> pdb=" O LEU F 280 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS F 285 " --> pdb=" O GLU F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 294 Processing helix chain 'F' and resid 295 through 306 removed outlier: 3.555A pdb=" N LYS F 299 " --> pdb=" O LEU F 295 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG F 301 " --> pdb=" O ALA F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 337 removed outlier: 3.658A pdb=" N ARG F 335 " --> pdb=" O ALA F 331 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP F 337 " --> pdb=" O ALA F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 370 removed outlier: 4.359A pdb=" N TYR F 345 " --> pdb=" O ASN F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 398 Processing helix chain 'F' and resid 401 through 412 Processing helix chain 'F' and resid 419 through 434 Processing helix chain 'F' and resid 436 through 446 removed outlier: 4.860A pdb=" N ARG F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TYR F 444 " --> pdb=" O PHE F 440 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER F 446 " --> pdb=" O GLU F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 453 removed outlier: 3.600A pdb=" N GLN F 452 " --> pdb=" O PRO F 449 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR F 453 " --> pdb=" O THR F 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 449 through 453' Processing helix chain 'F' and resid 508 through 513 removed outlier: 3.896A pdb=" N HIS F 512 " --> pdb=" O PRO F 509 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS F 513 " --> pdb=" O LYS F 510 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 178 removed outlier: 6.345A pdb=" N ASP A 178 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N GLU B 504 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 373 through 375 removed outlier: 3.503A pdb=" N GLN A 373 " --> pdb=" O VAL C 515 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 515 " --> pdb=" O GLN A 373 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 177 through 178 removed outlier: 6.445A pdb=" N ILE A 501 " --> pdb=" O TRP C 463 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU C 465 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N SER A 503 " --> pdb=" O LEU C 465 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 373 through 375 removed outlier: 3.698A pdb=" N GLN B 373 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 515 " --> pdb=" O GLN B 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 177 through 178 removed outlier: 6.259A pdb=" N ASP B 178 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N GLU C 504 " --> pdb=" O ASP B 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP B 463 " --> pdb=" O ILE C 501 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU C 505 " --> pdb=" O LEU B 465 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 373 through 375 Processing sheet with id=AA7, first strand: chain 'D' and resid 177 through 178 removed outlier: 6.453A pdb=" N ASP D 178 " --> pdb=" O LEU E 502 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N GLU E 504 " --> pdb=" O ASP D 178 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU E 505 " --> pdb=" O LEU D 465 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 373 through 375 removed outlier: 3.522A pdb=" N VAL F 515 " --> pdb=" O GLN D 373 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 177 through 178 removed outlier: 6.545A pdb=" N ILE D 501 " --> pdb=" O TRP F 463 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N LEU F 465 " --> pdb=" O ILE D 501 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER D 503 " --> pdb=" O LEU F 465 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 373 through 375 Processing sheet with id=AB2, first strand: chain 'E' and resid 177 through 178 removed outlier: 6.261A pdb=" N ASP E 178 " --> pdb=" O LEU F 502 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N GLU F 504 " --> pdb=" O ASP E 178 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP E 463 " --> pdb=" O ILE F 501 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU F 505 " --> pdb=" O LEU E 465 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 373 through 375 removed outlier: 3.554A pdb=" N GLN F 373 " --> pdb=" O VAL E 515 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL E 515 " --> pdb=" O GLN F 373 " (cutoff:3.500A) 1057 hydrogen bonds defined for protein. 3084 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.84 Time building geometry restraints manager: 4.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5040 1.34 - 1.45: 3423 1.45 - 1.57: 10341 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 18924 Sorted by residual: bond pdb=" C THR E 126 " pdb=" N PRO E 127 " ideal model delta sigma weight residual 1.336 1.391 -0.055 1.23e-02 6.61e+03 2.02e+01 bond pdb=" C THR C 126 " pdb=" N PRO C 127 " ideal model delta sigma weight residual 1.336 1.391 -0.055 1.23e-02 6.61e+03 2.01e+01 bond pdb=" C THR F 126 " pdb=" N PRO F 127 " ideal model delta sigma weight residual 1.336 1.391 -0.055 1.23e-02 6.61e+03 2.00e+01 bond pdb=" C THR D 126 " pdb=" N PRO D 127 " ideal model delta sigma weight residual 1.336 1.391 -0.055 1.23e-02 6.61e+03 2.00e+01 bond pdb=" C THR A 126 " pdb=" N PRO A 127 " ideal model delta sigma weight residual 1.336 1.390 -0.055 1.23e-02 6.61e+03 1.99e+01 ... (remaining 18919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 24959 2.41 - 4.83: 553 4.83 - 7.24: 75 7.24 - 9.66: 9 9.66 - 12.07: 6 Bond angle restraints: 25602 Sorted by residual: angle pdb=" CA PRO C 134 " pdb=" C PRO C 134 " pdb=" N PRO C 135 " ideal model delta sigma weight residual 117.93 122.49 -4.56 1.20e+00 6.94e-01 1.44e+01 angle pdb=" CA PRO B 134 " pdb=" C PRO B 134 " pdb=" N PRO B 135 " ideal model delta sigma weight residual 117.93 122.48 -4.55 1.20e+00 6.94e-01 1.44e+01 angle pdb=" CA PRO A 134 " pdb=" C PRO A 134 " pdb=" N PRO A 135 " ideal model delta sigma weight residual 117.93 122.46 -4.53 1.20e+00 6.94e-01 1.43e+01 angle pdb=" CA PRO F 134 " pdb=" C PRO F 134 " pdb=" N PRO F 135 " ideal model delta sigma weight residual 117.93 122.45 -4.52 1.20e+00 6.94e-01 1.42e+01 angle pdb=" CA PRO E 134 " pdb=" C PRO E 134 " pdb=" N PRO E 135 " ideal model delta sigma weight residual 117.93 122.43 -4.50 1.20e+00 6.94e-01 1.40e+01 ... (remaining 25597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.86: 10280 10.86 - 21.73: 886 21.73 - 32.59: 138 32.59 - 43.45: 36 43.45 - 54.32: 12 Dihedral angle restraints: 11352 sinusoidal: 4668 harmonic: 6684 Sorted by residual: dihedral pdb=" CB CYS D 145 " pdb=" SG CYS D 145 " pdb=" SG CYS D 149 " pdb=" CB CYS D 149 " ideal model delta sinusoidal sigma weight residual 93.00 38.68 54.32 1 1.00e+01 1.00e-02 4.00e+01 dihedral pdb=" CB CYS B 145 " pdb=" SG CYS B 145 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 38.69 54.31 1 1.00e+01 1.00e-02 4.00e+01 dihedral pdb=" CB CYS E 145 " pdb=" SG CYS E 145 " pdb=" SG CYS E 149 " pdb=" CB CYS E 149 " ideal model delta sinusoidal sigma weight residual 93.00 38.70 54.30 1 1.00e+01 1.00e-02 4.00e+01 ... (remaining 11349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1553 0.033 - 0.066: 908 0.066 - 0.099: 278 0.099 - 0.132: 152 0.132 - 0.166: 31 Chirality restraints: 2922 Sorted by residual: chirality pdb=" CB ILE D 431 " pdb=" CA ILE D 431 " pdb=" CG1 ILE D 431 " pdb=" CG2 ILE D 431 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.85e-01 chirality pdb=" CA LEU C 170 " pdb=" N LEU C 170 " pdb=" C LEU C 170 " pdb=" CB LEU C 170 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" CA LEU E 133 " pdb=" N LEU E 133 " pdb=" C LEU E 133 " pdb=" CB LEU E 133 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.73e-01 ... (remaining 2919 not shown) Planarity restraints: 3186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 134 " -0.046 5.00e-02 4.00e+02 6.86e-02 7.53e+00 pdb=" N PRO C 135 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 135 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 135 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 134 " 0.046 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO E 135 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 135 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 135 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 134 " -0.046 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO A 135 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 135 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 135 " -0.038 5.00e-02 4.00e+02 ... (remaining 3183 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 4322 2.79 - 3.32: 15949 3.32 - 3.85: 29623 3.85 - 4.37: 33278 4.37 - 4.90: 60477 Nonbonded interactions: 143649 Sorted by model distance: nonbonded pdb=" OG1 THR E 147 " pdb=" OD2 ASP F 213 " model vdw 2.269 3.040 nonbonded pdb=" OG1 THR B 147 " pdb=" OD2 ASP C 213 " model vdw 2.290 3.040 nonbonded pdb=" OG1 THR D 147 " pdb=" OD2 ASP E 213 " model vdw 2.352 3.040 nonbonded pdb=" O ARG D 207 " pdb=" OG SER D 211 " model vdw 2.381 3.040 nonbonded pdb=" O ARG B 207 " pdb=" OG SER B 211 " model vdw 2.381 3.040 ... (remaining 143644 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.16 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: 9.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 38.090 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 18930 Z= 0.228 Angle : 0.868 12.071 25614 Z= 0.482 Chirality : 0.050 0.166 2922 Planarity : 0.007 0.069 3186 Dihedral : 8.376 45.907 6978 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.15), residues: 2220 helix: -1.51 (0.11), residues: 1254 sheet: 0.50 (0.36), residues: 180 loop : -2.08 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP C 138 HIS 0.005 0.001 HIS D 340 PHE 0.039 0.003 PHE D 153 TYR 0.023 0.002 TYR D 200 ARG 0.015 0.001 ARG F 301 Details of bonding type rmsd hydrogen bonds : bond 0.13449 ( 1057) hydrogen bonds : angle 5.90207 ( 3084) SS BOND : bond 0.00034 ( 6) SS BOND : angle 0.90721 ( 12) covalent geometry : bond 0.00472 (18924) covalent geometry : angle 0.86775 (25602) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 511 time to evaluate : 1.953 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: 1.5545 time to fit residues: 877.2024 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 : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain D residue 459 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 0.0770 chunk 129 optimal weight: 0.9980 chunk 201 optimal weight: 0.6980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 273 GLN A 305 HIS A 373 GLN B 234 HIS B 245 GLN B 273 GLN B 305 HIS B 414 GLN C 215 ASN C 273 GLN C 305 HIS ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 GLN D 234 HIS D 273 GLN D 305 HIS D 414 GLN D 426 HIS E 247 GLN E 273 GLN E 305 HIS F 273 GLN F 305 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.138455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.109971 restraints weight = 24414.680| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.19 r_work: 0.3211 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18930 Z= 0.146 Angle : 0.606 11.284 25614 Z= 0.312 Chirality : 0.041 0.141 2922 Planarity : 0.005 0.058 3186 Dihedral : 4.651 28.228 2518 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.53 % Allowed : 11.13 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.17), residues: 2220 helix: 0.64 (0.14), residues: 1308 sheet: 0.84 (0.35), residues: 180 loop : -1.59 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 168 HIS 0.004 0.001 HIS A 269 PHE 0.019 0.002 PHE B 264 TYR 0.019 0.002 TYR D 216 ARG 0.007 0.001 ARG E 176 Details of bonding type rmsd hydrogen bonds : bond 0.04306 ( 1057) hydrogen bonds : angle 4.22363 ( 3084) SS BOND : bond 0.00665 ( 6) SS BOND : angle 2.96451 ( 12) covalent geometry : bond 0.00346 (18924) covalent geometry : angle 0.60224 (25602) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 313 time to evaluate : 2.242 Fit side-chains revert: symmetry clash REVERT: A 300 PHE cc_start: 0.7654 (m-10) cc_final: 0.6825 (t80) REVERT: A 337 ASP cc_start: 0.7425 (m-30) cc_final: 0.6936 (t0) REVERT: B 132 LEU cc_start: 0.7530 (mt) cc_final: 0.7311 (mt) REVERT: B 196 PHE cc_start: 0.7771 (t80) cc_final: 0.7468 (t80) REVERT: B 221 GLN cc_start: 0.7788 (mt0) cc_final: 0.7528 (mm110) REVERT: B 300 PHE cc_start: 0.7337 (m-10) cc_final: 0.6528 (t80) REVERT: B 442 GLU cc_start: 0.8172 (pp20) cc_final: 0.7796 (pp20) REVERT: C 132 LEU cc_start: 0.7551 (mt) cc_final: 0.7305 (mt) REVERT: C 198 VAL cc_start: 0.8476 (t) cc_final: 0.8205 (m) REVERT: C 251 THR cc_start: 0.8790 (t) cc_final: 0.8423 (m) REVERT: C 304 LYS cc_start: 0.8218 (ttmt) cc_final: 0.7551 (mttt) REVERT: C 306 MET cc_start: 0.7828 (mmm) cc_final: 0.7218 (mtm) REVERT: D 128 ILE cc_start: 0.7971 (mt) cc_final: 0.7714 (pp) REVERT: D 304 LYS cc_start: 0.8335 (ttmm) cc_final: 0.7372 (mtmt) REVERT: D 306 MET cc_start: 0.7970 (mmm) cc_final: 0.6853 (mtm) REVERT: D 334 ARG cc_start: 0.7941 (mmm-85) cc_final: 0.7656 (tpt90) REVERT: D 373 GLN cc_start: 0.7615 (pt0) cc_final: 0.7370 (pt0) REVERT: D 442 GLU cc_start: 0.8177 (pp20) cc_final: 0.7771 (pp20) REVERT: E 128 ILE cc_start: 0.8202 (mt) cc_final: 0.7787 (mm) REVERT: E 132 LEU cc_start: 0.7482 (mt) cc_final: 0.7139 (mt) REVERT: E 251 THR cc_start: 0.8800 (t) cc_final: 0.8428 (m) REVERT: E 300 PHE cc_start: 0.7679 (m-10) cc_final: 0.7293 (t80) REVERT: E 353 ARG cc_start: 0.8201 (mtt90) cc_final: 0.7874 (mtt90) REVERT: E 373 GLN cc_start: 0.7250 (tt0) cc_final: 0.7000 (mt0) REVERT: F 304 LYS cc_start: 0.8398 (ttmt) cc_final: 0.7520 (mttt) REVERT: F 306 MET cc_start: 0.7350 (mmm) cc_final: 0.6781 (mtp) REVERT: F 329 ILE cc_start: 0.6664 (OUTLIER) cc_final: 0.6227 (tt) REVERT: F 455 LYS cc_start: 0.8848 (mtpp) cc_final: 0.8609 (mptm) outliers start: 90 outliers final: 43 residues processed: 354 average time/residue: 1.4805 time to fit residues: 590.7773 Evaluate side-chains 306 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 262 time to evaluate : 2.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 138 TRP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain E residue 138 TRP Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain F residue 459 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 64 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 207 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 208 optimal weight: 0.6980 chunk 191 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 HIS B 305 HIS ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS C 215 ASN C 269 HIS C 305 HIS D 217 GLN D 247 GLN D 305 HIS E 269 HIS E 305 HIS F 217 GLN F 269 HIS F 305 HIS F 462 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.137309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108686 restraints weight = 24398.815| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.19 r_work: 0.3194 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18930 Z= 0.140 Angle : 0.585 13.536 25614 Z= 0.295 Chirality : 0.041 0.132 2922 Planarity : 0.005 0.053 3186 Dihedral : 4.364 29.411 2516 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.83 % Allowed : 13.70 % 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: 0.84 (0.18), residues: 2220 helix: 1.64 (0.15), residues: 1266 sheet: 1.17 (0.37), residues: 180 loop : -1.49 (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 0.014 0.002 PHE B 264 TYR 0.019 0.002 TYR D 222 ARG 0.009 0.000 ARG C 176 Details of bonding type rmsd hydrogen bonds : bond 0.04196 ( 1057) hydrogen bonds : angle 4.01857 ( 3084) SS BOND : bond 0.00418 ( 6) SS BOND : angle 1.46998 ( 12) covalent geometry : bond 0.00333 (18924) covalent geometry : angle 0.58441 (25602) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 300 time to evaluate : 3.728 Fit side-chains revert: symmetry clash REVERT: A 304 LYS cc_start: 0.8403 (ttmm) cc_final: 0.7356 (mttt) REVERT: A 337 ASP cc_start: 0.7268 (m-30) cc_final: 0.6832 (t0) REVERT: B 132 LEU cc_start: 0.7595 (mt) cc_final: 0.7181 (mt) REVERT: B 221 GLN cc_start: 0.7854 (mt0) cc_final: 0.7587 (mm110) REVERT: B 300 PHE cc_start: 0.7429 (m-10) cc_final: 0.6703 (t80) REVERT: C 132 LEU cc_start: 0.7354 (mt) cc_final: 0.7108 (mt) REVERT: C 194 PHE cc_start: 0.7838 (t80) cc_final: 0.7512 (t80) REVERT: C 251 THR cc_start: 0.8749 (t) cc_final: 0.8385 (m) REVERT: C 353 ARG cc_start: 0.8205 (mtt90) cc_final: 0.7909 (mtt90) REVERT: D 194 PHE cc_start: 0.8196 (t80) cc_final: 0.7882 (t80) REVERT: D 300 PHE cc_start: 0.7429 (m-10) cc_final: 0.6719 (t80) REVERT: D 334 ARG cc_start: 0.7984 (mmm-85) cc_final: 0.7597 (tpt90) REVERT: D 373 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7442 (pt0) REVERT: E 132 LEU cc_start: 0.7596 (mt) cc_final: 0.7272 (mt) REVERT: E 194 PHE cc_start: 0.8059 (t80) cc_final: 0.7559 (t80) REVERT: E 222 TYR cc_start: 0.7398 (t80) cc_final: 0.7062 (t80) REVERT: E 251 THR cc_start: 0.8752 (t) cc_final: 0.8376 (m) REVERT: E 304 LYS cc_start: 0.8305 (ttmm) cc_final: 0.7391 (mttt) REVERT: E 353 ARG cc_start: 0.8210 (mtt90) cc_final: 0.7884 (mtt90) REVERT: E 373 GLN cc_start: 0.7226 (tt0) cc_final: 0.6611 (mt0) REVERT: F 132 LEU cc_start: 0.7660 (mt) cc_final: 0.7289 (mt) REVERT: F 300 PHE cc_start: 0.7371 (m-10) cc_final: 0.6732 (t80) REVERT: F 304 LYS cc_start: 0.8422 (ttmt) cc_final: 0.7991 (tmtt) REVERT: F 306 MET cc_start: 0.7575 (mmm) cc_final: 0.7032 (mtp) REVERT: F 455 LYS cc_start: 0.8808 (mtpp) cc_final: 0.8598 (mptm) outliers start: 96 outliers final: 45 residues processed: 342 average time/residue: 1.5170 time to fit residues: 591.6285 Evaluate side-chains 300 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 254 time to evaluate : 3.160 ------------------------------------------------------------------------------- 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 416 ASN Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 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 355 LYS Chi-restraints excluded: chain C residue 416 ASN Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 373 GLN Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain E residue 442 GLU Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain F residue 459 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 34 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 93 optimal weight: 0.0980 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 213 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS A 305 HIS B 305 HIS ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN C 305 HIS D 221 GLN D 305 HIS E 217 GLN E 305 HIS F 305 HIS F 462 GLN F 512 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.135687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.106956 restraints weight = 24383.603| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.17 r_work: 0.3169 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18930 Z= 0.159 Angle : 0.595 15.869 25614 Z= 0.300 Chirality : 0.042 0.211 2922 Planarity : 0.005 0.049 3186 Dihedral : 4.344 33.234 2516 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.24 % Allowed : 15.11 % Favored : 79.66 % 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: 1.22 (0.18), residues: 2220 helix: 1.92 (0.15), residues: 1266 sheet: 1.63 (0.37), residues: 174 loop : -1.32 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 138 HIS 0.003 0.001 HIS E 426 PHE 0.015 0.002 PHE B 514 TYR 0.016 0.002 TYR C 222 ARG 0.008 0.000 ARG C 176 Details of bonding type rmsd hydrogen bonds : bond 0.04385 ( 1057) hydrogen bonds : angle 4.02845 ( 3084) SS BOND : bond 0.00343 ( 6) SS BOND : angle 1.08682 ( 12) covalent geometry : bond 0.00383 (18924) covalent geometry : angle 0.59508 (25602) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 288 time to evaluate : 2.018 Fit side-chains REVERT: A 300 PHE cc_start: 0.7480 (m-10) cc_final: 0.6847 (t80) REVERT: A 306 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.6294 (mtp) REVERT: B 132 LEU cc_start: 0.7407 (mt) cc_final: 0.7120 (mt) REVERT: B 221 GLN cc_start: 0.7848 (mt0) cc_final: 0.7636 (mm110) REVERT: B 300 PHE cc_start: 0.7474 (m-10) cc_final: 0.6854 (t80) REVERT: B 304 LYS cc_start: 0.8383 (ttmm) cc_final: 0.7881 (tmtt) REVERT: B 306 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7670 (mmm) REVERT: B 403 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7370 (tpp-160) REVERT: C 132 LEU cc_start: 0.7419 (mt) cc_final: 0.7169 (mt) REVERT: C 194 PHE cc_start: 0.7890 (t80) cc_final: 0.7581 (t80) REVERT: C 249 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8429 (mmp) REVERT: C 251 THR cc_start: 0.8759 (t) cc_final: 0.8395 (m) REVERT: C 304 LYS cc_start: 0.8446 (ttmm) cc_final: 0.7426 (mttt) REVERT: C 353 ARG cc_start: 0.8249 (mtt90) cc_final: 0.7952 (mtt90) REVERT: D 194 PHE cc_start: 0.8312 (t80) cc_final: 0.8096 (t80) REVERT: D 242 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: D 300 PHE cc_start: 0.7471 (m-10) cc_final: 0.6902 (t80) REVERT: D 306 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7589 (mmm) REVERT: D 334 ARG cc_start: 0.7934 (mmm-85) cc_final: 0.7561 (tpt90) REVERT: E 132 LEU cc_start: 0.7626 (mt) cc_final: 0.7289 (mt) REVERT: E 179 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8535 (mtm) REVERT: E 194 PHE cc_start: 0.7869 (t80) cc_final: 0.7485 (t80) REVERT: E 215 ASN cc_start: 0.7406 (OUTLIER) cc_final: 0.6449 (p0) REVERT: E 251 THR cc_start: 0.8768 (t) cc_final: 0.8394 (m) REVERT: E 304 LYS cc_start: 0.8382 (ttmm) cc_final: 0.7460 (mttt) REVERT: E 353 ARG cc_start: 0.8237 (mtt90) cc_final: 0.7924 (mtt90) REVERT: E 373 GLN cc_start: 0.7256 (tt0) cc_final: 0.6621 (mt0) REVERT: F 300 PHE cc_start: 0.7469 (m-10) cc_final: 0.6828 (OUTLIER) REVERT: F 304 LYS cc_start: 0.8457 (ttmt) cc_final: 0.8011 (tmtt) REVERT: F 306 MET cc_start: 0.7833 (mmm) cc_final: 0.7082 (mtp) outliers start: 104 outliers final: 59 residues processed: 331 average time/residue: 1.2244 time to fit residues: 460.7928 Evaluate side-chains 321 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 255 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 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 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 179 MET Chi-restraints excluded: chain E residue 192 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 215 ASN Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain 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: 1.9990 chunk 42 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 193 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 HIS ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 HIS ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 GLN E 305 HIS ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 HIS F 512 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.135472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.106640 restraints weight = 24450.679| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.16 r_work: 0.3174 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18930 Z= 0.157 Angle : 0.593 16.169 25614 Z= 0.298 Chirality : 0.042 0.208 2922 Planarity : 0.005 0.047 3186 Dihedral : 4.315 38.066 2516 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 5.14 % Allowed : 16.16 % 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: 1.34 (0.18), residues: 2220 helix: 2.01 (0.15), residues: 1266 sheet: 1.62 (0.36), residues: 174 loop : -1.24 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 458 HIS 0.005 0.001 HIS D 305 PHE 0.015 0.001 PHE B 514 TYR 0.015 0.001 TYR D 222 ARG 0.009 0.000 ARG F 176 Details of bonding type rmsd hydrogen bonds : bond 0.04356 ( 1057) hydrogen bonds : angle 4.00487 ( 3084) SS BOND : bond 0.00305 ( 6) SS BOND : angle 0.91566 ( 12) covalent geometry : bond 0.00383 (18924) covalent geometry : angle 0.59262 (25602) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 284 time to evaluate : 1.961 Fit side-chains REVERT: A 131 ILE cc_start: 0.6846 (OUTLIER) cc_final: 0.6571 (tt) REVERT: A 300 PHE cc_start: 0.7514 (m-10) cc_final: 0.6903 (t80) REVERT: A 304 LYS cc_start: 0.8431 (ttmm) cc_final: 0.7903 (tmtt) REVERT: A 306 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.6371 (ttp) REVERT: B 132 LEU cc_start: 0.7506 (mt) cc_final: 0.7082 (mt) REVERT: B 174 LYS cc_start: 0.7480 (mmtm) cc_final: 0.7265 (mmtt) REVERT: B 221 GLN cc_start: 0.7799 (mt0) cc_final: 0.7569 (mm110) REVERT: B 300 PHE cc_start: 0.7502 (m-10) cc_final: 0.6825 (t80) REVERT: B 304 LYS cc_start: 0.8358 (ttmm) cc_final: 0.7878 (tmtt) REVERT: B 403 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7351 (tpp-160) REVERT: C 132 LEU cc_start: 0.7436 (mt) cc_final: 0.7126 (mt) REVERT: C 194 PHE cc_start: 0.7824 (t80) cc_final: 0.7588 (t80) REVERT: C 251 THR cc_start: 0.8762 (t) cc_final: 0.8407 (m) REVERT: C 304 LYS cc_start: 0.8373 (ttmm) cc_final: 0.7403 (mttt) REVERT: C 353 ARG cc_start: 0.8248 (mtt90) cc_final: 0.7946 (mtt90) REVERT: D 242 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: D 251 THR cc_start: 0.8664 (t) cc_final: 0.8376 (m) REVERT: D 304 LYS cc_start: 0.8293 (ttmm) cc_final: 0.7436 (mtmt) REVERT: D 334 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7594 (ttp80) REVERT: E 132 LEU cc_start: 0.7600 (mt) cc_final: 0.7258 (mt) REVERT: E 194 PHE cc_start: 0.7850 (t80) cc_final: 0.7535 (t80) REVERT: E 215 ASN cc_start: 0.7392 (OUTLIER) cc_final: 0.6452 (p0) REVERT: E 251 THR cc_start: 0.8761 (t) cc_final: 0.8406 (m) REVERT: E 353 ARG cc_start: 0.8246 (mtt90) cc_final: 0.7937 (mtt90) REVERT: E 373 GLN cc_start: 0.7229 (tt0) cc_final: 0.6612 (mt0) REVERT: F 131 ILE cc_start: 0.6863 (OUTLIER) cc_final: 0.6552 (tt) REVERT: F 300 PHE cc_start: 0.7481 (m-10) cc_final: 0.6822 (OUTLIER) REVERT: F 304 LYS cc_start: 0.8434 (ttmt) cc_final: 0.7996 (tmtt) REVERT: F 306 MET cc_start: 0.7814 (mmm) cc_final: 0.7100 (mtp) outliers start: 102 outliers final: 65 residues processed: 329 average time/residue: 1.1186 time to fit residues: 417.6368 Evaluate side-chains 329 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 258 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 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 195 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 416 ASN Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 209 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 329 ILE Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 516 LEU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 487 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 43 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 chunk 185 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 198 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 HIS B 247 GLN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 HIS D 247 GLN ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 HIS F 305 HIS ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 462 GLN F 512 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.136596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.107716 restraints weight = 24571.427| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.17 r_work: 0.3178 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18930 Z= 0.138 Angle : 0.569 13.236 25614 Z= 0.287 Chirality : 0.041 0.174 2922 Planarity : 0.004 0.046 3186 Dihedral : 4.196 43.504 2516 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.98 % Allowed : 16.82 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.18), residues: 2220 helix: 2.30 (0.15), residues: 1236 sheet: 1.58 (0.35), residues: 174 loop : -1.25 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 458 HIS 0.005 0.001 HIS C 305 PHE 0.013 0.001 PHE F 429 TYR 0.013 0.001 TYR D 222 ARG 0.007 0.000 ARG F 176 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 1057) hydrogen bonds : angle 3.92107 ( 3084) SS BOND : bond 0.00288 ( 6) SS BOND : angle 0.82972 ( 12) covalent geometry : bond 0.00332 (18924) covalent geometry : angle 0.56931 (25602) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 274 time to evaluate : 2.116 Fit side-chains REVERT: A 131 ILE cc_start: 0.6951 (OUTLIER) cc_final: 0.6750 (tt) REVERT: A 300 PHE cc_start: 0.7529 (m-10) cc_final: 0.7211 (t80) REVERT: B 132 LEU cc_start: 0.7597 (mt) cc_final: 0.7191 (mt) REVERT: B 221 GLN cc_start: 0.7762 (mt0) cc_final: 0.7444 (mm110) REVERT: B 300 PHE cc_start: 0.7522 (m-10) cc_final: 0.6851 (t80) REVERT: B 403 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7357 (tpp-160) REVERT: C 132 LEU cc_start: 0.7507 (mt) cc_final: 0.7197 (mt) REVERT: C 194 PHE cc_start: 0.7836 (t80) cc_final: 0.7595 (t80) REVERT: C 251 THR cc_start: 0.8728 (t) cc_final: 0.8386 (m) REVERT: C 304 LYS cc_start: 0.8327 (ttmm) cc_final: 0.7400 (mttt) REVERT: C 353 ARG cc_start: 0.8241 (mtt90) cc_final: 0.7943 (mtt90) REVERT: D 242 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7636 (mp0) REVERT: D 251 THR cc_start: 0.8644 (t) cc_final: 0.8370 (m) REVERT: D 304 LYS cc_start: 0.8234 (ttmm) cc_final: 0.7418 (mtmt) REVERT: D 334 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7599 (ttp80) REVERT: E 132 LEU cc_start: 0.7588 (mt) cc_final: 0.7169 (mt) REVERT: E 194 PHE cc_start: 0.7839 (t80) cc_final: 0.7576 (t80) REVERT: E 214 ARG cc_start: 0.7180 (OUTLIER) cc_final: 0.6722 (mpt90) REVERT: E 215 ASN cc_start: 0.7556 (t0) cc_final: 0.6631 (p0) REVERT: E 221 GLN cc_start: 0.7510 (mm110) cc_final: 0.7086 (mm-40) REVERT: E 251 THR cc_start: 0.8715 (t) cc_final: 0.8375 (m) REVERT: E 304 LYS cc_start: 0.8365 (ttmm) cc_final: 0.7425 (mttt) REVERT: E 353 ARG cc_start: 0.8239 (mtt90) cc_final: 0.7913 (mtt90) REVERT: E 373 GLN cc_start: 0.7186 (tt0) cc_final: 0.6580 (mt0) REVERT: F 131 ILE cc_start: 0.6921 (OUTLIER) cc_final: 0.6651 (tt) REVERT: F 300 PHE cc_start: 0.7491 (m-10) cc_final: 0.6836 (OUTLIER) REVERT: F 304 LYS cc_start: 0.8448 (ttmt) cc_final: 0.8031 (tmtt) REVERT: F 487 ASP cc_start: 0.7054 (OUTLIER) cc_final: 0.6785 (t70) outliers start: 99 outliers final: 56 residues processed: 323 average time/residue: 1.1556 time to fit residues: 425.0803 Evaluate side-chains 323 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 261 time to evaluate : 1.913 ------------------------------------------------------------------------------- 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 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 209 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 416 ASN Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 138 TRP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 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 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 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 131 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 0.2980 chunk 23 optimal weight: 0.8980 chunk 178 optimal weight: 0.0370 chunk 15 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 HIS ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS D 221 GLN ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 GLN F 305 HIS F 340 HIS F 462 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.137586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108827 restraints weight = 24314.100| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.16 r_work: 0.3201 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18930 Z= 0.123 Angle : 0.563 11.474 25614 Z= 0.281 Chirality : 0.041 0.172 2922 Planarity : 0.004 0.045 3186 Dihedral : 4.086 45.619 2516 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.58 % Allowed : 17.22 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.18), residues: 2220 helix: 2.25 (0.15), residues: 1266 sheet: 1.55 (0.34), residues: 174 loop : -1.16 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 463 HIS 0.005 0.001 HIS C 305 PHE 0.014 0.001 PHE E 153 TYR 0.013 0.001 TYR B 222 ARG 0.005 0.000 ARG F 176 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 1057) hydrogen bonds : angle 3.84309 ( 3084) SS BOND : bond 0.00259 ( 6) SS BOND : angle 0.72430 ( 12) covalent geometry : bond 0.00293 (18924) covalent geometry : angle 0.56320 (25602) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 271 time to evaluate : 1.899 Fit side-chains REVERT: A 121 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6543 (pt) REVERT: A 131 ILE cc_start: 0.6838 (OUTLIER) cc_final: 0.6625 (tt) REVERT: A 221 GLN cc_start: 0.7466 (mm110) cc_final: 0.7187 (mm110) REVERT: A 304 LYS cc_start: 0.8354 (ttmm) cc_final: 0.7478 (mtmt) REVERT: B 132 LEU cc_start: 0.7620 (mt) cc_final: 0.7199 (mt) REVERT: B 221 GLN cc_start: 0.7691 (mt0) cc_final: 0.7391 (mm110) REVERT: B 300 PHE cc_start: 0.7511 (m-10) cc_final: 0.6923 (t80) REVERT: B 304 LYS cc_start: 0.8324 (ttmm) cc_final: 0.7811 (tmtt) REVERT: B 403 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7349 (tpp-160) REVERT: B 442 GLU cc_start: 0.8245 (pp20) cc_final: 0.7846 (pp20) REVERT: C 132 LEU cc_start: 0.7431 (mt) cc_final: 0.7143 (mt) REVERT: C 221 GLN cc_start: 0.7520 (mm110) cc_final: 0.7173 (mm110) REVERT: C 249 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8259 (mmp) REVERT: C 251 THR cc_start: 0.8687 (t) cc_final: 0.8365 (m) REVERT: C 304 LYS cc_start: 0.8343 (ttmm) cc_final: 0.7432 (mttt) REVERT: C 353 ARG cc_start: 0.8235 (mtt90) cc_final: 0.7938 (mtt90) REVERT: D 221 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7382 (mm110) REVERT: D 242 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7632 (mt-10) REVERT: D 304 LYS cc_start: 0.8199 (ttmm) cc_final: 0.7371 (mtmt) REVERT: D 334 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7659 (ttp80) REVERT: D 442 GLU cc_start: 0.8229 (pp20) cc_final: 0.7825 (pp20) REVERT: E 132 LEU cc_start: 0.7519 (mt) cc_final: 0.7156 (mt) REVERT: E 194 PHE cc_start: 0.7889 (t80) cc_final: 0.7610 (t80) REVERT: E 214 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6736 (mpt90) REVERT: E 215 ASN cc_start: 0.7544 (t0) cc_final: 0.6613 (p0) REVERT: E 221 GLN cc_start: 0.7542 (mm110) cc_final: 0.7145 (mm-40) REVERT: E 251 THR cc_start: 0.8686 (t) cc_final: 0.8357 (m) REVERT: E 304 LYS cc_start: 0.8343 (ttmm) cc_final: 0.7367 (mttt) REVERT: E 373 GLN cc_start: 0.7145 (tt0) cc_final: 0.6810 (tt0) REVERT: F 131 ILE cc_start: 0.7035 (OUTLIER) cc_final: 0.6800 (tt) REVERT: F 300 PHE cc_start: 0.7565 (m-10) cc_final: 0.6900 (t80) REVERT: F 304 LYS cc_start: 0.8372 (ttmt) cc_final: 0.7973 (tmtt) REVERT: F 403 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7292 (ttp80) REVERT: F 487 ASP cc_start: 0.7075 (OUTLIER) cc_final: 0.6815 (t70) outliers start: 91 outliers final: 45 residues processed: 316 average time/residue: 1.1782 time to fit residues: 422.7658 Evaluate side-chains 311 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 256 time to evaluate : 2.016 ------------------------------------------------------------------------------- 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 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 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 459 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 416 ASN Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 138 TRP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 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 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 131 ILE 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 403 ARG Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 487 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 195 optimal weight: 0.6980 chunk 136 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 204 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 216 optimal weight: 2.9990 chunk 18 optimal weight: 0.1980 chunk 142 optimal weight: 0.7980 chunk 201 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 GLN E 245 GLN E 247 GLN ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 462 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.138021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.109360 restraints weight = 24223.174| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.16 r_work: 0.3201 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: 0.8050 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18930 Z= 0.119 Angle : 0.555 11.284 25614 Z= 0.277 Chirality : 0.040 0.174 2922 Planarity : 0.004 0.045 3186 Dihedral : 4.013 45.327 2516 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.53 % Allowed : 17.32 % Favored : 78.15 % 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: 2.48 (0.15), residues: 1236 sheet: 1.53 (0.34), residues: 174 loop : -1.19 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 458 HIS 0.005 0.001 HIS E 305 PHE 0.014 0.001 PHE E 153 TYR 0.013 0.001 TYR B 222 ARG 0.005 0.000 ARG C 176 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 1057) hydrogen bonds : angle 3.80597 ( 3084) SS BOND : bond 0.00228 ( 6) SS BOND : angle 0.61194 ( 12) covalent geometry : bond 0.00280 (18924) covalent geometry : angle 0.55452 (25602) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 274 time to evaluate : 2.208 Fit side-chains REVERT: A 121 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6513 (pt) REVERT: A 131 ILE cc_start: 0.6836 (OUTLIER) cc_final: 0.6605 (tt) REVERT: A 221 GLN cc_start: 0.7481 (mm110) cc_final: 0.7210 (mm110) REVERT: A 304 LYS cc_start: 0.8352 (ttmm) cc_final: 0.7460 (mttt) REVERT: B 221 GLN cc_start: 0.7658 (mt0) cc_final: 0.7389 (mm110) REVERT: B 300 PHE cc_start: 0.7543 (m-10) cc_final: 0.6945 (t80) REVERT: B 304 LYS cc_start: 0.8330 (ttmm) cc_final: 0.7847 (tmtt) REVERT: B 403 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7317 (tpp-160) REVERT: C 132 LEU cc_start: 0.7438 (mt) cc_final: 0.7157 (mt) REVERT: C 249 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8252 (mmp) REVERT: C 251 THR cc_start: 0.8633 (t) cc_final: 0.8347 (m) REVERT: C 304 LYS cc_start: 0.8314 (ttmm) cc_final: 0.7405 (mttt) REVERT: C 353 ARG cc_start: 0.8225 (mtt90) cc_final: 0.7922 (mtt90) REVERT: D 221 GLN cc_start: 0.7526 (mm-40) cc_final: 0.7273 (mm110) REVERT: D 242 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7629 (mt-10) REVERT: D 251 THR cc_start: 0.8621 (t) cc_final: 0.8338 (m) REVERT: D 304 LYS cc_start: 0.8169 (ttmm) cc_final: 0.7378 (mtmt) REVERT: D 334 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7641 (ttp80) REVERT: E 132 LEU cc_start: 0.7660 (mt) cc_final: 0.7268 (mt) REVERT: E 194 PHE cc_start: 0.7871 (t80) cc_final: 0.7605 (t80) REVERT: E 214 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.6759 (mpt90) REVERT: E 215 ASN cc_start: 0.7591 (OUTLIER) cc_final: 0.6638 (p0) REVERT: E 221 GLN cc_start: 0.7442 (mm110) cc_final: 0.7070 (mm-40) REVERT: E 251 THR cc_start: 0.8673 (t) cc_final: 0.8373 (m) REVERT: E 304 LYS cc_start: 0.8258 (ttmm) cc_final: 0.7384 (mttt) REVERT: E 373 GLN cc_start: 0.7064 (tt0) cc_final: 0.6767 (tt0) REVERT: F 131 ILE cc_start: 0.6800 (OUTLIER) cc_final: 0.6506 (tt) REVERT: F 221 GLN cc_start: 0.7368 (mm110) cc_final: 0.7137 (mm110) REVERT: F 304 LYS cc_start: 0.8339 (ttmt) cc_final: 0.7526 (mtmt) REVERT: F 403 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7306 (ttp80) REVERT: F 487 ASP cc_start: 0.7008 (OUTLIER) cc_final: 0.6754 (t70) outliers start: 90 outliers final: 47 residues processed: 319 average time/residue: 1.1281 time to fit residues: 409.5577 Evaluate side-chains 319 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 261 time to evaluate : 2.085 ------------------------------------------------------------------------------- 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 198 VAL Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 416 ASN Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 138 TRP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 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 E residue 137 LEU Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 215 ASN Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain F residue 131 ILE 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 459 LEU Chi-restraints excluded: chain F residue 487 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 210 optimal weight: 0.4980 chunk 54 optimal weight: 0.7980 chunk 186 optimal weight: 0.0040 chunk 218 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 17 optimal weight: 0.0370 chunk 21 optimal weight: 0.8980 overall best weight: 0.3870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 HIS B 425 GLN C 221 GLN D 340 HIS D 425 GLN F 462 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.139756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.111053 restraints weight = 24324.013| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.16 r_work: 0.3224 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18930 Z= 0.109 Angle : 0.564 14.060 25614 Z= 0.277 Chirality : 0.040 0.198 2922 Planarity : 0.004 0.045 3186 Dihedral : 3.898 45.367 2516 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.37 % Allowed : 18.78 % Favored : 77.84 % 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: 1.76 (0.18), residues: 2220 helix: 2.39 (0.15), residues: 1266 sheet: 1.51 (0.34), residues: 174 loop : -1.06 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 458 HIS 0.005 0.001 HIS E 305 PHE 0.014 0.001 PHE E 153 TYR 0.013 0.001 TYR B 222 ARG 0.006 0.000 ARG E 176 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 1057) hydrogen bonds : angle 3.72714 ( 3084) SS BOND : bond 0.00256 ( 6) SS BOND : angle 0.67367 ( 12) covalent geometry : bond 0.00251 (18924) covalent geometry : angle 0.56355 (25602) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 269 time to evaluate : 2.169 Fit side-chains REVERT: A 121 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6615 (pt) REVERT: A 131 ILE cc_start: 0.6730 (OUTLIER) cc_final: 0.6505 (tt) REVERT: A 304 LYS cc_start: 0.8285 (ttmm) cc_final: 0.7417 (mtmt) REVERT: A 329 ILE cc_start: 0.6589 (OUTLIER) cc_final: 0.6261 (OUTLIER) REVERT: B 121 LEU cc_start: 0.7678 (pp) cc_final: 0.7448 (pt) REVERT: B 221 GLN cc_start: 0.7608 (mt0) cc_final: 0.7352 (mm110) REVERT: B 300 PHE cc_start: 0.7536 (m-10) cc_final: 0.6943 (t80) REVERT: B 304 LYS cc_start: 0.8298 (ttmm) cc_final: 0.7828 (tmtt) REVERT: B 403 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7351 (tpp-160) REVERT: B 442 GLU cc_start: 0.8185 (pp20) cc_final: 0.7880 (pp20) REVERT: C 132 LEU cc_start: 0.7397 (mt) cc_final: 0.7147 (mt) REVERT: C 304 LYS cc_start: 0.8285 (ttmm) cc_final: 0.7410 (mttt) REVERT: D 221 GLN cc_start: 0.7488 (mm-40) cc_final: 0.7228 (mm110) REVERT: D 304 LYS cc_start: 0.8172 (ttmm) cc_final: 0.7360 (mtmt) REVERT: D 334 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7591 (ttp80) REVERT: D 442 GLU cc_start: 0.8157 (pp20) cc_final: 0.7845 (pp20) REVERT: E 132 LEU cc_start: 0.7568 (mt) cc_final: 0.7174 (mt) REVERT: E 194 PHE cc_start: 0.7877 (t80) cc_final: 0.7651 (t80) REVERT: E 214 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6668 (mpt90) REVERT: E 215 ASN cc_start: 0.7627 (OUTLIER) cc_final: 0.6701 (p0) REVERT: E 221 GLN cc_start: 0.7352 (mm110) cc_final: 0.7088 (mm-40) REVERT: E 304 LYS cc_start: 0.8277 (ttmm) cc_final: 0.7430 (mttt) REVERT: E 373 GLN cc_start: 0.6882 (tt0) cc_final: 0.6581 (tt0) REVERT: F 131 ILE cc_start: 0.6807 (OUTLIER) cc_final: 0.6510 (tt) REVERT: F 221 GLN cc_start: 0.7366 (mm110) cc_final: 0.7146 (mm110) REVERT: F 304 LYS cc_start: 0.8296 (ttmt) cc_final: 0.7507 (mtmt) REVERT: F 403 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7296 (ttp80) outliers start: 67 outliers final: 39 residues processed: 305 average time/residue: 1.1489 time to fit residues: 397.7220 Evaluate side-chains 295 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 248 time to evaluate : 1.918 ------------------------------------------------------------------------------- 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 198 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 416 ASN 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 206 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 416 ASN Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 138 TRP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 198 VAL 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 487 ASP Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 215 ASN Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 462 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 159 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 152 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 128 optimal weight: 0.5980 chunk 32 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 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** 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 = 0.3703 r_free = 0.3703 target = 0.137688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108948 restraints weight = 24427.015| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.16 r_work: 0.3193 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18930 Z= 0.135 Angle : 0.579 12.677 25614 Z= 0.289 Chirality : 0.041 0.159 2922 Planarity : 0.004 0.045 3186 Dihedral : 4.007 46.372 2516 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.12 % Allowed : 19.84 % Favored : 77.04 % 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: 1.77 (0.18), residues: 2220 helix: 2.50 (0.15), residues: 1236 sheet: 1.56 (0.34), residues: 174 loop : -1.10 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 458 HIS 0.006 0.001 HIS F 305 PHE 0.013 0.001 PHE A 429 TYR 0.012 0.001 TYR B 222 ARG 0.008 0.000 ARG B 176 Details of bonding type rmsd hydrogen bonds : bond 0.03886 ( 1057) hydrogen bonds : angle 3.82970 ( 3084) SS BOND : bond 0.00200 ( 6) SS BOND : angle 0.56015 ( 12) covalent geometry : bond 0.00324 (18924) covalent geometry : angle 0.57877 (25602) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 255 time to evaluate : 2.067 Fit side-chains REVERT: A 121 LEU cc_start: 0.6906 (OUTLIER) cc_final: 0.6602 (pt) REVERT: A 131 ILE cc_start: 0.6807 (OUTLIER) cc_final: 0.6606 (tt) REVERT: A 233 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8098 (OUTLIER) REVERT: A 304 LYS cc_start: 0.8275 (ttmm) cc_final: 0.7345 (mttt) REVERT: B 221 GLN cc_start: 0.7624 (mt0) cc_final: 0.7370 (mm110) REVERT: B 300 PHE cc_start: 0.7554 (m-10) cc_final: 0.6936 (t80) REVERT: B 304 LYS cc_start: 0.8314 (ttmm) cc_final: 0.7846 (tmtt) REVERT: B 403 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7359 (tpp-160) REVERT: B 442 GLU cc_start: 0.8185 (pp20) cc_final: 0.7796 (pp20) REVERT: C 121 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.7092 (pt) REVERT: C 132 LEU cc_start: 0.7473 (mt) cc_final: 0.7040 (mt) REVERT: C 251 THR cc_start: 0.8660 (t) cc_final: 0.8428 (m) REVERT: C 304 LYS cc_start: 0.8290 (ttmm) cc_final: 0.7420 (mttt) REVERT: D 221 GLN cc_start: 0.7545 (mm-40) cc_final: 0.7297 (mm110) REVERT: D 242 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: D 304 LYS cc_start: 0.8189 (ttmm) cc_final: 0.7394 (mtmt) REVERT: D 334 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7600 (ttp80) REVERT: D 442 GLU cc_start: 0.8156 (pp20) cc_final: 0.7757 (pp20) REVERT: E 132 LEU cc_start: 0.7678 (mt) cc_final: 0.7257 (mt) REVERT: E 194 PHE cc_start: 0.7957 (t80) cc_final: 0.7658 (t80) REVERT: E 214 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.6714 (mpt90) REVERT: E 215 ASN cc_start: 0.7634 (t0) cc_final: 0.6707 (p0) REVERT: E 221 GLN cc_start: 0.7382 (mm110) cc_final: 0.7106 (mm-40) REVERT: E 304 LYS cc_start: 0.8252 (ttmm) cc_final: 0.7372 (mttt) REVERT: E 373 GLN cc_start: 0.7087 (tt0) cc_final: 0.6785 (tt0) REVERT: F 131 ILE cc_start: 0.6792 (OUTLIER) cc_final: 0.6506 (tt) REVERT: F 221 GLN cc_start: 0.7411 (mm110) cc_final: 0.7161 (mm110) REVERT: F 233 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.8057 (OUTLIER) REVERT: F 304 LYS cc_start: 0.8297 (ttmt) cc_final: 0.7514 (mtmt) REVERT: F 403 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7326 (ttp80) outliers start: 62 outliers final: 39 residues processed: 291 average time/residue: 1.1222 time to fit residues: 372.7516 Evaluate side-chains 295 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 247 time to evaluate : 2.037 ------------------------------------------------------------------------------- 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 198 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 416 ASN 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 206 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 416 ASN Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 138 TRP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 206 VAL 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 44 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 175 optimal weight: 1.9990 chunk 204 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 18 optimal weight: 0.0770 chunk 74 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 overall best weight: 0.6342 ------------------------------------------------------------------------------- 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** C 269 HIS F 462 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.137198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108719 restraints weight = 24353.391| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.14 r_work: 0.3195 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18930 Z= 0.131 Angle : 0.580 12.262 25614 Z= 0.290 Chirality : 0.041 0.143 2922 Planarity : 0.004 0.045 3186 Dihedral : 3.998 47.075 2516 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.47 % Allowed : 19.59 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.18), residues: 2220 helix: 2.46 (0.15), residues: 1236 sheet: 1.56 (0.34), residues: 174 loop : -1.10 (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 F 305 PHE 0.013 0.001 PHE A 429 TYR 0.012 0.001 TYR B 222 ARG 0.008 0.000 ARG B 176 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 1057) hydrogen bonds : angle 3.84023 ( 3084) SS BOND : bond 0.00229 ( 6) SS BOND : angle 0.60068 ( 12) covalent geometry : bond 0.00315 (18924) covalent geometry : angle 0.57984 (25602) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13272.51 seconds wall clock time: 229 minutes 59.85 seconds (13799.85 seconds total)